Bio-ontologies are digital frameworks for handling biological and biomedical data. They consist of theoretical entities and relations with explicitly defined logical structures and precise definitions, whose purpose is to provide a shared language for representing information to be distributed and integrated across diverse scientific contexts. It is tempting to view bio-ontologies as clear and formal expressions of a scientific community’s ontological commitments about their domain of inquiry, and to view their integration as tantamount to the metaphysical unification of (...) science that some philosophers have envisaged. However, I argue that the local, practical, social and technological factors that influence their design prevent us from straightforwardly reading metaphysical conclusions from them. I discuss these complications and suggest how they can be overcome, revealing more general lessons for the development of a well-founded scientific metaphysics. (shrink)

Traditionally, ontology, or at least western ontology, bas been an anthropocentric enterprise, that takes only human experiences into account. In this paper I argue that a prolific biocentric ontology can be based on UexkülI's Umwelt theory. UexkülI offers the basis of an ontology according to which the study of experiences is a much wider field than it is as depicted by classical ontology and contemporary philosophy of consciousness. Based on the thoughts of the contemporary philosopher Thomas Nagel I claim that (...) there might very well be Iifeforms that are totally unimaginable to us. I argue that this view is compatible with the Umwelt theory, and that it should be adopted by biosemioticians. Furthermore, I argue that a biosemiotic possibilism should be implemented. Followingly, one should not claim to know which characteristics of living beings are universally and necessarily valid, but restrict oneself to statements about life as we know it. (shrink)

Ontology languages for the Semantic Web have their strengths and weaknesses, in particular in the light of deploying them for biological and medical information systems. We survey and compare the Description Logics-based OWL languages, and the DL-Lite and DLR families of languages. Language choices that an ontology developer has to make are, among others, expressivity with n-ary relations (where n > 2) and more role properties versus ontology usage for data-intensive tasks. Guidelines are suggested to facilitate choosing the language best (...) fitted for a task. (shrink)

Ontologies are being developed throughout the biomedical sciences to address standardization, integration, classification and reasoning needs against the background of an increasingly data-driven research paradigm. In particular, ontologies facilitate the translation of basic research into benefits for the patient by making research results more discoverable and by facilitating knowledge transfer across disciplinary boundaries. Addressing and adequately treating mental illness is one of our most pressing public health challenges. Primary research across multiple disciplines such as psychology, psychiatry, biology, neuroscience (...) and pharmacology needs to be integrated in order to promote a more comprehensive understanding of underlying processes and mechanisms, and this need for integration only becomes more pressing with our increase in understanding of differences among individuals and populations at the molecular level concerning susceptibility to specific illnesses. Substance addiction is a particularly relevant public health challenge in the developed world, affecting a substantial percentage of the population, often co-morbid with other illnesses such as mood disorders. Currently, however, there is no straightforward automated method to combine data of relevance to the study of substance addiction across multiple disciplines and populations. In this contribution, we describe a framework of interlinked, interoperable bio-ontologies for the annotation of primary research data relating to substance addiction, and discuss how this framework enables easy integration of results across disciplinary boundaries. We describe entities and relationships relevant for the description of addiction within the Mental Functioning Ontology, Chemical Entities of Biological Interest Ontology, Protein Ontology, Gene Ontology and the Neuroscience Information Framework ontologies. (shrink)

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data (...) on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

There are few successful applications of automated reasoning over OWL-formalised bio-ontologies, and requirements are often unclearly formulated. Of what is available, usage and prospective scenarios of automated reasoning is often different from the straightforward classification and satisfiability. We list nine types of scenarios and specify the requirements in more detail. Several of these requirements are already possible in practice or at least in theory, others are in need of further research, in particular regarding the linking of the OWL ontology (...) to data, reasoning over roles, and dynamically linking modular ontologies. (shrink)

Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus Principle: realist, (...) contextual-best, and coordinative. Contrasted with the realist program of the Open Biomedical Ontologies Foundry, we argue that historical practices in systematic biology provide an important and overlooked alternative based on coordinative consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or “settled” science. (shrink)

According to enactivism all living systems, from single cell organisms to human beings, are ontologically endowed with some form of teleological and sense-making agency. Furthermore, enactivists maintain that: there is no fixed pregiven world and as a consequence all organisms “bring forth” their own unique “worlds” through processes of sense-making. The first half of the paper takes these two ontological claims as its central focus and aims to clarify and make explicit the arguments and motivations underlying them. Our analysis here (...) highlights three distinct but connected problems for enactivism: these arguments do not and cannot guarantee that there is no pregiven world, instead, they end up generating a contradiction whereby a pregiven world seems to in fact be tacitly presupposed by virtue of a reliance on a tacit epistemic perspectivalism which is also inherently representationalist and as a consequence makes it difficult to satisfactorily account for the ontological plurality of worlds. Taking these considerations on board, the second half of the paper then aims to develop a more robust ontologically grounded enactivism. Drawing from biosemiotic enactivism, science and technology studies and anthropology, the paper aims to present an account which both rejects a pregiven world and coherently accounts for how organisms bring forth ontologically multiple worlds. (shrink)

In The Onlife Manifesto: Being Human in a Hyperconnected Era Luciano Floridi and his associates examine various aspects of the contemporary meaning of humanity. Yet, their insights give less thought to the political economy of techno-capitalism that in large measure creates ICTs and leads to their further innovation, development and commercialization. This article responses to Floridi’s work and examines political economy of the blurred distinction between human, machine and nature in the postdigital context. Taking lessons from early history of the (...) Internet across the Eastern and the Western Bloc, it examines ideological underpinnings of development of information and communication technologies. The paper points towards the postdigital challenge of the rising importance of biological sciences, their mutual connection with information sciences, and the society at large. It introduces the concept of bio-informational capitalism, and closely examines the relationships between biology and information... (shrink)

The sociobiological and socio-political aspects of human existence have been the subject of techno-rationalistic control and manipulation. The investigation of the mutual complementarity of anthropological and ontological paradigms under these circumstances is the main purpose of present publication. The comparative conceptual analysis of the bio-power and bio-politics in the mentality of the modern technological civilization is a main method of the research. The methodological and philosophical analogy of biological and social engineering allows combining them in the nature and social implications (...) as part of a High Hume technologies class. As result of the transformation of somatic foundations of the human being and his behavior, stereotypes in the object of control and management the technogenic risk reached the existential level. The rapidly growing status of biopower and biopolitics in the conceptual field of contemporary political science becomes by phenomenological expression of these processes. (shrink)

According to enactivism all living systems, from single cell organisms to human beings, are ontologically endowed with some form of teleological and sense-making agency. Furthermore, enactivists maintain that: there is no fixed pregiven world and as a consequence all organisms “bring forth” their own unique “worlds” through processes of sense-making. The first half of the paper takes these two ontological claims as its central focus and aims to clarify and make explicit the arguments and motivations underlying them. Our analysis here (...) highlights three distinct but connected problems for enactivism: these arguments do not and cannot guarantee that there is no pregiven world, instead, they end up generating a contradiction whereby a pregiven world seems to in fact be tacitly presupposed by virtue of a reliance on a tacit epistemic perspectivalism which is also inherently representationalist and as a consequence makes it difficult to satisfactorily account for the ontological plurality of worlds. Taking these considerations on board, the second half of the paper then aims to develop a more robust ontologically grounded enactivism. Drawing from biosemiotic enactivism, science and technology studies and anthropology, the paper aims to present an account which both rejects a pregiven world and coherently accounts for how organisms bring forth ontologically multiple worlds. (shrink)

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

A comparison of six alternative definitions of the term 'cellular pathway' against the background of ontological realism.

Transmodern ethics establishes moral norms on liberal, pluralist and pragmatic principles. We see a comeback of the negation morals, however not of ontology-anchored morals, as is the case of the God who picks favourites or of the jealous God paradigm, and not even of morals anchored in a contractualist perspective, as is the case in the modern period. The preferred focus is on the value of positivism, of cooperation as a source of efficiency, of personal enrichment, be it cultural, spiritual, (...) or moral, derived from the access to alterity. Tolerance as an ethical value is legitimised by a new, utilitarian humanism. The ethical construction of identity revolves around the value of loyalty to a tradition, a dogma, a mentality, and by extension to any coherent system liable to generate a sense of belonging. Postindustrial ethics uses for instance the value of loyalty as a strategy in marketing, organisational development, political propaganda etc. The policies used in order to increase the loyalty of a shop's customers, the employee's loyalty for the company she works for, the supporter's loyalty to his team, are the translation in layman terms of the loyalty ethics that in spiritual terms was one of the foundations of orthodoxy as loyalty to the tradition of the holy fathers. The values of equality, liberty and fraternity have been more than that, as they have laid the foundations of the modern society. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever-changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

An ontology is a domain of knowledge structured through formal rules so that it can be interpreted and used by computers. Ontologies are becoming increasingly important in bioinformatics because they can be linked to the information in databases and their knowledge then used to query the databases. Typical examples in current use are the Gene Ontology, which incorporates much of our knowledge about gene products, and ontologies of developmental anatomy, which, for example, facilitate tissue‐based queries to gene expression (...) databases both textually and spatially. This article considers the production, formulation and types of bio‐ontologies together with the reasons why they are so useful. © BioEssays 25:501–506, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

This collection provides English readers with a critical update on current debates on biopolitics in and around Italian thought. More than a decade after the publication of seminal books such as Agamben’s _Homo Sacer_ and Hardt and Negri’s _Empire_, the names of, among others, Roberto Esposito, Paolo Virno, Christian Marazzi, and Andrea Fumagalli have recently been brought to the attention of Anglophone scholars and political activists. Several authors have rightly emphasised the evanescent character of biopolitics, and the difficulty in providing (...) a definition of it that could embrace all the conflicting theories of its most celebrated critics and supporters. The present collection is structured around the basic contention that bio-economy, human nature, and Christianity are the three visible contemporary manifestations of the theoretical object/problem of biopolitics in, respectively, Italian post-workerist economics, post-Marxist philosophical anthropology, and post-structuralist ontology. This book was originally published as a special issue of _Angelaki_. (shrink)

All eyes are turned towards genomic data and models as the source of knowledge about whether human races exist or not. Will genomic science make the final decision about whether racial realism (e.g., racial population naturalism) or anti-realism (e.g., racial skepticism) is correct? We think not. We believe that the results of even our best and most impressive genomic technologies underdetermine whether bio-genomic races exist, or not. First, different sub-disciplines of biology interested in population structure employ distinct concepts, aims, measures, (...) and models, producing cross-cutting categorizations of population subdivisions rather than a single, universal bio-genomic concept of "race." Second, within each sub-discipline (e.g., conservation biology, phylogenetics), genomic results are consistent with, and map multiply to, racial realism and anti-realism. Indeed, racial ontologies are constructed conventionally, rather than discovered. We thus defend a /constructivist conventionalism/ about bio-genomic racial ontology. Choices and conventions must always be made in identifying particular kinds of groups. Political agendas, social programs, and moral questions premised on the existence of naturalistic race must accept that no scientifically grounded racial ontology is forthcoming, and adjust presumptions, practices, and projects accordingly. (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)

Bio‐banking in research elicits numerous ethical issues related to informed consent, privacy and identifiability of samples, return of results, incidental findings, international data exchange, ownership of samples, and benefit sharing etc. In low and middle income (LMICs) countries the challenge of inadequate guidelines and regulations on the proper conduct of research compounds the ethical issues. In addition, failure to pay attention to underlying indigenous worldviews that ought to inform issues, practices and policies in Africa may exacerbate the situation. In this (...) paper we discuss how the African context presents unique and outstanding cultural thought systems regarding the human body and biological materials that can be put into perspective in bio‐bank research. We give the example of African ontology of nature presented by John Samwel Mbiti as foundational in adding value to the discourse about enhancing relevance of bio‐bank research in the African context. We underline that cultural rites of passage performed on the human body in majority of communities in Africa elicit quintessential perspective on beliefs about handling of human body and human biological tissues. We conclude that acknowledgement and inclusion of African indigenous worldviews regarding the human body is essential in influencing best practices in biobank research in Africa. (shrink)

A longstanding philosophical premise perceives simplicity as a desirable attribute of scientific theories. One of several raised justifications for this notion is that simple theories are more likely to indicate the true makeup of natural systems. Qualitatively parsimonious hypotheses and theories keep to a minimum the number of different postulated entities within a system. Formulation of such ontologically simple working hypotheses proved to be useful in the experimental probing of narrowly defined bio systems. It is less certain, however, whether qualitatively (...) parsimonious theories are effective indicators of the true nature of complex biological systems. This paper assesses the success of ontologically simple theories in envisaging the makeup of three complex systems in bacteriology, immunology, and molecular biology. Evidence shows that parsimonious theories completely misconstrued the actual ontologically complex constitutions of the three examined systems. Since evolution and selective pressures typically produce ontologically intricate rather than simple bio systems, qualitatively parsimonious theories are mostly inapt indicators of the true nature of complex biological systems. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Extractivist OntologiesLithium Mining and Anthropocene Imaginaries in Chile's Atacama DesertMauricio F. Collao Quevedo (bio)The term energy transition generally refers to efforts to switch from one energy system to another. In light of the current climate crisis, energy transition projects have sought to move societies away from their reliance on fossil fuels and toward a renewables-based energy system. Yet such projects have not been easy to undertake. As Marie Forget (...) and Vincent Bos point out, an energy system based on renewables requires a transformation of energy "regulatory frameworks, technical and organizational structures, geographic forms and network practices" (1). More specifically, current energy transition models rely on the expansion of lithium production, accompanying systems of private property rights, and complex logistical and technical strategies. This article examines the interplay between lithium extraction, national development, and Anthropocene imaginaries in Chile's Atacama Desert, arguing that the green brand of extractivism that characterizes the industry relies on elaborate institutional arrangements aimed at expanding and protecting extractivist ontological and epistemological regimes in the politically contested region. As such, struggles over lithium in Chile's Atacama region demonstrate the extent to which efforts to decolonize the Anthropocene and make possible non-extractive futures of collective survival must unfold on ontological grounds, against the consolidation of the Age of Man.Mining, Water Rights, and Indigenous Communities in the Atacama DesertAmong today's most promising energy sources and materials are sodium, copper, sulfur, nickel, cobalt, rare earth metals, and lithium. These [End Page 78] have become central to energy transition strategies and states seeking to attract investors for development (Lunde Seefeldt). As a report by the World Bank points out, demand for transition minerals like lithium, cobalt, and graphite could increase by 500% by 2050 ("Climate-Smart Mining"), highlighting the extent to which global energy transition efforts are counting on greater extraction of transition minerals and the expansion of extractive frontiers to previously unexplored or unexploited regions (Moore, Capitalism; World Bank Group). Lithium is at the center of this economic and technological shift toward green economies.Global lithium demand is growing rapidly, with investment and production rates growing significantly in recent years (Narins) and catching the attention of states (e.g., China) and corporate tech giants (e.g., Tesla) that are already trying to secure greater shares of the global market. The light metal's popularity is largely due to its internal chemistry, which meets many of the technical and practical requirements associated with green energy transition. Lithium is light, conducive, and energy-dense, which in the context of batteries means faster recharge, lower costs, and charge-holding abilities that make lithium-ion batteries more efficient than a nickel-metal hybrid equivalent (Perotti and Coviello). Because of this, lithium is increasingly being considered as promising for human development and survival as its energy predecessors, inspiring labels such as "white gold," "white petroleum," "the new copper," "the 21st century's petroleum," or the "new gasoline" of sustainability (Acuña and Tironi; Lunde Seefeldt; Voskoboynik and Andreucci).But the industry is not without its downsides. The negative impacts of lithium extraction in Chile's Atacama Desert have been challenged by local communities for whom the metal does not exist as a discrete entity that can be easily extracted from its socioecological context. For many of these communities, lithium is more than a transition metal found in an appropriable and materially heterogenous underground brine: it is an ontologically contested, socioecological entity that sustains and participates in complex webs of life-supporting, place-based, and more-than-human relations. Such accounts of the brine are radically incompatible with "official" state accounts of it, which are maintained through an institutional architecture that allows the ontological basis of the brine to be manipulated for extractive purposes by both corporate and state actors.In the following pages, I examine the ways in which Chile's legal and institutional arrangements, informed by imaginaries of green modernization, [End Page 79] create conditions under which extralocal actors can manipulate along extractivist lines the ontological ambiguity and material heterogeneity of lithium-containing brines in the salt flats of the Atacama Desert. Through an analysis of the ways in which lithium industries in the... (shrink)

Applied technological developments are represented by (1) genetic engineering as management tools of biological evolution and (2) socio-economic engineering as management tools of civilizational and socio-cultural development. This binary structure logically follows from the postulated three-module organization of the sustainable evolutionary strategy of the sentient human being. Naturphilosophy once again acquires the status of the basis of the theory of evolution in an explicit way. There is a system of metaphysical postulates and ontological categories derived from the anthropic principle of (...) participation. For modern neoliberal political democracy, bio-power and biopolitics look like the most effective technology for stabilizing the scenarios and trends of the global evolutionary process that are optimal within this ideological system. Conclusions.Transbipolitics in our understanding is a political problematic related to the rationalization of the global evolutionary process. In the coming decades transbipolitics will become the carrier element of the global process of evolution of the noosphere with the consequent complication and increase of cohesion between the individual socio-cultural types that are part of the system of modern globalizing civilization. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

Clearly in contrast to the sociosymbolic approaches that underlie the positions of Butler or Derrida, this article delves into a materialist and machinic reading of the ontology of Deleuze and Guattari. This ontology is the basis of a posthumanist conception that allows to join political philosophy, technology and biology understood as complex rhizomatic systems. From this point of view, we propose to construct an antagonistic posthumanist politics that is an alternative to the pluriversal ethics defended by Braidotti. We believe that (...) the latter maintains an excessively liberal position that prioritizes inclusion as a new form of consensus in the face of conflict. (shrink)

This essay is an occasion to discuss the critical trajectories of a now common field of enquiry concerned with the impact of biomediatic technologies on politics and culture. Thacker's book The Global Genome importantly sits between debates about biopower as the governance of life and biopolitics as the transformation of what life can be. In particular, the book advances the hypothesis that as information produces `life itself', so it has become central to a political economy of excess and surplus value. (...) In other words, information does not dematerialize biology. Bioinformatics and biotech informationalize the living and rematerialize biology. As biotech becomes central to biopower, the global genome comes to reigning profit, labour, racism, biocolonialism, biosecurity, and bioart. However, Thacker's reliance on a bio-ontology of life grounding all relations of power leaves no space for process-events to break the chain of life's perpetual reproduction. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a (...) framework for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Persons are biological beings who participate in social environments. Is human sociality different from that of insects? Is human sociality different from that of a computer or robot with elaborate rules for social interaction in its program memory? What is the relationship between the biology of humans and the sociality of persons? I argue that persons constitute an emergent ontological level that develops out of the biological and psychological realm, but that is largely social in its own constitution. This requires (...) a characterization of the relationships between the bio/psychological and the social, and of the developmental process of emergence. It also requires a framework for modeling the bio/psychological level that makes any such emergence possible. Neither attachment theory nor information processing frameworks, for example, will do — the major orientations toward human sociality today make understanding that sociality ultimately impossible. Only an action framework, such as that of Peirce or Piaget2, suffices. (shrink)

The Cell Cycle Ontology (CCO) has the aim to provide a 'one stop shop' for scientists interested in the biology of the cell cycle that would like to ask questions from a molecular and/or systems perspective: what are the genes, proteins, and so on involved in the regulation of cell division? How do they interact to produce the effects observed in the regulation of the cell cycle? To answer these questions, the CCO must integrate a large amount of knowledge from (...) diverse sources; the irregularity and incompleteness of this information suggests an ontology can act as the means of this integration. The volatility and continued expansion of biological knowledge means the content and modelling of the CCO will have to be frequently changed and updated. The CCO is generated from the input data automatically once every two months. This makes it easy to change the representation to enable certain queries; incorporate new knowledge; and consistently apply design patterns across the CCO. The automatic process also allows the CCO to be delivered in a variety of representations that suit the needs of various CCO customers and the abilities of existing toolsets. In this paper we present the CCO and its characteristics of utility and flexibility, that, from our perspective, make it a beautiful ontology. (shrink)

This paper analyses Agamben’s notion of homo sacer, showing how it should not be confined to the field of a negative critique of biopolitics. In his work, Agamben cautiously delineates a positive figure of homo sacer, whom, according to him, we all virtually are. Such figure would be able to subvert the form in which the relation between bare life and political existence has so far been both thought and lived in the West. How and when is this passage from (...) negative to positive sacredness historically accomplished for Agamben? Is such transit after all thinkable? These are the two basic questions he both unintentionally formulates and leaves undecided in his book Homo Sacer . Agamben further elaborates his investigation of biopolitics in the book he dedicates to Saint Paul, The Time That Remains . Chiesa suggests that, in this volume, the figure of homo sacer as earthly hero is transposed onto that of the messianic man. This can only be achieved by means of a detailed Christian—and more specifically Franciscan—development of the ontological notion of ‘form of life’. Problematically enough, Agamben is able to carry out a transvaluation of biopolitics only in the guise of a bio-theo-politics. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Ontological and Other AssumptionsLloyd A. Wells (bio) and Sandra J. Rackley (bio)Fahrenberg and Cheetham have conducted an immensely thought-provoking study of the assumptions about human nature made by 800 students and pose a question about the future impact of these assumptions on individuals’ practice in professions including medicine and psychotherapy.This work represents a branch of “philosophical anthropology,” which considers assumptions people make about human nature. The authors used a (...) questionnaire, much of which was newly designed, to assess the assumptions made by university students studying psychology, philosophy, sciences, and other disciplines. Most of the respondents were studying at Freiburg, but some were sampled at several other universities in both the former East and West Germanies. Questions involved consciousness and the brain, evolution, free will, belief in God, the meaning of life, and theodicy.Given the importance of these beliefs and assumptions in so many peoples’ lives, it is quite surprising that there are so few modern data available, and this study ventures an important first step in assessing these assumptions. However, there are many problems inherent in this study (and any like it).The first, for us, is the validity of the questionnaire itself, an issue that was not specifically addressed in the paper. Face validity is a problem even in the few questions quoted directly in the paper. For example, some statements contain two clauses, and one could well agree with one without agreeing with another: “I do not know whether a God exists and I do not believe it is possible to know.” This is the most relevant answer for a true agnostic, but the assumption that “I do not know whether a God exists” does not necessarily link at all with “I do not believe it is possible to know.” Similarly, a theist might have trouble with the two clauses, “I know God really exists” and “I do not doubt this.” (Technically, knowledge does imply a lack of doubt, but belief certainly does not.) Particularly in the trilemmas, where various patterns of response were analyzed, these multiple-clause statements may have led students to respond in a manner inconsistent with their true beliefs and assumptions. Furthermore, many of the questions contain terms that may have been unfamiliar to first-year university students. The authors explain their rationale in not defining terms, but the lack of clarity about definitions may have led some of the students to not fully understand the questions asked and to perhaps influence the answers they chose.Misunderstanding of the questions may account for some of the disparities reported in the results. Other apparent inconsistencies, however, do not seem to be a result of unclear questions. For example, sixty percent of the students agreed with the statement that “I believe in … existence after death,” whereas forty-seven percent agreed with the statement that “when my brain is dead my consciousness and my person cease to be.” These [End Page 203] findings do not add up, and this study has several similar sets of data. People contradict themselves in long and complex questionnaires, and this may be a simple explanation for these findings, but is this the only explanation? How seriously did the students take the questionnaire, often given as part of their class? How honest were their responses?How generalizable are the findings of this study? It is very difficult even to speculate about this. The statistics are incomprehensible in light of the data given, and one must essentially take them on faith, wherever one falls on the God/theodicy questions. The design has many flaws, but we do learn how a subsample of German university students rate important factors about the meaning of life. Statements are made in the paper that the students’ results correlate with similar results for the general population, but this assertion seems to be based on a very few questions. One would like much more delineation of this apparent correlation, because we wonder about the juxtaposition of developmental factors with the answers the students gave to this questionnaire. First-year university students are at a critical developmental point, and it would be fascinating to follow this large cohort of students over time to see whether... (shrink)

Human persons exist longer than a single moment in time; they persist through time. However, so far it has not been possible to make this natural and widespread assumption metaphysically comprehensible. The philosophical debate on personal identity is rather stuck in a dilemma: reductionist theories explain personal identity away, while non-reductionist theories fail to give any informative account at all. This chapter argues that this dilemma emerges from an underlying commitment, shared by both sides of in the debate, to an (...) ontology which that gives the priority to static unchanging things. The claim defended here is that the dilemma of personal identity can be overcome if we acknowledge the biological nature of human persons and switch to a process- ontological framework that takes process and change to be ontologically primary. Human persons are biological higher-order processes, rather than things, and their identity conditions can be scientifically investigated. (shrink)

How and why, historian of science Lily Kay asks, did the ‘biological problem of DNA-based protein synthesis’ come to be represented ‘as an information code and a writing technology?’ What sort of metaphor was ‘code’ for these bio-geneticists? One whose run-away expansion, Derrida noted in Of Grammatology (1967), urgently required philosophical justification. Yet, 60 years later, there is still fundamental disagreement about its meaning and epistemic status. If the metaphor lacks ontological purchase, what accounts for its effectiveness? If, on the (...) other hand, scriptural metaphors get at the common root of culture and biology, what do we now mean by ‘code’? In this article, I trace several influential accounts of the metaphor’s effectiveness—making explicit the opposing notions of ‘code’ that animate them—and argue that each is too limited. Greater attention to the metaphoricity of ‘code’ yields a more philosophically productive and critical account of the metaphor of code. (shrink)

Christopher Boorse’s Health care ethics: an introduction, Temple University Press, Philadelphia, pp 359–393, 1987; in Humber, Almeder, Totowa What is disease?, Humana Press, New York City, pp 1–134, 1997; J Med Philos, 39:683–724, 2014) Bio-Statistical Theory comprehends diseases in terms of departures from natural norms, which involve an objectively describable deviation from the proper physiological or psychological functioning of parts of the human organism. I argue that while recent revisions and additional considerations shield the BST from a number of issues (...) raised by critics, they give rise to significant new challenges. These are related to the attribution of epistemic authority, the possibility of multiple concepts in the authoritative literature, and the framing of BST as “philosophical explication.” The conclusion is that, in its current form, the BST is unable to provide a robust framework for a naturalist classification. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Vice and Naturalistic OntologyChristopher R. Williams (bio)Keywordscausality, criminality, determinism, medical model, positivismThese questions have been posed: Is vice (encompassing criminal and other wrongful conduct) best regarded as “sick” behavior, “immoral” behavior, or some other type altogether? Are we to understand vice in natural-medical terms, or are we better served by utilizing a moral framework? Is criminality reducible to and best categorized as a metaphysical type the essential features of (...) which are neurological or otherwise biological in nature? Or, perhaps, is criminality closer to a (non-natural) sociological type, the essential features of which can be understood only through reference to social norms and cultural conventions? These are torturously involved philosophical and theoretical questions that have given rise to an equally torturous volume of literature. Without pretending to do justice to these questions or their corresponding literature, several key considerations that must be inserted into and accounted for within the discursive pursuit of these inquiries are worth noting.Where a naturalistic ontology is employed within the study of vice, we reduce the intricacies of deviant behavioral phenomena to what we presume to be their underlying medical/biological properties. It is worth remembering that behavior itself cannot rightfully be said to be “sick”; rather, what we mean to say is that the behavior in question—in our case, various forms of “vice”—is symptomatic of some underlying illness or medical/biological condition. The presumed underlying sickness and the behavior itself are distinct, ontologically linked only through their theorized relationship to one another. This, then, is a key assumption of the medical approach to vice and its ontological classification as a natural-medical kind: that there exists a relationship between the behavior (a symptom) and the underlying illness or medical condition, and that the relationship is of the causal kind. Vice, it is suggested, is a change in state that is caused by (or, at the very least, is a direct consequence of) sickness or illness. Second, to legitimate such attributions, the illness supplying the requisite causal force must be identifiable and its causal connection to the behavior must be or be capable of being sufficiently explicated. In other words, once we have identified the relevant medical/biological properties and the behavior to which they stand in causal relatedness, we must be prepared to characterize this dynamic—we must be able to show exactly how and why such and such a condition gives rise to such and such a behavior.Problematically, causation itself is and has always been a contentious metaphysical specimen. Hume (1955) reminded us of the troubling reality [End Page 39] that we cannot ever “see” one thing cause or necessitate another. We are left, rather, to merely presume the existence of causal relationships between things. How is it, exactly, that disorder in neurodevelopment can necessitate certain behavioral outcomes? Even if we can “see” (in the empirical sense) the disorder and equally “see” the behavior, we cannot of course witness the precise causal action of the former upon the latter. Even if we are content inferring causal action in such cases, we still need to demonstrate the basic conditions of causality. To show that Condition X is causally related Behavior Y, we need to show that they are regularly associated with one another, that Condition X temporally preceded Behavior Y and, most challengingly, that no other conditions or factors have an intervening (e.g., additive, synergistic) influence. Hypothetically, if we were to posit a causal relationship between schizotypal personality traits and violent behavior, we would need to establish: (1) that schizotypal traits and violent behavior regularly coexist; (2) that those traits presented before the manifestation of the violent behavior; and (3) that no other factors (biological, psychological, and/or sociological) contributed in any meaningful way to those manifestations. We would thus need to systematically rule out family dynamics, income, education, intelligence, substance use, and so forth, as contributing factors. If, in turn, we were to determine that the presence of schizotypal traits alone is not sufficient—even if a necessary condition—to produce violent behavior but, rather, that those traits act in concert with other variables to produce the behavior, then we would not truly be... (shrink)

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and (...) dispositions, to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (shrink)

The author attempts to advance and substantiate a novel theoretical - cosmist1 - approach to reaching the end of integrative universal, truly humane, bio-science.2The work is performed on the original basis of philosophical cosmology, ontology of Absolute Cosmist Wholism, cosmist epistemology, anthropology, and the core principle of CosmoBiotypology. Cosmist theory leads to a person-driven science that is able to integrate subjective and objective knowledge: humankind's personal experience with psychological, biological, and sociological knowledge about the person. In this, the cosmist approach (...) rises to a novel - cosmist functional universal - level of bio-reductionism that relies ultimately on objective scientific knowledge but, at the same time, is primarily person-driven: based on the feelings and perceptions of a person. The core notion of the theory is a person's Basic (Cosmist) Functionality, the realization of which leads to man's3entire ontogenetic well-being.4. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)