A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

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)

Gregory Rocca's nuanced discussion prevents Aquinas's thought from being capsulized in familiar slogans and is an antidote to unilateralist or monochrome views about God-talk.

This paper critically examines a prominent and perennial strategy—found in thinkers as diverse as Kant and Shamik Dasgupta—of simultaneously embracing the Principle of Sufficient Reason and also limiting it so as to avoid certain apparently negative consequences of an unrestricted PSR. I will argue that this strategy of taming the PSR faces significant challenges and may even be incoherent. And for my purposes, I will enlist a generally derided argument by Leibniz for the PSR which will help us to see (...) the connections between the PSR and a radical form of monism. (shrink)

The Parmenidean Ascent is a full-throated and wide-ranging defense of an extreme form of monism or the denial of all distinctions, a form of monism rarely seen since the time of the pre-Socratic philosopher, Parmenides. At once historically sensitive and deeply engaged with trends in recent and contemporary metaphysics, philosophy of action, epistemology, and philosophy of language, The Parmenidean Ascent aims, on rationalist grounds and in a skeptical spirit, to challenge the content of-and to overturn the methods of much of (...) contemporary philosophy. (shrink)

Spinoza's response to a certain radical form of scepticism has deep and surprising roots in his rationalist metaphysics. I argue that Spinoza's commitment to the Principle of Sufficient Reason leads to his naturalistic rejection of certain sharp, inexplicable bifurcations in reality such as the bifurcations that a Cartesian system posits between mind and body and between will and intellect. I show how Spinoza identies and rejects a similar bifurcation between the representational character of ideas or mental states and the epistemic (...) status of these ideas, a bifurcation to which Spinoza sees the radical sceptic committed. Spinoza's rejection of this bifurcation helps to explain some of his most cryptic statements concerning scepticism and also reveals a promising and highly metaphysical strategy for understanding and responding to scepticism. (shrink)

Engineering ethics is usually focused on engineers’ ethics, engineers acting as individuals. Certainly, these professionals play a central role in the matter, but engineers are not a singularity inside engineering ; they exist and operate as a part of a complex network of mutual relationships between many other people, organizations and groups. When engineering ethics and engineers’ ethics are taken as one and the same thing the paradigm of the ethical engineer which prevails is that of the heroic engineer, a (...) certain model of the ideal engineer: someone both quite individualistic and strong enough to deal with all the moral challenges that could arise. We argue that this is not the best approach, at least today in our interrelated world. We have achieved a high degree of independence from nature by means of technology. In exchange for this autonomy we have become increasingly tied up with very complex systems to which we constantly delegate new tasks and powers. Concerns about safety keep growing everywhere due to the fact that now we have a sensitive awareness of the huge amount of power we are both consuming and deploying, thus, new forms of dialogue and consensus have to be incorporated at different levels, in different forums and at different times. Within these democratic channels of participation not just the needs and interests, but also the responsibilities and mutual commitments of all parties should be taken into account. (shrink)

This paper offers a defense of a much-maligned Leibnizian argument for the Principle of Sufficient Reason, the principle according to which whatever is has a sufficient reason or explanation. While Leibniz’s argument is widely thought to rely on a question-begging premise, the paper offers a wholly original and non-question-begging defense of that premise, a defense that Leibniz did not anticipate. The paper does not present this defense of Leibniz's argument as an interpretation of Leibniz; rather, the paper—more modestly in one (...) way, less modestly in another—simply claims that this argument succeeds. (shrink)

This paper presents an argument for the Principle of Sufficient Reason, the PSR, the principle according to which each thing that exists has an explanation. I begin with several widespread and extremely plausible arguments that I call explicability arguments in which a certain situation is rejected precisely because it would be arbitrary. Building on these plausible cases, I construct a series of explicability arguments that culminates in an explicability argument concerning existence itself. This argument amounts to the claim that the (...) PSR is true. The plausibility of the initial cases in the series provides the basis of an argument for the PSR, an argument that can be rebutted only by drawing a line between the plausible early cases in the series and the apparently unacceptable later cases. I argue that no principled reason for drawing this line has been found and that one cannot draw an unprincipled or arbitrary line without begging the question. The paper concludes that, therefore, this defense of the PSR remains unrebutted and that we have a powerful, new reason to embrace the PSR. (shrink)

In some developed nations, corporations are today legally regarded as “people”. But if that were literally true of the Weyland‐Yutani Corporation in the Alien franchise, the least it would deserve is a swift left‐hook to the jaw from Ripley and the few unfortunate persons who survive with her in each of the movies. The question of what constitutes good business practices is what business ethics is all about. In Alien, Carter Burke is the quintessential corporate weasel, and in many ways (...) it's almost as if Gordon Gekko was transported into science fiction. The problem of deferring accountability is unavoidable in any large company, and Weyland‐Yutani is no exception. There are two major approaches to ethics that can help us to understand the extent to which cost‐benefit reasoning is ethical. The first, defended and popularized by Immanuel Kant, is deontology. The second major approach to ethics is utilitarianism, whose most famous early proponent was John Stuart Mill. (shrink)

The notion of ‘omnipotence’ (potentia dei) runs through the history of medieval philosophy especially after the contribution of Augustine’s thought. Augustine thus traces ethical developments from the idea of God’s sovereignty to the construction of an order of things comparable with his power of creation. Augustine was the first Christian thinker to introduce and document the notion of potentia dei in an ethical context, proving at the same time that the ambivalence of God’s power results either from the activity of (...) ordering, or from the impossibility of God’s duplication, or from the incapacity to destroy the world in respect to a rational configuration of laws and events. (shrink)

Escribir sobre ética —y en particular sobre ética médica— en los tiempos que corren comporta un cierto riesgo, no sólo por la posible incompetencia del autor, sino porque éste se encuentra algo desubicado en un entorno de crisis moral propiciada por el cientifismo como nueva religión laica y la voracidad de los mercados. La preocupación de los legos por la creciente dificultad en discernir aquello que es ético o bueno de lo que no lo es constituye en la actualidad un (...) dilema universal, al menos por cuanto respecta a nuestra civilización occidental. Dicha preocupación se encuentra plasmada en decenas de textos dedicados no ya a los aspectos más abstractos o filosóficos de la ética general, sino a las “éticas particulares” aplicables a las profesiones, las empresas o al ámbito político. Así, se habla de una ética periodística, del compliance industrial, de la investigación, de la banca, de las redes de sociales y, por supuesto de la medicina. (shrink)

This first extensive study of Spinoza's philosophy of mind concentrates on two problems crucial to the philosopher's thoughts on the matter: the requirements for having a thought about a particular object, and the problem of the mind's relation to the body. Della Rocca contends that Spinoza's positions are systematically connected with each other and with a principle at the heart of his metaphysical system: his denial of causal or explanatory relations between the mental and the physical. In this way, (...) Della Rocca's exploration of these two problems provides a new and illuminating perspective on Spinoza's philosophy as a system. (shrink)

Scientific risk evaluations are constructed by specific evidence, value judgements and biological background assumptions. The latter are the framework-setting suppositions we apply in order to understand some new phenomenon. That background assumptions co-determine choice of methodology, data interpretation, and choice of relevant evidence is an uncontroversial claim in modern basic science. Furthermore, it is commonly accepted that, unless explicated, disagreements in background assumptions can lead to misunderstanding as well as miscommunication. Here, we extend the discussion on background assumptions from basic (...) science to the debate over genetically modified (GM) plants risk assessment. In this realm, while the different political, social and economic values are often mentioned, the identity and role of background assumptions at play are rarely examined. We use an example from the debate over risk assessment of stacked genetically modified plants (GM stacks), obtained by applying conventional breeding techniques to GM plants. There are two main regulatory practices of GM stacks: (i) regulate as conventional hybrids and (ii) regulate as new GM plants. We analyzed eight papers representative of these positions and found that, in all cases, additional premises are needed to reach the stated conclusions. We suggest that these premises play the role of biological background assumptions and argue that the most effective way toward a unified framework for risk analysis and regulation of GM stacks is by explicating and examining the biological background assumptions of each position. Once explicated, it is possible to either evaluate which background assumptions best reflect contemporary biological knowledge, or to apply Douglas' 'inductive risk' argument. (shrink)

By invoking surprising rationalist considerations that Bernard Williams does not anticipate, this paper defends Williams’s claim that that moral criticism on the basis of purported external reasons amounts to ‘bluff’. After strengthening this rejection of external reasons by drawing parallels to compelling rationalist arguments in other domains, the paper mounts a similarly rationalist critique of internal reasons invoked by Kantian moral philosophers. The paper closes with an apocalyptic line of thought that develops the preceding rationalist arguments into a challenge to (...) the notion of acting for reasons in general. (shrink)

This paper analyzes and evaluates Spinoza way of carrying out his naturalistic program in psychology. I begin by examining Spinoza’s general metaphysical doctrine according to which each thing strives to preserve itself. While this doctrine cannot be true in its unqualified form, it does receive some support from Spinoza’s views on the nature of complex individuals. I then explore the problematic way in which Spinoza applies the doctrine of self -preservation to human psychology. The paper goes on the investigate the (...) naturalistic character of Spinoza’s views on such topics as irrational action, prudence, altruism, mental causation and the nature and classification of affects. (shrink)

The intelligibility of change in Descartes Content Type Journal Article DOI 10.1007/s11016-010-9494-0 Authors Michael Della Rocca, Department of Philosophy, Yale University, P.O. Box 208306, New Haven, CT 06520-8306, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

Se busca dar cuenta del origen y naturaleza de la noción ética y psicoanalítica de culpa. Tanto Freud como Nietzsche se han ocupado de la genealogía de este concepto; cada uno, desde ámbitos distintos, pero que en forma sorprendente confluyen. Asimismo se examina como la noción de culpa es el motivo literario y clave hermenéutica de la sobrecogedora obra de Kafka, lector de Freud. Obras como El proceso, La condena, etc., lo evidencian. La tesis central que aúna este amplio registro (...) de obras y autores referidos ―y en la que radica el valor de este trabajo― es la idea freudiana que la conciencia de culpa preexiste a la falta, esto es, de la existencia de una culpabilidad constitutiva o internalizada que podría ser atribuida a la tradición judeo-cristiana, según la imputación de Nietzsche que se funda en un entramado genealógico más complejo. (shrink)

The introduction of Linear Logic extends the Curry-Howard Isomorphism to intensional aspects of the typed functional programming. In particular, every formula of Linear Logic tells whether the term it is a type for, can be either erased/duplicated or not, during a computation. So, Linear Logic can be seen as a model of a computational environment with an explicit control about the management of resources.