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)

The Parmenides is arguably the pivotal text for understanding the Platonic corpus as a whole. I offer a critical analysis that takes as its key the closely constructed dramatic context and mimetic irony of the dialogue. Read with these in view, the contradictory characterizations of the "one" in the hypotheses dissolve and reform as stages in a systematic response to the objections that Parmenides earlier posed to the young Socrates' notions of forms and participation, potentially liberating Socrates from his dependence (...) on sensible simile and yielding a distinctively conceptual articulation of the difference and relation of forms and their sensible participants. The dialogue as a whole thereby functions as the means for the "conversion" of the soul to eidetic being for which Plato has the elder Socrates call in Republic VII. (shrink)

An effort to track the movement of thought in the proem of the poem in order to discover in it the context for the disclosure of the "is" in fr. s 2 and 8. Close attention to symbolic imagery and historical allusions, and to the philosophical power of the unthinkable "nothing". (For a renewed and expanded effort, see the author's "Ambiguity and Transport: Reflections on the Proem to Parmenides' Poem," Oxford Studies in Ancient Philosophy xxx [2006], 1-47.).

Do the laws of nature supervene on ordinary, non-nomic matters of fact? Lange's criticism of Humean supervenience (HS) plays a key role in his account of natural laws. Though we are sympathetic to his account, we remain unconvinced by his criticism. We focus on his thought experiment involving a world containing nothing but a lone proton and argue that it does not cast sufficient doubt on HS. In addition, we express some concern about locating the lawmakers in an ontology of (...) primitive subjunctive facts and suggest that a 'mixed' metaphysics to the lawmaker question might be attractive. (shrink)

What happens to the inner light of consciousness with the death of the individual body and brain? Reductive materialism assumes it simply fades to black. Others think of consciousness as indicating a continuation of self, a transformation, an awakening or even alternatives based on the quality of life experience. In this issue, speculation drawn from theoretic research are presented. -/- Table of Contents Epigraph: From “The Immortal”, Jorge Luis Borges iii Editor’s Introduction: I Killed a Squirrel the Other Day, Gregory (...) M. Nixon iv-xi Research Essays The Tilde Fallacy and Reincarnation: Variations on a "Skeptical" Argument Teed Rockwell 862-881 Death, Consciousness, and Phenomenology, Steve Bindeman 882-899 The Idealist View of Consciousness After Death, Bernardo Kastrup 900-909 Consciousness, a Cosmic Phenomenon—A Hypothesis, Eva Déli 910-930 The Theory of a Natural Afterlife: A Newfound, Real Possibility for What Awaits Us at Death, Bryon K. Ehlmann 931-950 Near-Death Cases Desegregating Non-Locality/Disembodiment via Quantum Mediated Consciousness: An Extended Version of the Cell-Soul Pathway, Contzen Pereira & J Shashi Kiran Reddy 951-968 On the Possible Existence of Quantum Consciousness After Brain Death, Massimo Pregnolato & Alfredo Pereira Jr. 969-991 Science and Postmortem Survival, Edward F. Kelly 992-1011 Explorations ISS Theory: Cosmic Consciousness, Self, and Life Beyond Death in a Hyperdimensional Physics, Chris H. Hardy 1012-1035 Does the Consciousness End, Remain Awake, or Transform After Death? Radivoj Stankovich (with Micho Durdevich) 1036-1050 Big Bang Spirituality, Life, and Death, Ken Bausch 1051-1063 Death, Consciousness and the Quantum Paradigm, Ronald Peter Glasberg 1064-1077 Living With Limits: The Continuum of Consciousness, Donald Brackett 1078-1098 Mysticism, Consciousness, Death, Mike Sosteric 1099-1118 What Dies? Eternalism and the Afterlife in William James, Jonathan Bricklin 1119-1140 Theories of Consciousness and Death: Does Consciousness End, Continue, Awaken, or Transform When the Body Dies? Roger Cook 1141-1153 It’s the Other Way Around: Matter is a Form of Consciousness and Death is the End of the Illusion of Life in the World, James P. Kowall & Pradeep B. Deshpande 1154-1208 Statements A Feminine Vision for the World Consciousness, & a New Outrageous Ontology, Lorna Green 1209-1217 The Mask of Eternity: The Quest for Immortality and the Afterlife, Iona Miller 1218-1228 Are We Really “such stuff as dreams are made on”? Chris Nunn 1229-1225 Is the Afterlife a Non-Question? (Let's Hope Not), Deepak Chopra 1226-1230 Life After Death? An Improbable Essay, Stuart Kauffman 1231-1236. (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)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

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)

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

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

Investigation of neural and cognitive processes underlying individual variation in moral preferences is underway, with notable similarities emerging between moral- and risk-based decision-making. Here we specifically assessed moral distributive justice preferences and non-moral financial gambling preferences in the same individuals, and report an association between these seemingly disparate forms of decision-making. Moreover, we find this association between distributive justice and risky decision-making exists primarily when the latter is assessed with the Iowa Gambling Task. These findings are consistent with neuroimaging studies (...) of brain function during moral and risky decision-making. This research also constitutes the first replication of a novel experimental measure of distributive justice decision-making, for which individual variation in performance was found. Further examination of decision-making processes across different contexts may lead to an improved understanding of the factors affecting moral behaviour. (shrink)

Initial responses to questionnaires used to assess participants' understanding of informed consent for malaria vaccine trials conducted in the United States and Mali were tallied. Total scores were analyzed by age, sex, literacy (if known), and location. Ninety-two percent (92%) of answers by United States participants and 85% of answers by Malian participants were correct. Questions more likely to be answered incorrectly in Mali related to risk, and to the type of vaccine. For adult participants, independent predictors of higher scores (...) were younger age and female sex in the United States, and male sex in Mali. Scores in the United States were higher than in Mali (P = 0.005). Despite this difference participants at both sites were well informed overall. Although interpretation must be qualified because questionnaires were not intended as research tools and were not standardized among sites, these results do not support concerns about systematic low understanding among research participants in developing versus developed countries. (shrink)

Hoerl & McCormack posit two systems – the temporal updating system and the temporal reasoning system – and suggest that they explain an inherent contradiction in people's naïve theory of time. We suggest there is no contradiction. Something does, however, require explanation: the tension between certain sophisticated beliefs about time, and certain phenomenological states or beliefs about those phenomenological states. The temporal updating mechanism posited by H&M may contribute to this tension.

Stein has characterized one of the central problems in accounting for our knowledge in physics as that of getting the laboratory, or observatory, inside the theory -- that is, of understanding how the mathematical structures of fundamental physical theories have empirical content. He has argued that physicists respond to this problem by giving schematic representations of observers and experiments. In addition, Stein emphasizes the importance of regarding knowledge as an enterprise, with current theories providing guidance for future inquiry. I will (...) explore some ramifications of this way of thinking about the structure of scientific theories for contemporary cosmology. One goal of observational cosmology is to measure the six basic parameters appearing in the standard model of cosmology. These parameters are well-defined if the universe is suitably approximated at some scale by a perturbed FLRW model. The enormous extrapolations involved in the standard model are often justified by the consistent determination of these parameters via a variety of methods. Here I will consider two recent debates regarding this approach to cosmology, inspired by Stein's work. The first debate regards the impact of different ways of characterizing the propagation of light through a cosmological spacetime on the determination of cosmological parameters (such as H_0). The second regards how the highly symmetric FLRW models relate to describing the real universe, at small scales where it is very lumpy. (shrink)

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory (...) of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the “bottom up” approach) and (4) how to infer the nature of the last universal common ancestor (the “top down” approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin.We also describe another family of paths motivated by a” circularity” approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question. (shrink)

This issue of Technoetic Arts: A Journal of Speculative Research (TA) encompasses eight articles by artists and scholars from around the globe who engage with methodologies of art practice within research that reflects on technological and ecological change, contributing to the discourse on the inclusion of subjective experience in research. The articles by authors Dulmini Perera, Kate Doyle, Nora S. Vaage, Merete Lie, Nikita Peresin Meden, Kristina Pranjić, Peter Purg, Nicolaas H. Jacobs, Marth Munro, Chris Broodryk, Semi Ryu, Rahul (...) Mahata, Doreswamy, Sana Altaf and Aqib Javid Parry form a collection that crosses disciplines and genres to engage in fundamental critique of existing modes of enquiry and conclusion. The texts situate art and design methodologies in particular cultural contexts and in relation to frameworks defined by research methodologies of the sciences and humanities to gain agency for critique and to counter a sense of inevitability that has come to mark the most recent crises. (shrink)

This special edition brings together (1) the recent methodological worries of the moralism/realism and ideal/non-ideal theory debates with (2) the soaring ambition of work in international or global political theory, as found in, say, theories of global justice. Contributors are as follows: Chris Bertram, Jonathan Floyd, Aaron James, Terry MacDonald, David Miller, Shmulik Nili, Mathias Risse and Matt Sleat.

According to Conceptual Role Semantics, the meaning of a representation is the role of that representation in the cognitive life of the agent, e.g. in perception, thought and decision-making. It is an extension of the well known "use" theory of meaning, according to which the meaning of a word is its use in communication and more generally, in social interaction. CRS supplements external use by including the role of a symbol inside a computer or a brain. The uses appealed to (...) are not just actual, but also counterfactual: not only what effects a thought does have, but what effects it would have had if stimuli or other states had differed. The view has arisen separately in philosophy and in cognitive science. The source of the view is Wittgenstein and Sellars, but the source in contemporary philosophy is a series of papers by Harman and Field. Other proponents in philosophy have included Block, Horwich, Loar, McGinn and Peacocke. In cognitive science, they include Woods and Miller and Johnson-Laird. (shrink)

Benjamin Libet's celebrated experiments concerning freedom elicited numerous attempts of _philosophical_ repudiation. Ten years ago, however, Judy Trevena and Jeff Miller published a _technical_ objection; they claim to have detected a,,smearing artifact" in Libet's calculations. This rests on a misunderstanding of Libet's methodology. In my reconstruction of Libet's argument, he draws an abductive inference to the best explanation. Now, Trevena's and Miller's objection does indeed lead to alternative explanations of Libet's measurements. These alternatives are _ad hoc_ and extremely (...) improbable. They constitute worse explanations than the explanation offered by Libet. _German_ Benjamin Libets bahnbrechende Experimente zur Willensfreiheit aus den Achtziger Jahren des vorigen Jahrhunderts gehören längst zu den Klassikern der Experimentalkunst. Aus _philosophischer_ Perspektive sind sie oft kritisiert worden; unabhängig davon ist zu Beginn des neuen Jahrtausends ein _technischer_ Einwand gegen Libet prominent geworden, der von Freiheitsfreunden gerne zitiert wird. Er geht auf Judy Trevena und Jeff Miller zurück und besteht in dem Vorwurf, dass Libet mit seiner Berechnung der _gemittelten_ Bereitschaftspotential-Kurven die wahren Verhältnisse verschmiere und dabei aus mathematischen Gründen den Anstiegs-Zeitpunkt des Bereitschaftspotentials künstlich nach vorne verschiebe – das ist der Vorwurf des sog. Verschmierungsartefakts. Ich zeige, dass der Vorwurf nicht sticht. Er beruht auf einem Missverständnis der Schlussmethode Libets. Laut meiner wissenschaftstheoretischen Rekonstruktion zieht Libet weder deduktive noch induktive Schlüsse aus seinen Einzelbeobachtungen; er schließt abduktiv, d.h. er schließt auf die beste Erklärung seiner Einzelbeobachtungen. Wie eine genaue arithmetische Analyse zeigt, bieten die Alternativ-Erklärungen, unter denen sich das Verschmierungsartefakt bewahrheiten würde, schlechtere Erklärungen als Libets Erklärung – sie sind an den Haaren herbeigezogen und extrem unwahrscheinlich. (shrink)

Philosophy of science is expanding via the introduction of new digital data and tools for their analysis. The data comprise digitized published books and journal articles, as well as heretofore unpublished material such as images, archival text, notebooks, meeting notes, and programs. The growth in available data is matched by the extensive development of automated analysis tools. The variety of data sources and tools can be overwhelming. In this article, we survey the state of digital work in the philosophy of (...) science, showing what kinds of questions can be answered and how one can go about answering them. (shrink)

Argumentation schemes can be described as abstract structures representing the most generic types of argument, constituting the building blocks of the ones used in everyday reasoning. This paper investigates the structure, classification, and uses of such schemes. Three goals are pursued: 1) to describe the schemes, showing how they evolved and how they have been classified in the traditional and the modern theories; 2) to propose a method for classifying them based on ancient and modern developments; and 3) to outline (...) and show how schemes can be used to describe and analyze or produce real arguments. To this purpose, we will build on the traditional distinctions for building a dichotomic classification of schemes, and we will advance a modular approach to argument analysis, in which different argumentation schemes are combined together in order to represent each step of reasoning on which a complex argument relies. Finally, we will show how schemes are applied to formal systems, focusing on their applications to Artificial Intelligence, AI & Law, argument mining, and formal ontologies. (shrink)

Public health is concerned with increasing the health of the community at whole. Insofar as health is a ‘good’ and the community constitutes a ‘public’, public health by definition promotes a ‘public good’. But ‘public good’ has a particular and much more narrow meaning in the economics literature, and some commentators have tried to limit the scope of public health to this more narrow meaning of a ‘public good’. While such a move makes the content of public health less controversial, (...) it also strips important goals from the realm of public health, goals that traditionally have been, and morally should be, a part of it. Instead, I will argue, while public health should be defined by public goods, it should be defined by a broader conception of public goods that I shall call ‘normative public goods’, goods that ought to be treated as if they were public goods in the more narrow sense. (shrink)

The current industrial revolution is said to be driven by the digitization that exploits connected information across all aspects of manufacturing. Standards have been recognized as an important enabler. Ontology-based information standard may provide benefits not offered by current information standards. Although there have been ontologies developed in the industrial manufacturing domain, they have been fragmented and inconsistent, and little has received a standard status. With successes in developing coherent ontologies in the biological, biomedical, and financial domains, an effort called (...) Industrial Ontologies Foundry (IOF) has been formed to pursue the same goal for the industrial manufacturing domain. However, developing a coherent ontology covering the entire industrial manufacturing domain has been known to be a mountainous challenge because of the multidisciplinary nature of manufacturing. To manage the scope and expectations, the IOF community kicked-off its effort with a proof-of-concept (POC) project. This paper describes the developments within the project. It also provides a brief update on the IOF organizational set up. (shrink)

Being able to ask others to do things, and thereby giving them reasons to do those things, is a prominent feature of our interpersonal lives. In this paper, I discuss the distinctive normative status of requests – what makes them different from commands and demands. I argue for a theory of this normative phenomenon which explains the sense in which the reasons presented in requests are a matter of discretion. This discretionary quality, I argue, is something that other theories cannot (...) accommodate, though it is a significant aspect of the relations that people stand in to one another, and the kinds of practical reasons that flow from those relations. (shrink)

The scientific community, we hold, often provides society with knowledge—that the HIV virus causes AIDS, that anthropogenic climate change is underway, that the MMR vaccine is safe. Some deny that we have this knowledge, however, and work to undermine it in others. It has been common to refer to such agents as “denialists”. At first glance, then, denialism appears to be a form of skepticism. But while we know that various denialist strategies for suppressing belief are generally effective, little is (...) known about which strategies are most effective. We see this as an important first step toward their remediation. This paper leverages the approximate comparison to various forms of philosophical skepticism to design an experimental test of the efficacy of four broad strategies of denial at suppressing belief in specific scientific claims. Our results suggest that assertive strategies are more effective at suppressing belief than questioning strategies. (shrink)

Some astronomers believe that we have discovered that Pluto is not a planet. I contest this assessment. Recent discoveries of trans-Neptunian Pluto-sized objects do not require that we exclude Pluto from the planets. But the obvious alternative, that classificatory revision is a matter of arbitrary choice, is also unpalatable. I argue that this classificatory controversy — which I compare to the controversy about the classification of the platypus — illustrates how our classificatory practices are laden with normative commitments of a (...) distinctive kind. I argue that the “norm-ladenness” of classification has philosophically significant ramifications for how we think about scientific disputes and debates in the metaphysics of classification such as the monism/pluralism debate. (shrink)

There are a bewildering variety of claims connecting Darwin to nineteenth-century philosophy of science—including to Herschel, Whewell, Lyell, German Romanticism, Comte, and others. I argue here that Herschel’s influence on Darwin is undeniable. The form of this influence, however, is often misunderstood. Darwin was not merely taking the concept of “analogy” from Herschel, nor was he combining such an analogy with a consilience as argued for by Whewell. On the contrary, Darwin’s Origin is written in precisely the manner that one (...) would expect were Darwin attempting to model his work on the precepts found in Herschel’s Preliminary Discourse on Natural Science. While Hodge has worked out a careful interpretation of both Darwin and Herschel, drawing similar conclusions, his interpretation misreads Herschel’s use of the vera causa principle and the verification of hypotheses. The new reading that I present here resolves this trouble, combining Hodge’s careful treatment of the structure of the Origin with a more cautious understanding of Herschel’s philosophy of science. This interpretation lets us understand why Darwin laid out the Origin in the way that he did and also why Herschel so strongly disagreed, including in Herschel’s heretofore unanalyzed marginalia in his copy of Darwin’s book. (shrink)

As we look beyond our terrestrial boundary to a multi-planetary future for humankind, it becomes paramount to anticipate the challenges of various human factors on the most likely scenario for this future: permanent human settlement of Mars. Even if technical hurdles are circumvented to provide adequate resources for basic physiological and psychological needs, Homo sapiens will not survive on an alien planet if a dysfunctional psyche prohibits the utilization of these resources. No matter how far we soar into the stars, (...) our psychologies for future generations will be forever tethered to the totality of our surroundings. By shaping our environment toward survival and welfare during the voyage to Mars and in a Martian colony, we indirectly shape our psyches and prepare them for a mission of unprecedented alienation and duration. Once on Mars, human factors such as leadership structure, social organization and code of conduct, group size, gender balance, developmental cycle, mobility, length of stay and the ecological settings and type and manner of subsistence, will create a novel Martian culture. The degree that settlers are severed from the Earth will affect how radically foreign this culture will be when compared with cultures on Earth. (shrink)

We can clarify a certain difficulty with regard to the phrase ‘the best and most perfect virtue’ in Aristotle’s definition of the human good in Nicomachean Ethics I 7 if we make use of two related distinctions: Donnellan’s attributive–referential distinction and Kripke’s distinction between speaker’s reference and semantic reference. I suggest that Aristotle is using the phrase ‘the best and most perfect virtue’ attributively, not referentially, and further that even though the phrase may refer to a specific virtue (semantic reference), (...) Aristotle is not using the phrase to refer to a specific virtue (speaker’s reference). (shrink)

In recent years there has been a number of promising technical and institutional developments regarding use of ontologies in industry. At the same time, however, most industrial ontology development work remains within the realm of academic research and is without significant uptake in commercial applications. In biomedicine, by contrast, ontologies have made significant inroads as valuable tools for achieving interoperability between data systems whose contents derive from widely heterogeneous sources. In this position paper, we present a set of principles learned (...) from the successful Open Biomedical Ontologies (OBO) Foundry initiative to guide the design and development of the Industrial Ontologies Foundry (IOF), which is a counterpart to the OBO Foundry initiative for the manufacturing industry. We also illustrate the potential utility of these principles by sketching the conceptual design of a framework for sustainable IOF development. (shrink)

Since nothing about God is passive, and the perception of pain is inherently passive, then it seems that God does not know what it is like to experience pain. Nor would he be able to cause us to experience pain, for his experience would then be a sensation (which would require God to have senses, which he does not). My suggestion is that Berkeley avoids this situation by describing how God knows about pain “among other things” (i.e. as something whose (...) identity is intelligible in terms of the integrated network of things). This avoids having to assume that God has ideas (including pain) apart from his willing that there be perceivers who have specific ideas that are in harmony or not in harmony with one another. (shrink)

Plagiarism detection is the process of finding similarities on electronic based documents. Recently, this process is highly required because of the large number of available documents on the internet and the ability to copy and paste the text of relevant documents with simply Control+C and Control+V commands. The proposed solution is to investigate and develop an easy, fast, and multi-language support plagiarism detector with the easy of one click to detect the document plagiarism. This process will be done with the (...) support of intelligent system that can learn, change and adapt to the input document and make a cross-fast search for the content on the local repository and the online repository and link the content of the file with the matching content everywhere found. Furthermore, the supported document type that we will use is word, text and in some cases, the pdf files –where is the text can be extracting from them- and this made possible by using the DLL file from Word application that Microsoft provided on OS. The using of DLL will let us to not constrain on how to get the text from files; and will help us to apply the file on our Delphi project and walk throw our methodology and read the file word by word to grantee the best working scenarios for the calculation. In the result, this process will help in the uprising the documents quality and enhance the writer experience related to his work and will save the copyrights for the official writer of the documents by providing a new alternative tool for plagiarism detection problem for easy and fast use to the concerned Institutions for free. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Wie wollen und können wir die Zukunft gestalten? Wie die Herausforderungen, die technische Innovationen, Digitalisierung und Künstliche Intelligenz (KI) mit sich bringen, meistern? In diesem Band kommen Philosophen, Ingenieur- und Naturwissenschaftler ebenso zu Wort wie Juristen, Bildungswissenschaftler und Ökonomen. Sie alle blicken vom speziellen Standpunkt ihres Fachs auf die Gestaltung der Zukunft. Als Brücke erweist sich dabei die Philosophie, welche die verschiedenen Perspektiven verknüpft und eint. Das Selbstverständnis von APHIN, des wissenschaftlichen und gemeinnützigen Arbeitskreises philosophierender Ingenieure und Naturwissenschaftler, – die (...) Offenheit für die Fragen und Probleme des jeweils anderen – ist damit in allen Beiträgen gegenwärtig. (shrink)

Recent studies show that racism still exists in the American medical profession, the fact of which legitimizes the historically long-legacy of mistrust towards medical profession and health authorities among African Americans. Thus, it was suspected that the participation of black patients in end-of-life care has always been significantly low stemmed primarily from their mistrust of the medical profession. On the other hand, much research finds that there are other reasons than the mistrust which makes African Americans feel reluctant to the (...) end-of-life care, such as cultural-religious difference and genuine misunderstanding of the services. If so, two crucial questions are raised. One is how pervasive or significant the mistrust is, compared to the other factors, when they opt out of the end-of-life care. The other is if there is a remedy or solution to the seemingly broken relationship. While no studies available answer these questions, we have conducted an experiment to explore them. The research was performed at two Philadelphia hospitals of Mercy Health System, and the result shows that Black patients’ mistrust is not too great to overcome and that education can remove the epistemic obstacles as well as overcome the mistrust. (shrink)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

This paper is about conjunctions and disjunctions in the scope of non-doxastic atti- tude verbs. These constructions generate a certain type of ignorance implicature. I argue that the best way to account for these implicatures is by appealing to a notion of contex- tual redundancy (Schlenker, 2008; Fox, 2008; Mayr and Romoli, 2016). This pragmatic approach to ignorance implicatures is contrasted with a semantic account of disjunctions under `wonder' that appeals to exhausti cation (Roelofsen and Uegaki, 2016). I argue that (...) exhausti cation-based theories cannot handle embedded conjunctions, so a pragmatic account of ignorance implicatures is superior. (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build is the domain mid-level (...) ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

This volume offers a rich and accessible introduction to contemporary research on Buddhist ethical thought. It includes contributions of many of the leading scholars in this field, on topics including the nature of Buddhist ethics, karma and rebirth, mindfulness, narrative, intention, free will, politics, anger, and equanimity.

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

The 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)