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)

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)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (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)

A lineage of prominent philosophers who have discussed the second-person relation can be regarded as advancing structural accounts. They posit that the second-person relation effects one transformative change to the structure of practical reasoning. In this paper, I criticise this orthodoxy and offer an alternative, substantive account. That is, I argue that entering into second-personal relations with others does indeed affect one's practical reasoning, but it does this not by altering the structure of one's agential thought, but by changing what (...) reasons can become available. The importance of second-personal thought for action is heterogenous. Second-person relations make possible the emergence of a wide variety of different kinds of practical reasons: creating some, revealing others. Recognising this diminishes the appeal of the traditional, structural accounts of the practical significance of such second-personal relations. Moving away from structural accounts facilitates a more thorough understanding of the intersubjective form of action. (shrink)

In his Posterior Analytics Aristotle confronted a problem that threatened his vision of scientific knowledge as an axiomatic system: if scientific knowledge is demonstrative in character, and if the axioms of a science cannot themselves be demonstrated, then the most basic of all scientific principles will remain unknown. In the famous concluding chapter of this work (II 19), he claimed to solve this problem by distinguishing two kinds of knowledge: we cannot have epistêmê of the first principles, but we can (...) have nous of them. This ‘solution’ has struck many students of his thought as hopelessly ad hoc and unpersuasive. And nowhere is Aristotle less persuasive than when he appeals to a faculty of intuition or a priori insight which arrives on the scene precisely when it is most needed. I defend Aristotle’s account by showing how nous is not properly characterized as a faculty of intuition which operates independently of sense experience. Rather, nous is a kind of knowledge that is available to us whenever our mind advances from the perception of particular individuals to grasp the relevant universal concept or general principle. (shrink)

It is common for people to be sensitive to aesthetic qualities in one another’s speech. We allow the loveliness or unloveliness of a person’s voice to make impressions on us. What is more, it is also common to allow those aesthetic impressions to affect how we are inclined to feel about the speaker. We form attitudes of liking, trusting, disliking or distrusting partly in virtue of the aesthetic qualities of a person’s speech. In this paper I ask whether such attitudes (...) could ever be legitimate. This is a microcosm of the broader issue of whether people’s aesthetic qualities in general can justify the interpersonal valuing-attitudes that they so often cause. I draw from recent discussions of body aesthetics to articulate a pair of challenges. One challenge says that aesthetic judgements of speech are reliant on unjustifiable prejudices. The other holds that a person’s aesthetic qualities are irrelevant to whether they should be liked. Against these challenges I argue that some speech can bear aesthetic qualities which are not reliant on prejudice and which are relevant to whether the speaker should be liked. I develop this argument through an analysis of the concept of lyricism. (shrink)

Computer and information ethics, as well as other fields of applied ethics, need ethical theories which coherently unify deontological and consequentialist aspects of ethical analysis. The proposed theory of just consequentialism emphasizes consequences of policies within the constraints of justice. This makes just consequentialism a practical and theoretically sound approach to ethical problems of computer and information ethics.

Some reasons are thought to depend on relations between people, such as that of a promiser to a promisee. It has sometimes been assumed that all reasons that are relational in this way are moral obligations. I argue, via a counter example, that there are non-obligatory relational reasons. If true, this has ramifications for relational theories of morality.

In book Zeta of the Metaphysics and elsewhere Aristotle appears to commit himself to the following propositions: (1) No universal can be substance; (2) Form is a universal; and (3) Form is that which is most truly substance. These propositions appear to constitute an inconsistent triad lying at the heart of Aristotle’s ontology. A number of attempts have been made to rescue Aristotle from the charge of inconsistency. Some have claimed that Aristotle did not subscribe to (1), but only to (...) the proposition that nothing predicated universally can be substance. Others hold that, contrary to (2), form is not a universal but peculiar to each individual. Still others argue that the sense of ‘substance’ in which the species form is a substance is not the sense in which no universal is substance. I argue that none of these attempts to rescue Aristotle from the charge of inconsistency is ultimately defensible. (shrink)

This paper is about the similarity between the appreciation of a piece of art, such as a cherished music album, and the loving appreciation of a person whom one knows well. In philosophical discussion about the rationality of love, the Qualities View (QV) says that love can be justified by reference to the qualities of the beloved. I argue that the oft-rehearsed trading-up objection fails to undermine the QV. The problems typically identified by the objection arise from the idea that (...) love-worthy qualities could be coarse-grained, when in fact they must be fine-grained. The analogy with appreciation of aesthetic qualities helps to draw out this point. Once the fine-grained nature of love-worthy qualities is properly understood, it is clear that critics of the QV cannot rely on the trading-up objection to motivate its rejection. Moreover, the paper’s core argument helps to illuminate the persistently aesthetic nature of interpersonal affections. (shrink)

The ethical philosophy of Emmanuel Levinas is typically associated with a punishing conception of responsibility rather than freedom. In this chapter, our aim is to explore Levinas’s often overlooked theory of freedom. Specifically, we compare Levinas’s account of freedom to the Kantian (and Fichtean) idea of freedom as autonomy and the Hegelian idea of freedom as relational. Based on these comparisons, we suggest that Levinas offers a distinctive conception of freedom—“finite freedom.” In contrast to Kantian autonomy, finite freedom constitutively involves (...) standing in certain social relations with others. And in contrast to Hegelian relational freedom, the social relations involved in finite freedom are not defined by mutual recognition, but by feelings of separation and even antagonism. Along the way, we promote a reading Levinas’s Totality and Infinity as a Hegel-style story of Bildung (development), and show how, on Levinas’s view, freedom can develop or mature in the life of the individual. (shrink)

Parmenides may fairly be said to have undertaken two parallel efforts: first, to offer a persuasive account of the nature of ‘what-is’ (to eon); and second, to establish ‘it is’ as the only true and trustworthy way of speaking and thinking about what-is. Fragment 7.3-6 plays a crucial role in this latter effort when Parmenides’ goddess directs the youth to put aside all information obtained through sense perception and instead ‘judge by reason the poludêris elenchos spoken by me.’ Although the (...) meaning of the phrase has been variously understood, I argue that it is properly taken to mean ‘a much-contested testing’ (of the possible ways of inquiry). In characterizing the elenchos as poludêris or ‘much contested’ the goddess is asserting that the decision to follow the ‘it is’ route of inquiry must be continually reaffirmed against the pull of custom and sense experience. (shrink)

Xenophanes of Colophon (fl. 530 BC) is widely regarded as the first skeptic in the history of Western philosophy, but the character of his skepticism as expressed in his fragment B 34 has long been a matter of debate. After reviewing the interpretations of B 34 defended by Hermann Fränkel, Bruno Snell, and Sir Karl Popper, I argue that B 34 is best understood in connection with a traditional view of the sources and limits of human understanding. If we hold (...) that mortal beings can achieve certain knowledge only with the assistance of divine powers, while rejecting any possibility of bridging the divine-human gap, a broad skepticism concerning the prospects for human knowledge becomes inevitable. It is therefore of some relevance that Xenophanes repudiated the practice of divination through signs (mantikê) and offered entirely naturalistic explanations of phenomena popularly regarded as indications of the divine will (thunder, lightning, eclipses, rainbows, etc.). (shrink)

This article is the SECOND of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This short article provides intriguing evidence that the Bible was encoded by its original redactors. It then proposes innovative interpretations of some of the Bible's important words and stories.

Arthur Danto claims that knowing that S is not a property of some individual knower M but a relation between M and some object O in the world, where O is what makes S true. For if knowledge were a property of M it would be possible to determine whether M knew simply by examining M, which is typically not the case (i.e. unless S happens to be about M). I argue that Danto errs in: (1) claiming that we can (...) determine whether or not some assertion S is true only by observing the truth conditions for S; (2) claiming that we cannot determine whether s is true by examining M; and (3) claiming that since the statement that M knows that S ‘says something about both M and the world’ it must assert a relation between M and the world. (shrink)

Keith Lehrer has put forward an argument for skepticism which trades on the possibility that a group of creatures in another galaxy (Googols) may be rendering our beliefs about reality largely false (this is ‘Lehrer’s Skeptical Hypothesis’). Since there are no arguments against the Lehrer-Googol hypothesis, it cannot be rejected as unjustified. But since we can be completely justified in believing that p only when hypotheses which conflict with our belief are unjustified, we cannot be completely justified in believing that (...) p. Hence, we can never know that p. I argue that Lehrer’s argument fails in so far as believers on both sides of a question may be completely justified in their beliefs. Since this is so, one can be completely justified in believing p, and thereby know that p, even when an opposing view is itself completely justified. (shrink)

At the heart of Levinas’s work is the apparently simple idea that through the encounter with another person, we are forced to give up our self-concern and take heed of the ethical relation between us. But, while simple on the surface, when one tries to characterize it in more detail, it can be hard to fit together the various ways in which Levinas talks about this relation and to identify precisely what he took its normative structure to be, as this (...) is described in a number of apparently different ways, that are not obviously compatible or equivalent, such as “command,” “call,” “summons,” “demand,” and so on. In this chapter, we intend to focus on these different characterizations and show what makes them different while also endeavoring to find a way in which Levinas’s conception may nonetheless be fitted together into a coherent account of the face-to-face encounter that is at the heart of his ethics. We will begin by considering the different normative terms used to characterize the encounter in that text and show how they are conceptually distinct from one another; we will then offer a way to read Levinas’s position to nonetheless show how these different normative relations can be fitted together into a stable position. (shrink)

I argue that these inconsistencies in wording and practice reflect the existence of two distinct Aristotelian views of inquiry, one peculiar to the Posterior Analytics and the other put forward in the Physics and practiced in the Physics and in other treatises. Although the two views overlap to some degree (e.g. both regard a rudimentary understanding of the subject as an essential first stage), the view of the syllogism as the workhorse of scientific investigation and the related view of inquiry (...) as a search for the ‘missing middle terms’ turn out to be ideas peculiar to the Analytics. Conversely, the techniques of analysis and differentiation highlighted in the Physics account receive only cursory attention in the Analytics. However, when we consider the character of Aristotle’s own inquiries, on both scientific and philosophical topics, it becomes clear that it is the Physics rather than the Posterior Analytics that gives us Aristotle’s considered view the path to knowledge. (shrink)

This article is the SIXTH of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

A. E. Taylor states the widely held view that Plato’s Euthyphro posed a question which figured prominently in later ethical controversies: “It amounts to asking whether acts of piety, or more generally virtuous acts, derive their character of being right from the mere fact of being commanded or are commanded because they are antecedently intrinsically right.” I argue against this characterization of the Euthyphro. The argument Socrates deploys against Euthyphro’s third and most serious definition of holiness or piety (to hosion) (...) is not the opening round in the debate over divine command theory nor is a discussion of the nature of holiness ipso facto an exercise in ethical theory. (shrink)

Genetic explanations of religious belief, such as Freud’s analysis of theism as ‘a neurotic relic’, pose a problem for theists: how far do such explanations establish the irrationality of religious belief? I argue that genetic analyses of belief suffer from a number of limitations. Showing that some reason-irrelevant factor or factors were sufficient to produce conviction on some occasion would not establish that they were necessary in every case of religious conviction. Showing that reason-irrelevant factors were both necessary and sufficient (...) to produce conviction would not establish that reason-relevant factors were entirely absent. And showing that reason-relevant factors played no role in the adoption of the belief would not establish that they were absent in its continued retention. I conclude that we will profitably investigate the plausibility of religious beliefs by attending to the reasons that can be given for or against them rather than by speculating about their causes. (shrink)

This article is the FIFTH of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This article is the FOURTH of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This article is the FIRST of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This article is the THIRD of several excerpts from my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book is posted on this site). “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find (...) a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This book compares Hindu nondual philosophy to that of Baruch Spinoza, demonstrating the similarity of Spinoza’s ideas to Kashmiri Pratyabhijñā Shaivism. The book is well researched, but it is written in an informal style suitable for both scholars and the educated general public. There is already some scholarly literature comparing Spinoza’s philosophy to Śaṅkara’s Vedānta, but none of it has focused, as this book does, on philosophy of mind, and none of it has included nondual Kashmiri Shaivism in the comparison. (...) Among other things, the important distinction between Śaṅkara’s Vedānta and nondual Kashmiri Shaivism is brought to the fore by looking at those two philosophies through the lens of Spinoza. “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

This single pdf includes ALL SEVEN of my Dogma Revue articles, which together comprise the entirety of my book The Nondual Mind: Vedānta, Kashmiri Pratyabhijñā Shaivism, and Spinoza (the full book in manuscript form is also posted on this site). The book compares Hindu nondual philosophy to that of Baruch Spinoza, demonstrating the similarity of Spinoza’s ideas to Kashmiri Pratyabhijñā Shaivism. The book is well researched, but it is written in an informal style suitable for both scholars and the educated (...) general public. There is already some scholarly literature comparing Spinoza’s philosophy to Śaṅkara’s Vedānta, but none of it has focused, as this book does, on philosophy of mind, and none of it has included nondual Kashmiri Shaivism in the comparison. Among other things, the important distinction between Śaṅkara’s Vedānta and nondual Kashmiri Shaivism is brought to the fore by looking at those two philosophies through the lens of Spinoza. “I liked James H. Cumming’s The Nondual Mind a lot. It is beautifully written, thoughtful, and very clear.” (Prof. Yitzhak Y. Melamed, Charlotte Bloomberg Professor of Philosophy, Johns Hopkins University) “James H. Cumming’s scholarly interpretation of Spinoza’s works, persuasively showing how 17th century European ideas that ushered in the Enlightenment find a precursor in 10th century Kashmir, is a masterpiece of reason and philosophy that will leave the reader with profound thoughts on the meaning of history, God, and life itself. As a senior staff attorney in my chambers for many years at the California Supreme Court and a top scholar of ethics and philosophy of law, Mr. Cumming never ceased to amaze me with his outstanding research and intellect. This scholarly book is a must read for all who want to know why Spinoza continues to influence contemporary philosophy and how his work is still relevant in today’s challenging, interconnected world.” (Hon. Ming W. Chin, Associate Justice (Retired), Supreme Court of California, 1996–2020). (shrink)

Amidst the lively and often highly positive reception of this best-selling collection of six essays in feminist philosophy, some critics have complained that it does not seem to argue for very much...

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

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

This "book review" was published as the preface of Karl Renz's entertaining book If You Wake Up, Don't Take It Personally: Dialogues in the Presence of Arunachala (Aperion 2011). The subject matter is Neo-Vedānta.

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)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

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

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

Creationists who object to evolution in the science curriculum of public schools often cite Jonathan Well’s book Icons of Evolution in their support (Wells 2000). In the third chapter of his book Wells claims that neither paleontological nor molecular evidence supports the thesis that the history of life is an evolutionary process of descent from preexisting ancestors. We argue that Wells inappropriately relies upon ambiguities inherent in the term ‘Darwinian’ and the phrase ‘Darwin’s theory’. Furthermore, he does not accurately distinguish (...) between the overwhelming evidence that supports the thesis of common descent and controversies that pertain to causal mechanisms such as natural selection. We also argue that Wells’ attempts to undermine the evidence in support of common descent are flawed and his characterization of the relevant data is misleading. In particular, his assessment of the ‘Cambrian explosion’ does not do justice to the fossil record. Nor do his selective references to debate about molecular and paleontological phylogenies constitute a case against common descent. We conclude that the fossil and molecular evidence is more than sufficient to warrant science educators to present common descent as a well-established scientific fact. We also argue that diagrams depicting the ‘tree of life’ can be pedagogically useful as simplified representations of the history of life. (shrink)

The Universal Core (UCore) is a central element of the National Information Sharing Strategy that is supported by multiple U.S. Federal Government Departments, by the intelligence community, and by a number of other national and international institutions. The goal of the UCore initiative is to foster information sharing by means of an XML schema providing consensus representations for four groups of universally understood terms under the headings who, what, when, and where. We here describe a project to create an ontology-based (...) supporting layer for UCore, entitled ‘Universal Core Semantic Layer’ (UCore SL), and describe how UCore SL can be applied to further UCore’s information sharing goals. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

Children continue to be overlooked as a topic of concern in discussions around the ethical use of people’s data and information. Where children are the subject of such discussions, the focus is often primarily on privacy concerns and consent relating to the use of their data. This paper highlights the unique challenges children face when it comes to online interferences with their decision-making, primarily due to their vulnerability, impressionability, the increased likelihood of disclosing personal information online, and their developmental capacities. (...) These traits allow for practices such as hypernudging to be executed on them more accurately and with more serious consequences, specifically by potentially undermining their autonomy. We argue that children are autonomous agents in the making and thus require additional special protections to ensure that the development of their autonomy is safeguarded. This means that measures should be taken to prohibit most forms of hypernudging children and thus ensure that they are protected from this powerful technique of digital manipulation. (shrink)

I offer an interpretation of Carnap and Quine’s views on cognitive significance and insignificance. The basic idea behind their views is as follows: to judge an expression is insignificant is to recommend it not be used in or explicated into languages used to express truth-valued judgments in inquiry; to judge an expression is significant is to recommend it be used in or explicated into such languages. These judgments are pragmatic judgments, made in light of purposes for language use in inquiry. (...) For Carnap at least, these pragmatic judgments are non-cognitive. This basic idea is only a roughly correct statement of their views. This is because the details of the scientific languages they recommend for inquiry are necessary to understand their views and the way they understand their own views. Even so, I offer two reasons to suggest that this basic idea is worthy of our consideration today. First, it provides a conception of significance that captures the natural thought that epistemological concerns can lead us to consider expressions to be insignificant without requiring an objectionable form of verificationism. Second, if we appeal also to Carnap and Quine’s pluralistic attitude toward explication, we can make a pragmatic judgment that an expression is insignificant while judging it to be significant on a distinct explication of significance fit for describing and explaining natural language. (shrink)

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

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...) comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

This synthesis of 5 prominent conflict management paradigms uses power differential as the single most contributing variable to their process and outcome of conflict. Efforts of scholars to integrate or synthesize conflict paradigms have been unsuccessful or clumsy by the scholars’ own assessments. The 5 selected paradigms represent an interdisciplinary set of normative and descriptive paradigms from different social contexts and intellectual frameworks. The 5 share the common traits of rival goals, three levels of socially constructed power differential, and outcomes (...) relative to the total value of the rival goal. An inverse relationship between power differential and the total value of conflict outcomes is supported by all 5 paradigms and empirical data. Explanatory metatheory is the methodology used for synthesis. An increase in power differential results in a decrease in total value of the rival goal. Power differential is constructed using Max Weber’s ideal-type method. The power differentials are abstracted from the paradigms themselves. Empirical work form secondary sources and case studies complete the analysis. (shrink)

This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...) to which the introduction of an UBI would meet these criteria is then examined, with a focus on the social role that stands to be most affected by an UBI, namely that of the worker-earner. It is argued that while an UBI is likely to be only partially effective as an instrument of specifically social freedom, its main justification lies not here, but in securing a basis for the subjective freedom that social freedom presupposes. (shrink)

I suggest that the post-Hegelian tradition presents us with three contrasting normative models of work. According to the first model, the core norms of work are those of means-ends rationality. In this model, the modern world of work is constitutively a matter of deploying the most effective means to bring about given ends. The rational kernel of modern work, the core norm that has shaped its development, is on this view instrumental reason, and this very same normative core, in the (...) shape of advanced technology and more efficient, time-saving production, can help to liberate it. The second model, by contrast, takes the core norms of work to be internal to working activity. Rather than work gaining its normativity from something external to it, from ends to which the work is a contingent means, on this second view the core norms of work are expressions of values or meanings that are immanent to working practices themselves. The expressive model of work regards the actual world of work to be constituted historically by work-specific norms, norms which working subjects themselves have invoked and mobilised around in the course of their struggles for emancipation. According to the third model, the core norms of work have to do neither with instrumental rationality nor authentic self-expression. Rather they concern norms that relate either to individual achievement or contribution through work (in the form of esteem) or to the conditions that must in place for individuals to participate in the exchange of services by which market societies reproduce themselves (in the form of mutual respect). (shrink)