Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Harvard University Press takes pride in publishing the third edition of a work whose depth, scope, and wisdom have gained it international recognition as a classic in its field. Harry Austryn Wolfson, world-renowned scholar and most lucid of scholarly writers, here presents in ordered detail his long-awaited study of the philosophic principles and reasoning by which the Fathers of the Church sought to explain the mysteries of the Trinity and the Incarnation. Professor Wolfson first discusses the problem of the (...) relation of faith and reason. Starting with Paul, who, differentiating between the wisdom of God and the wisdom of the world, averred that he was not going to adorn his teachings with persuasive arguments based on the wisdom of the world, Professor Wolfson describes the circumstances and influences which nevertheless brought about the introduction of philosophy into matters of faith and analyzes the various attitudes of the Fathers towards philosophy. The Trinity and the Incarnation are Professor Wolfson's next concern. He analyzes the various ways in which these topics are presented in the New Testament, and traces the attempts on the part of the Fathers to harmonize these presentations. He shows how the ultimate harmonized formulation of the two doctrines was couched in terms of philosophy; how, as a result of philosophic treatment, there arose with regard to the Trinity the problem of three and one and with regard to the Incarnation the problem of two and one; and how, in their attempts to solve these problems, the Fathers drew upon principles which in philosophy were made use of in the solution of certain aspects of the problem of the one and the many. In the final part of this volume, entitled "The Anathematized," he deals with Gnosticism and other heresies which arose during the Patristic period with regard to the Trinity and the Incarnation. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Nietzsche and MetaphorKarsten HarriesNietzsche and Metaphor, by Sarah Kofman; translated by Duncan Large; xivi & 239 pp. Stanford: Stanford University Press, 1993, $37.50 cloth, $12.95 paper.Since its first publication in 1972, Sarah Kofman’s Nietzsche et la métaphore has become a minor classic; reason enough to welcome this readable translation, accompanied with the translator’s unusually informative introduction, which resituates the work “in the context in which it first appeared, (...) at the high-water mark during an extraordinary surge of interest in ‘the new Nietzsche’ which swept over France in the 1960s and early 1970s” (p. ix), and concludes with a brief glance at the similarly extraordinary growth of interest in Nietzsche today in the English speaking countries, which should assure this translation of a warm reception. The addition of thoughtful notes and a complete bibliography of Kofman’s writings reinforces the impression that a major work of a major writer has finally been made available in English.Indeed, anyone interested in the metaphor-intoxicated, “new Nietzsche,” will be required to turn to this book, which has made such an important contribution to the discourse that constructed this Nietzsche. Rather short (without Kofman’s appended review of Granier’s Heideggerian Nietzsche, just 119 pp.) and readable, it invites us to confront this “new Nietzsche” with Nietzsche himself, or rather with the texts he published and—here we must be on our guard—with texts that for different reasons he left unpublished.The way this book gives precedence to the unpublished over the published works invites challenge, and here again it is not The Will to Power, but rather early material that comes in for intense scrutiny where, by now quite expectedly, “The Philosopher: Reflections on the Struggle Between Art and Knowledge” and even more “On Truth and Lie in a Nonmoral Sense,” come in for special attention—chapter 3, “The Forgetting of Metaphor,” and chapter 4, which bears the title “Metaphorical Architectures,” offer themselves as a partial commentary on the latter brief and never completed text. But still only a partial commentary, and as revealing as the passages Kofman chooses to discuss are those passed over. As expected one meets with Nietzsche’s famous description of truth as “A mobile army of metaphors, metonymies, and anthropomorphisms” (p. 58) and a great many related passages, pointing in the same general direction. But we should not allow ourselves to be carried away by the flow of Nietzsche’s youthful prose: only a one-sided reading of this text will overlook how close, despite his use of architectural metaphors to call into question the architecture of philosophy, Nietzsche here remains to one of the paradigmatic philosophical builders, to Kant, and even more to Schopenhauer—both mentioned only in passing by Kofman. That we ourselves have constituted the world of science is for Nietzsche no reason to question “the eternal consistency, omnipresence, and infallibility of the laws of nature” (“On Truth and Lie in a Nonmoral Sense”). Quite the opposite, he goes on, the [End Page 153] turn to the subject allowed a thinker like Kant to conclude that, in Nietzsche’s words, “so far as we can penetrate here—from the telescopic heights to the microscopic depths—everything is secure, complete, infinite, regular, and without any gaps. Science will be able to dig successfully in this shaft forever, and all the things that are discovered will harmonize with and not contradict each other.” Nietzsche advances no considerations to dispute such confidence. Readers of this text focused on the many ways in which Nietzsche here emphasizes “the artistic process of metaphor formation” should keep in mind his insistence that this process, with which every sensation is said to begin, is also said to presuppose Kant’s pure intuitions, time and space, and therefore “relationships of succession and number.” “The only way in which the possibility of subsequently constructing a new conceptual edifice from metaphors themselves can be explained is by the firm persistence of these original forms. That is to say, this conceptual edifice is an imitation of temporal, spatial, and numerical relationships in the domain of metaphor. Every explanation of metaphor formation is here said to... (shrink)

As cross-border trade and cross-border financing continue to increase while security rights over tangible property are governed by the law of the place where the moveable is situated, comparative knowledge of national secured transactions law is crucial for everyone using security rights over tangibles in a cross-border context. This book provides an in-depth examination of the key issues that arise when security rights are created, perfected and enforced in different European countries. Authored by experts on German, English, Dutch, French, Belgian, (...) Italian and Spanish law, the national reports use practical cases and highlight differences and similarities. A special focus is placed on the way in which national courts deal with security interests created elsewhere. A comprehensive introductory chapter analyzes significant secured transactions issues, summarises the comparative data and compares them with Art. 9 of the Uniform Commercial Code and suggests guiding principles for a European harmonization measure or national reform efforts. The book will assist market participants and their counsel to better understand secured transactions law and relevant private international law rules of their own and other countries and assist those involved in national, EU and global law reform efforts. (shrink)

This is an eminently sensible book with a clear and strightforwardly argued thesis, that to pursue ideals impossible to achieve in practice is not always irrational, but is often useful and productive of good results. Professor Rescher maintains that, while “must” in practical matters certainly implies “can,” “ought” does not; so that “cannot,” while it excuses failure, does not abrogate obligation to try. This, he claims disposes of many theoretical problems about moral dilemmas, which certainly may arise with respect to (...) what one should do, but which cannot exist with respect to what, in the given circumstances, one must do. To decide what the latter obligation is, is indeed difficult and complicated. It involves priorities unattainable in the prevailing conditions, for others considered more important. But once the priorities have been settled, what must be done is unequivocal and further conflict of duties is precluded. A moral code, says Rescher, is intended as a guide to conduct, which it could not be if it were specific in every detail. Rules must therefore be general, and particular situations require their modification in order to ensure the best results. This leaves room for, and requires, casuistry the balancing and harmonizing of potentially conflicting demands to achieve the best possible in the circumstances. (shrink)

A Scientific Integrity Consortium developed a set of recommended principles and best practices that can be used broadly across scientific disciplines as a mechanism for consensus on scientific integrity standards and to better equip scientists to operate in a rapidly changing research environment. The two principles that represent the umbrella under which scientific processes should operate are as follows: Foster a culture of integrity in the scientific process. Evidence-based policy interests may have legitimate roles to play in influencing aspects of (...) the research process, but those roles should not interfere with scientific integrity. The nine best practices for instilling scientific integrity in the implementation of these two overarching principles are Require universal training in robust scientific methods, in the use of appropriate experimental design and statistics, and in responsible research practices for scientists at all levels, with the training content regularly updated and presented by qualified scientists. Strengthen scientific integrity oversight and processes throughout the research continuum with a focus on training in ethics and conduct. Encourage reproducibility of research through transparency. Strive to establish open science as the standard operating procedure throughout the scientific enterprise. Develop and implement educational tools to teach communication skills that uphold scientific integrity. Strive to identify ways to further strengthen the peer review process. Encourage scientific journals to publish unanticipated findings that meet standards of quality and scientific integrity. Seek harmonization and implementation among journals of rapid, consistent, and transparent processes for correction and/or retraction of published papers. Design rigorous and comprehensive evaluation criteria that recognize and reward the highest standards of integrity in scientific research. (shrink)

This is an eminently sensible book with a clear and strightforwardly argued thesis, that to pursue ideals impossible to achieve in practice is not always irrational, but is often useful and productive of good results. Professor Rescher maintains that, while “must” in practical matters certainly implies “can,” “ought” does not; so that “cannot,” while it excuses failure, does not abrogate obligation to try. This, he claims disposes of many theoretical problems about moral dilemmas, which certainly may arise with respect to (...) what one should do, but which cannot exist with respect to what, in the given circumstances, one must do. To decide what the latter obligation is, is indeed difficult and complicated. It involves priorities unattainable in the prevailing conditions, for others considered more important. But once the priorities have been settled, what must be done is unequivocal and further conflict of duties is precluded. A moral code, says Rescher, is intended as a guide to conduct, which it could not be if it were specific in every detail. Rules must therefore be general, and particular situations require their modification in order to ensure the best results. This leaves room for, and requires, casuistry the balancing and harmonizing of potentially conflicting demands to achieve the best possible in the circumstances. (shrink)

While recent studies have shed some light on the significance of the electrical activity of the nervous system, there has been no adequate explanation for the wave formation or synchronization of this electrical activity. Adrian sums up the problem. “The origin of the 10-a-second rhythm is still uncertain, though the evidence points to some widespread organization, probably involving the central masses as well as the cortex. There are abundant nervous connexions for coordinating the beat, and when the rhythm is well (...) developed it is possible to record impulse discharges in phase with it passing to and fro in the nerve fibers of the white matter below the cortex. But in some areas no impulse could be detected entering or leaving the cell layers, though the potential waves keep more or less in step with those elsewhere. There is no proof that the waves are kept in phase by some means which does not involve nervous signalling, for impulses in axons of small diameter might well be missed, but it is not altogether unlikely that the synchronization is due in part to a direct electrical influence of one group of nerve cells on another. Gerard and Libet have shown that synchronization can occur between the two halves of a frog's brain cut in two and then placed in contact, and more recently Arvanitaki has shown that individual nerve cells may influence one another if they are brought close together in a conducting medium. At all events there are many examples of synchronized rhythmic activity in large collections of nerve-or-muscle cells. In the optic ganglion of the water beetle, for instance, there may be both a slow rhythm when the eye is in darkness and a rapid one when the eye is exposed to a bright light. The change from a slow to a fast rhythm is curiously reminiscent of that in the cerebral cortex when a sensory stimulus abolishes the 10-a-second rhythm and substitutes one at 40–60 a second. Such resemblances in preparations of quite different structures may be quite fortuitous, but they make it difficult to resist the suggestion that the rhythms of the brain may be dependent on the general properties of cell masses rather than on any special anatomical arrangement of them. Whatever its origin, the 10-a-second rhythm of the cortex corresponds to the resting, drowsy, or inattentive state and there is no such uniform pulsation when the brain is alert.”. (shrink)

Chrysippus claims that some propositions perish. including some true conditionals whose consequent is impossible and antecedent is possible, to which he appeals against Diodorus?s Master Argument. On the standard interpretation. perished propositions lack truth values. and these conditionals are true at the same time as their antecedents arc possible and consequents impossible. But perished propositions are false, and Chrysippus?s conditionals are true when their antecedent and consequent arc possible, and false when their antecedent is possible and consequent impossible. The claim (...) of the Master Argument that Chrysippus rejects, then, is stronger ihan usually supposed. (shrink)

In Principles of Human Knowledge Berkeley speaks of the sensible qualities of an apple as being its parts. The paper argues that our words for sense-qualities play a role so unlike that of part-words that verbal atrocities would result from treating qualities as parts. Berkeley lends a surface plausibility to this move by focusing on a narrow selection of the normal linguistic accompaniment of the noun 'apple'. He puts out of mind the language of 'doing things with apples'— peeling, dicing, (...) and so on— which when recalled shows how strikingly far apart are the two categories he tries to mingle. (shrink)

The task of understanding Wittgenstein’s Philosophical Investigations is more like that of understanding a difficult person than of grasping difficult ideas. It makes heavy demands upon the reader. He must first of all have the patience to stare at slight variations in language-uses until they look as marked as Wittgenstein wants them to look. Then he must be prepared for what looks like impassable break-offs in line of thought. Next, if he is a philosopher, he must listen to a great (...) many hard sayings about philosophy—some of them prepared for, others thrown in as crotchety asides. Through all this, he must also come to see that here is suggested a radically new way of looking at language. Without some grasp of this new way, he cannot hope to feel the main force of the work. Instead of trying to summarize the Investigations, therefore, I will try to draw together some of the principal ideas which seem to me to give sense and unity to its details. This will not amount to seeing the book as a whole. Also, I expect that the result will misrepresent some of those ideas, I hope not grievously. (shrink)

The ordinary justification for my not doubting that the next bread I eat will nourish me as in the past is that we humans do not bother ourselves with doubts except where life actually prompts a doubt. Hume, however, represents this not-doubting as an inference we repeatedly draw, and not a very strong one since it concludes to a future-tense judgement from past-tense premisses. Thus Hume creates the impression that the commonest ways of leaning on past experience as a guide (...) involve a woefully weak type of inference, and this paper challenges that impression. (shrink)

Much of the literature on the question “Is a human essentially distinct from every possible machine?” proceeds on the assumption that we know what a man essentially is, namely a living body with such attributes as consciousness, freedom, feeling and linguistic competence. Is a man essentially that? The paper contrasts that picture of man with Kierkegaard’s account of man as essentially self. Hard limits of machine subjectivity begin to appear in the failure of certain everyday concepts involving ‘self’ to engage (...) at all with the concept ‘machine’. (shrink)

Much of the literature on the question “Is a human essentially distinct from every possible machine?” proceeds on the assumption that we know what a man essentially is, namely a living body with such attributes as consciousness, freedom, feeling and linguistic competence. Is a man essentially that? The paper contrasts that picture of man with Kierkegaard’s account of man as essentially self. Hard limits of machine subjectivity begin to appear in the failure of certain everyday concepts involving ‘self’ to engage (...) at all with the concept ‘machine’. (shrink)

Dutch science flourished in the late sixteenth and in the seventeenth century thanks to the immigration of cartographers, botanists, mathematicians, astronomers and the like from the Southern Netherlands after the Spanish army had captured the city of Antwerp in 1585, and thanks to the religious and the socio‐economic situation of the country. A strong impulse for practical scientific activities started from the Reformation, mainly thanks to its anti‐traditional attitude, which had an anti‐rationalistic tendency. Therefore, in the Northern Netherlands there was (...) no ‘warfare’ between science and religion and the biblical arguments leading to Galileo's condemnation were not used.Although the growth of the exact sciences and of technology in the late sixteenth and the seventeenth centuries in Protestant cirles may be partly attributed to the expansion of trade, industry, navigation and so on, this does not explain why there was also at the same time a great interest in subjects as botany and zoology, which had no immediate economic utility. There were discussions about Copernicanism and Cartesianism. So a number of astronomers and theologians rejected the earth's movement on scientific and religious grounds, but there were also those who did not reject the Copernican system on biblical grounds. In the seventeenth century there was much discussion between science and religion in the Northern Netherlands, but that discussion was not followed by censure by the Church of the State. In the Republic there was a large amount of intellectual freedom in the study of the natural sciences, thanks to practical and ideological considerations. In the eighteenth century the seventheenth century tension between science and religion changed into a physicotheological natural science. It was believed that investigations into the workings of nature should lead to a better understanding of its Creator. So Bernard Nieuwentijt in his well‐known book: The right use of‐world views for the conviction of atheists and unbelievers (1715) intended to prove the existence of God on the basis of teleological arguments. (shrink)