© 2016 Elsevier Ltd All rights reserved.Crystallographic studies of ligands bound to biological macromolecules represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ∼75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery and design, and the goodness-of-fit of ligand models (...) to electron-density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide PDB/Cambridge Crystallographic Data Center/Drug Design Data Resource Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30-31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the PDB? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated. (shrink)

Peter Abelard held two views that imply a form of Mereological Essentialism: first, a thing is nothing other than all its parts taken together and second, no thing has more parts at one time than it does at another. This paper situates Abelard’s theses within their historical context. The paper first examines Boethius’s suggestive remarks about the dependence of the whole upon its parts and it highlights several of the choices that were open to twelfth-century students of Boethius’s mereology. Then (...) there is a brief survey of Abelard’s understanding of Mereological Essentialism. Finally, the paper examines some of the more interesting challenges to Mereological Essentialism that were posed by Abelard’s contemporaries. The paper focuses in particular on a set of fragments that have been attributed to the school of Joscelin of Soissons. (shrink)

Peter Abelard held two views that imply a form of Mereological Essentialism: first, a thing is nothing other than all its parts taken together and second, no thing has more parts at one time than it does at another. This paper situates Abelard’s theses within their historical context. The paper first examines Boethius’s suggestive remarks about the dependence of the whole upon its parts and it highlights several of the choices that were open to twelfth-century students of Boethius’s mereology. Then (...) there is a brief survey of Abelard’s understanding of Mereological Essentialism. Finally, the paper examines some of the more interesting challenges to Mereological Essentialism that were posed by Abelard’s contemporaries. The paper focuses in particular on a set of fragments that have been attributed to the school of Joscelin of Soissons. (shrink)

This book offers a major reassessment of Peter Abelard's modal logic and theory of modalities, presenting them as far more uniform and consistent than was until now recognized. Irene Binini offers new ways of connecting Abelard's modal views with other parts of his logic, semantics, metaphysics and theology. Further, the work also provides a comprehensive study of the logical context in which Abelard's theories originated and developed, by presenting fresh evidence about many 11th- and 12th-century sources that are still unpublished. (...) This analysis sheds new light on the relations between Abelard and ancient authors such as Aristotle, Boethius, and Priscian, as well as between Abelard and his contemporaries, such as Anselm of Canterbury, William of Champeaux, Joscelin of Soissons, and Alberic of Paris. (shrink)

Aristotle gave seven arguments for the law of non-contradiction. The first one is against a special case of dialetheism, the view that only some contradictions are true, and other six arguments are mostly against trivialism, the view that everything and consequently every contraction is true. Aristotle never argued that dialetheism entails trivialism. Unlike Aristotle, Avicenna, in his defense of LNC, not only considers trivialism and argues against it, but also argues that dialetheism entails trivialism. The argument that dialetheism entails trivialism (...) is called explosion. It is usually known that the first argument for explosion is given by the twelfth century logician William of Soissons. In this paper, we will meet Avicenna’s different argument for explosion and then I will demonstrate that this argument is a non-sequitur. (shrink)

The Trinity. This chapter examines Abelard’s first major writing about the divine Trinity, the Theologia ‘Summi boni’, written in 1119–20 and condemned as expounding heresy at the Council of Soissons in 1121. Abelard emphasizes the capacity of pagan philosophers to gain insight into the supreme good as much as prophets of the Old Testament. He applies his theory of language to words used about God to explain how Christians can speak of three divine persons as names given to signify different (...) attributes of God, namely his power, wisdom and goodness. (shrink)

This chapter investigates the connection between memory and drawing. It looks at how they played a role in the training of visual artists in Europe between the thirteenth and the fourteenth centuries. _The Craftsman’s Handbook_ (ca. 1400) by Cennino Cennini suggests that the assimilation of a great master’s style is achieved by the training of memory through daily drawing exercises. Collections of drawings by individual draftsmen offer a starting point for the study of an artist’s visual memory. An analysis of (...) a drawing in the portfolio made by Villard de Honnecourt between 1220 and 1240 and of a miniature in the Gospels of St. Medard of Soissons from ca. 800, which was the likely model chosen by Villard, offers evidence on how he trained his own hand and memory. The purpose of drawing is not always clear, but it seems to function as both a form of memory-training and a way to elicit recollections and trigger visual imagination. (shrink)

A Christian Theologia. This chapter considers Abelard’s Theologia Christiana, his revision and development of the treatise condemned at Soissons. In this work, Abelard deepens his understanding of the Holy Spirit, and starts to consider ethical insights, as communicated by pagan philosophy. Written while Abelard was teaching at the oratory he founded in honor of the Paraclete, the work reflects new ideas in the theory of language, and contains in embryo many of the theological ideas he would develop in the 1130s. (...) The chapter also considers other writings, such as the Sic et Non, that Abelard composed during the 1120s, while teaching both philosophy and theology. (shrink)

The identification of two possible readings – de re and de dicto – of modal claims is considered one of the greatest achievements of Abelard’s logic. In the Dialectica and the Logica “Ingredientibus,” Abelard uses this distinction as a basis for his modal semantics and theory of modalities. Rather than focusing on Abelard’s own theory, the aim of this article is to pay attention to a number of sources that – like Abelard’s logical works – are datable to the first (...) decades of the twelfth century, to investigate whether the de re–de dicto distinction was already adopted and debated in them. It argues that, even if there is no systematic theorization of the distinction in these sources, Abelard’s contemporaries put forward a number of questions concerning the syntax and the signification of modal claims that contributed to set the stage for the distinction’s identification and later development. (shrink)

In 1931 the mathematical logician Kurt Godel published a revolutionary paper that challenged certain basic assumptions underpinning mathematics and logic. A colleague of Albert Einstein, his theorem proved that mathematics was partly based on propositions not provable within the mathematical system and had radical implications that have echoed throughout many fields. A gripping combination of science and accessibility, Godel’s Proof by Nagel and Newman is for both mathematicians and the idly curious, offering those with a taste for logic and philosophy (...) the chance to satisfy their intellectual curiosity. (shrink)

David Gauthier in his article, Maximization constrained: the rationality of cooperation, tries to defend of the joint strategy in situations which no outcome is both equilibrium and optimal. Prisoner’s Dilemma is the most familiar example of these situations. He first starts with some quotes by Hobbes in Leviathan; Hobbes, in chapter 15 discusses an objection by someone is called Foole, and then will reject his view. In response to Foole, Hobbes presents two strategies (i.e. joint and individual) and two kinds (...) of agents in such problems including Prisoner’s Dilemma – i.e. straightforward maximizer (SM) and constrained maximizer(CM). Then he considers two arguments respectively for SM and CM, and he will show that why in an ideal and transparent situation, the first argument fails and the second one would be the only valid argument. likewise, in the following part of his article, he considers more realistic situations with translucency and he concludes that under some conditions, joint strategy would be still the rational decision. (shrink)

The first major work in the history of philosophy to bear the title "Metaphysics" was the treatise by Aristotle that we have come to know by that name. But Aristotle himself did not use that title or even describe his field of study as 'metaphysics'; the name was evidently coined by the first century C.E. editor who assembled the treatise we know as Aristotle's Metaphysics out of various smaller selections of Aristotle's works. The title 'metaphysics' -- literally, 'after the Physics' (...) -- very likely indicated the place the topics discussed therein were intended to occupy in the philosophical curriculum. They were to be studied after the treatises dealing with nature (ta phusika). In this entry, we discuss the ideas that are developed in Aristotle's treatise. (shrink)

Sebastian Gardner competently tackles one of Sartre's more complex and challenging works in this new addition to the Reader's Guides series.

This article examines the reception and portrayal of Immanuel Kant’s (1724–1804) legacy in Latvia from 2011 to 2024, focusing on academic discourse, public debates, and commemorative activities. It explores historical connections, translations, scholarly research, and public commemorations through the lens of Pierre Bourdieu’s (1930–2002) theory of cultural and symbolic capital, illustrating how Kant’s legacy is contextualized and appropriated within Latvian intellectual traditions. The study examines Kant’s physical and symbolic presence in Latvian public spaces, such as monuments and plaques, highlighting the (...) relationship between historical memory, cultural narratives, and myth-making. By providing a comprehensive account of Kant’s significance in Latvia, the study contributes to broader discussions on the integration of global intellectual heritage into national and local contexts. (shrink)

In Carnap’s autobiography, he tells the story how one night in January 1931, “the whole theory of language structure” in all its ramifications “came to [him] like a vision”. The shorthand manuscript he produced immediately thereafter, he says, “was the first version” of Logical Syntax of Language. This document, which has never been examined since Carnap’s death, turns out not to resemble Logical Syntax at all, at least on the surface. Wherein, then, did the momentous insight of 21 January 1931 (...) consist? We seek to answer this question by placing Carnap’s shorthand manuscript in the context of his previous efforts to accommodate scientific theories and metalinguistic claims within Wittgenstein’s Tractatus theory of meaning. The breakthrough of January 1931 consists, from this viewpoint, in the rejection of the Tractatus theory in favor of the meta-mathematical perspective of Hilbert, Gödel, and Tarski. This was not yet the standpoint of the published Logical Syntax, as we show, but led naturally to the “principle of tolerance” and thus to Carnap’s mature philosophy, in which the inconsistencies between this first view and the principle of tolerance, which survived into the published Syntax, were overcome. (shrink)

This essay concerns Dedekind’s “mathematical structuralism,”by which we mean methodological features characteristic for the approach to mathematics in his mature writings. The discussion starts with some background on forerunners, especially Gauss, Dirichlet, and Riemann, whose “conceptual” style of work influenced him strongly. But Dedekind went further than them, by making methodological choices that are more distinctly and fully “structuralist”. This includes his resolute acceptance of actually infinite systems, understood within a “logical” framework, and studied not just axiomatically, but also in (...) terms of isomorphisms and related notions (since 1871). As an illustration, the essay discusses his early adoption and strikingly modern transformation of Galois theory, together with his contributions to algebraic number theory. After that, the essayturns to Dedekind’s more “foundational” contributions, i.e., his writings on the real numbers, the natural numbers, and set theory. It shows that the same methodological choices inform them. Yet his approach kept evolving in subtle ways too, especially in terms of the centrality of functions (_Abbildungen_, mappings). (shrink)

István Hont identified a point in the history of political thought at which republicanism and commercialism became separated. According to Hont, Emmanuel Sieyès proposed that a monarchical republic should be formed. By contrast the Jacobins, in favour of a republic led by the people, rejected not only Sieyès’s political proposal, but also the economic ideology that went with it. Sieyès was in favour of a commercial republic; the Jacobins were not. This was, according to Hont, a defining moment in the (...) history of political thought. In this article, I offer a different analysis of that particular moment in the history of the commercial republic, one that instead of focusing on Sieyès and the Jacobins, looks at the thought of Girondins philosophers Nicolas de Condorcet and Sophie de Grouchy. I argue that their arguments provide sound models for a commercial republic, reconciling late 18th century republican ideals in which virtue was central, with the need for a flourishing and internationally active market economy. (shrink)

As these opening quotes acknowledge, the Prisoner’s Dilemma (PD) represents a core puzzle within the formal mathematics of game theory.3 Its rise in conspicuity is evident figure 2.1 above demonstrating a relatively steady rise in incidences of the phrase’s usage between 1960 to 1995, with a stable presence persisting into the twenty first century. This famous two-person “game,” with a stock narrative cast in terms of two prisoners who each independently must choose whether to remain silent or speak, each advancing (...) self-interest at the expense of the other and thereby achieving a mutually suboptimal outcome, mires any social interaction it is applied to into perplexity. The logic of this game proves the inverse of Adam Smith’s invisible hand: individuals acting on self interest will achieve a mutually suboptimal outcome. However, as this chapter illuminates, the assumptions underlying game theory drive this conclusion. (shrink)

Critical discussion of J.M.E. Moravcsik's paper on Plato's method of division.

Geoffrey Rose’s prevention paradox points to a tension between two prima facie plausible moral principles: that we should save the greater number and that weshould save the most at risk. This paper argues that a novel moral theory, ex-ante contractualism, captures our intuitions in many prevention paradox cases, regardless of our interpretation of probability claims. However, it goes on to show that it might be impossible to square ex-ante contractualism with all of our moral intuitions. It concludes that even if (...) ex-ante contractualism cannot furnish an entire ethics of risk, it does identify important considerations for any such theory. (shrink)

Among various cases that equally admit of evidentialist reasoning, the supposedly evidentialist solution has varying degrees of intuitive attractiveness. I suggest that cooperative reasoning may account for the appeal of apparently evidentialist behavior in the cases in which it is intuitively attractive, while the inapplicability of cooperative reasoning may account for the unattractiveness of evidentialist behaviour in other cases. A collective causal power with respect to agreed outcomes, not evidentialist reasoning, makes cooperation attractive in the Prisoners' Dilemma. And a natural (...) though unwarranted assumption of such a power may account for the intuitive appeal of the one-box response in Newcomb's Problem. (shrink)

Kant’s dissertation for the Master’s degree Succinct Exposition of Some Meditations on Fire was written in Latin in 1755 as a sample (specimen) preceding a Master’s exam, but its first printing did not appear until 1838. What is the relevance of this Master’s dissertation for historical and philosophical studies? To answer this question I analyse the structure and give a brief summary of the dissertation, look at the history of its writing and try to identify the place of this work (...) among Kant’s other papers on natural philosophy. I then demonstrate that Kant’s concept of ether as an elastic matter of fire, heat and light containing the forces of attraction and repulsion originates in the dissertation On Fire. I identify the provisions in Kant’s early works which he later develops in the Master’s dissertation and establish continuity between the text of On Fire and the so-called Physical Monadology, draw parallels between the ideas enunciated by Kant in his first dissertation and the interpretation of ether in the printed works that followed. Finally, I put forward the hypothesis of the heuristic potential of the On Fire treatise for the analysis of Kant’s manuscript legacy. Perhaps this dissertation will enable researchers to clear up some tangled propositions in Kant’s Opus Postumum. However, a series of further studies is needed to verify the hypothesis. (shrink)

This volume gathers together for the first time are all the key texts in a crucial debate in modern philosophy, centered on Leibniz's famous 1695 essay, the "New System of the Nature of Substances and their Communication," in which he introduced his strikingly original theory of metaphysics. His "system" became increasingly famous and drew him into discussion and development of these ideas, both in public and in private, with a variety of thinkers, most notably the great French philosopher Pierre Bayle. (...) Woolhouse's and Francks's new English edition gives the only full representation of this debate, and will therefore be essential reading for anyone who wishes to gain a proper understanding of Leibniz's philosophy and its intelletual context. All the texts are newly translated and extensively annotated; many appear in English for the first time. (shrink)