The prediction of protein–protein interactions based on independently obtained structural information for each interacting partner remains an important challenge in computational chemistry. Procedures where hypothetical interaction models (or decoys) are generated, then ranked using a biochemically relevant scoring function have been garnering interest as an avenue for addressing such challenges. The program PatchDock has been shown to produce reasonable decoys for modeling the association between pig alpha-amylase and the VH-domains of camelide antibody raised against it. We designed a biochemically relevant (...) method by which PatchDock decoys could be ranked in order to separate near-native structures from false positives. Several thousand steps of energy minimization were used to simulate induced fit within the otherwise rigid decoys and to rank them. We applied a partial free energy function to rank each of the binding modes, improving discrimination between near-native structures and false positives. Sorting decoys according to strain energy increased the proportion of near-native decoys near the bottom of the ranked list. Additionally, we propose a novel method which utilizes regression analysis for the selection of minimization convergence criteria and provides approximation of the partial free energy function as the number of algorithmic steps approaches infinity. (shrink)

This Is A New Release Of The Original 1868 Edition.

“Opt-out” organ procurement policies based on presumed consent are typically advertised as being superior to “opt-in” policies based on explicit consent at securing organs for transplantation. However, Michael Gill has argued that presumed consent policies are also better than opt-in policies at respecting patient autonomy. According to Gill’s Fewer Mistakes Argument, we ought to implement the procurement policy that results in the fewest frustrated wishes regarding organ donation. Given that the majority of Americans wish to donate their organs, it is (...) plausible that a presumed consent policy would result in fewer frustrated wishes compared to the current opt-in policy. It follows that we ought to implement a policy of presumed consent. In this paper, I first consider and find wanting an objection to the Fewer Mistakes Argument developed recently by Douglas MacKay. I also consider an objection put forth by James Taylor but argue that there is a methodological reason to prefer my own argument to Taylor’s. Finally, I argue for two theses: first, that Gill’s major argument in favor of the crucial premise of the Fewer Mistakes Argument is flawed, and second, that the major premise of the Fewer Mistakes Argument is false. (shrink)

Unlike some other reproductions of classic texts (1) We have not used OCR(Optical Character Recognition), as this leads to bad quality books with introduced typos. (2) In books where there are images such as portraits, maps, sketches etc We have endeavoured to keep the quality of these images, so they represent accurately the original artefact. Although occasionally there may be certain imperfections with these old texts, we feel they deserve to be made available for future generations to enjoy.

Human rights law has been called upon to help with the problem of persistently high greenhouse gas emissions. An obligation on states and other legal entities to lower their emissions (mitigation) is said to be deducible from that body of law. I refute this thesis. First, I consider two practical difficulties—causality and non-triviality—that face a plaintiff who, with emission mitigation as the objective, attempts to prove a human rights violation using the regular pattern of proof for a violation. Proponents of (...) the “human rights approach” to mitigation have held that proof of an emission “contribution” by the defendant together with proof of an “impact” by climate change on the plaintiff’s human rights are sufficient to discharge the evidentiary burden for the proof of causation. The rest of the causation chain is simply presumed. Thus, the original proof pattern for a human rights violation is abandoned. The proponents’ answer to the triviality difficulty has been to aggregate emitters into very large entities and sue _them_. However, aggregation can be shown to lead to a _reductio ad absurdum_. In my argument’s second part, I identify a more fundamental difficulty with the human rights approach to mitigation: The defendant’s emissions do not amount to a norm violation. Everyone contributes emissions without legislative or other prohibition. Treaty law on climate change itself recognizes emitting behaviour as lawful and permits the continuation of state emissions through to at least 2050. A rise in global warming from preindustrial levels to 1.5° Celsius with room for an even greater rise to close to 2° Celsius has been _budgeted for_ by the Paris Agreement on Climate Change. The setting up of a budget affirms the normalized status of within-budget emissions. This universal license to emit denies the human rights approach to mitigation the very conditions of application of human rights law. (shrink)

Book Review: P.P. Tolochko. Ukraine between Russia and the West: Historical and Nonfiction Essays. Saint Petersburg: Saint Petersburg University of Humanities and Social Sciences, 2018. - 592 pp. ISBN 978-5-7621-0973-4This author discusses the problem of scientific objectivity and reviews a book written by the medievalist-historian P.P. Tolochko, full member of the National Academy of Sciences of Ukraine, honorable director of the NASU Institute of Archaeology. The book was published by the Saint Petersburg University of Humanities and Social Sciences in the (...) autumn of 2018. The book presents a collection of articles and reports devoted to processes in Ukraine and, first of all, in Ukrainian historical science, which, at the moment, is experiencing an era of serious reformation of its interpretative models. The author of the book shows that these models are being reformed to suit the requirements of the new ideology, with an obvious disregard for the conduct of objective scientific research. In this regard, the problem of objectivity of scientific research becomes the subject of this review because the requirement of objectivity can be viewed not only as a methodological requirement but also as a moral and political position, opposing the rigor of scientific research to the impact of ideological, political and moral systems and judgments. It is concluded that in this sense the position of P.P. Tolochko can be considered as the act of profound ethical choice. (shrink)

Peter Lipton argues that inference to the best explanation involves the selection of a hypothesis on the basis of its loveliness. I argue that in optimal cases of IBE we may be able to eliminate all but one of the hypotheses. In such cases we have a form of eliminative induction takes place, which I call ‘Holmesian inference’. I argue that Lipton’s example in which Ignaz Semmelweis identified a cause of puerperal fever better illustrates Holmesian inference than Liptonian IBE. I (...) consider in detail the conditions under which Holmesian inference is possible and conclude by considering the epistemological relations between Holmesian inference and Liptonian IBE.Keywords: Inference to the best explanation; Peter Lipton; Abduction; Holmesian inference; Eliminative induction. (shrink)

In this article, we focus on the scholarly and policy debate on autonomous weapon systems and particularly on the objections to the use of these weapons which rest on jus ad bellum principles of proportionality and last resort. Both objections rest on the idea that AWS may increase the incidence of war by reducing the costs for going to war or by providing a propagandistic value. We argue that whilst these objections offer pressing concerns in their own right, they suffer (...) from important limitations: they overlook the difficulties of calculating ad bellum proportionality; confuse the concept of proportionality of effects with the precision of weapon systems; disregard the ever-changing nature of war and of its ethical implications; mistake the moral obligation imposed by the principle of last resort with the impact that AWS may have on political decision to resort to war. Our analysis does not entail that AWS are acceptable or justifiable, but it shows that ad bellum principles are not the best set of ethical principles for tackling the ethical problems raised by AWS; and that developing adequate understanding of the transformations that the use of AWS poses to the nature of war itself is a necessary, preliminary requirement to any ethical analysis of the use of these weapons. (shrink)

In this paper I outline my conception of the epistemology of science, by reference to my published papers, showing how the ideas presented there fit together. In particular I discuss the aim of science, scientific progress, the nature of scientific evidence, the failings of empiricism, inference to the best (or only) explanation, and Kuhnian psychology of discovery. Throughout, I emphasize the significance of the concept of scientific knowledge.

Let us call a property that is essentially dispositional a potency.1 David Armstrong thinks that potencies do not exist. All sparse properties are essentially categorical, where sparse properties are the explanatory properties of the type science seeks to discover. An alternative view, but not the only one, is that all sparse properties are potencies or supervene upon them. In this paper I shall consider the differences between these views, in particular the objections Armstrong raises against potencies.

Ame, vie, souffle, qui saurait bien les distinguer exactement?1like heartburn, a pronounced discomfort with the very idea of consciousness followed the early days of experimental psychology. Received wisdom has it that psychologists came to mistrust consciousness for largely behaviorist reasons—they are supposed to have worried about the alleged impossibility of performing quantifiable, repeatable measurements on an essentially private phenomenon.2 But this is a historical distortion, one that obscures some interesting and earlier philosophical concerns about the scientific study of consciousness.Behaviorists rejected (...) the scientific respectability of consciousness, to be sure. But by the... (shrink)

Volume 20, Issue 6, June 2020, Page 30-32.

Alexander George’s lucid interpretation of Hume’s “Of Miracles” provides fresh insights into this provocative text, explaining the concepts and claims involved. He also shows why Hume’s argument fails to engage with committed religious thought and why philosophical argumentation so often proves ineffective in shaking people’s deeply held beliefs.

Financial conflicts of interest in medical research foster deviations from research standards and evidentially lead to the suppression of research findings that are at odds with commercial interests of pharmaceutical companies. Questionable research practices prevent data from being created, made available, or given suitable recognition. They run counter to codified principles of responsible conduct of research, such as honesty, openness or respect for the law. Resulting in ignorance, misrepresentation and suspension of scientific self-correction, suppression of medical evidence in its various (...) forms is both a threat to the epistemic and the moral integrity of medical science. This paper discusses an example of the suppression of medical evidence in recent influenza research and develops a conceptual framework for the description and assessment of questionable research practices applied in research and publication processes to suppress evidence. (shrink)

Dispositions are related to conditionals. Typically a fragile glass will break if struck with force. But possession of the disposition does not entail the corresponding simple (subjunctive or counterfactual) conditional. The phenomena of finks and antidotes show that an object may possess the disposition without the conditional being true. Finks and antidotes may be thought of as exceptions to the straightforward relation between disposition and conditional. The existence of these phenomena are easy to demonstrate at the macro-level. But do they (...) exist at the fundamental level also? While fundamental finkish dispositions may be excluded fairly straightforwardly, the existence of fundamental antidotes is more open. Nonetheless I conclude that the phenomenon is likely to be less widespread than at the macro level and that fundamental antidotes may be eliminable. According to the dispositional essentialist, the laws of nature can be explained by taking natural properties to be essentially dispositional. This account can be extended to show that the existence of finks and antidotes explains ceteris paribus laws. Consequently the existence or otherwise of fundamental finks and antidotes sheds some light on the question of whether fundamental laws may also be ceteris paribus laws. (shrink)

We provide a general theorem implying that for a (strongly) dependent theory T the theory of sufficiently well-behaved pairs of models of T is again (strongly) dependent. We apply the theorem to the case of lovely pairs of thorn-rank one theories as well as to a setting of dense pairs of first-order topological theories.

We characterize þ-independence in a variety of structures, focusing on the field of real numbers expanded by predicate defining a dense multiplicative subgroup, G, satisfying the Mann property and whose pth powers are of finite index in G. We also show such structures are super-rosy and eliminate imaginaries up to codes for small sets.

The article shows that Kuhn's concept of incommensurability emphasizes mainly the objective dimension of communication. To the thesis about the incommensurability of the meanings of scientific concepts in competing paradigms, we oppose the idea of a three-dimensional space of communicative dimensions. We supplement the objective dimension of communication, within which the environmental evolutionary selection of the best knowledge is carried out, with equal social and temporal horizons.

According to Immanuel Kant, legality means the quality of an action being merely and simply in conformity with a law. The article defends the significance of this notion and explains how it indicates the existence of a legal relation. The legal relation, in turn, is the result of resolving an antinomy between the social and the substantive dimension of moral judgment.

The value of resting electroencephalogram (EEG) in revealing neural constitutes of consciousness (NCC) was examined. We quantified the dynamic repertoire, duration and oscillatory type of EEG microstates in eyes-closed rest in relation to the degree of expression of clinical self-consciousness. For NCC a model was suggested that contrasted normal, severely disturbed state of consciousness and state without consciousness. Patients with disorders of consciousness were used. Results suggested that the repertoire, duration and oscillatory type of EEG microstates in resting condition quantitatively (...) related to the level of consciousness expression in brain-damaged patients and healthy-conscious subjects. Specifically, results demonstrated that (a) decreased number of EEG microstate types was associated with altered states of consciousness, (b) unawareness was associated with the lack of diversity in EEG alpha-rhythmic microstates, and (c) the probability for the occurrence and duration of delta-, theta- and slow-alpha-rhythmic microstates were associated with unawareness, whereas the probability for the occurrence and duration of fast-alpha-rhythmic microstates were associated with consciousness. In conclusion, resting EEG has a potential value in revealing NCC. This work may have implications for clinical care and medical–legal decisions in patients with disorders of consciousness. (shrink)

I present an argument that encapsulates the view that theory is underdetermined by evidence. I show that if we accept Williamson's equation of evidence and knowledge, then this argument is question-begging. I examine ways of defenders of underdetermination may avoid this criticism. I also relate this argument and my critique to van Fraassen's constructive empiricism.

That government agencies and public bodies can be liable for damages when they induce and then frustrate people’s legitimate expectations is an important and distinctive feature of administrative law in Europe. This article sets out to establish a set of moral principles and ideals that might justify this legal institution. The notion of security of expectations found in the work of utilitarian writers provides a starting point. Having examined the strengths and weaknesses of this approach, I then turn to consider (...) an alternative argument based on finding a solution to the problem of credible commitments. Finally, I look for suitable moral arguments in the liberal and Kantian political theorising of John Rawls. I argue that if we see the function of the rule of law as not merely to maximise aggregate utility and to make policymakers’ decisions seem credible but also to ensure Justice as Fairness for individuals, then this provides a more robust and satisfactory way to justify the liability of public bodies for legitimate expectations they induce and then frustrate. (shrink)

I defend against criticism the following claims concening Thomas Kuhn: (i) there is a strong naturalist streak in The structure of scientific revolutions, whereby Kuhn used the results of a posteriori enquiry in addressing philosophical questions; (ii) as Kuhn's career as a philosopher of science developed he tended to drop the naturalistic elements and to replace them with more traditionally philosophical a prior approaches; (iii) at the same there is a significant residue of positivist thought in Kuhm, which Kuhn did (...) not recognise as such; (iv) the naturalist elements referred to in (i) are the most original and fruitful elements of Kuhn's thinking; (v) the positivistic elements referred to in (iii) vitiated his thought and acted as factors in preventing Kuhn from developing the naturalistic elemtns and from following the path taken by much subsequent philosophy of science. Preston presents an alternative reading of Kuhn which emphasizes the Wittgensteinian elements in Kuhn. I argue that this alternative view is, descriptively, poorly supported by the textual evidence and the facts of the history of philosophy of science in the twentieth century. I provide some defence of the naturalistic approach and related themes. (shrink)

Although the first ‘pragmatist aesthetics’ was devised by John Dewey in his Art as Experience, Richard Shusterman has been the only scholar to use the notion of “pragmatist aesthetics” in his Pragmatist Aesthetics. In this paper, I show that Dewey already refuses the gap between the practices of the ‘artworld’ and that of everyday life. In Art as Experience, he criticizes the ‘museum conception’ of art to argue that some aesthetic experiences in our daily life have the same essential structure (...) as the experience of art. While Rorty has revised Dewey’s basic premises, Shusterman has rather restated them. Since the end of the 1980s, he has started developing his own philosophical project, named ‘somaesthetics’. Shusterman’s somaesthetics does not simply incorporate many Deweyan views, but also develops them further. Accepting a Deweyan framework, Shusterman rejects the sharp dualism of the so-called “lower and higher levels of art”. What is more, he considers philosophy as an art of the living, embracing in somaesthetics the ancient Greek and Asian traditions. (shrink)

This book explores a range of traditional and contemporary metaphysical themes that figure in the writings of E. J. Lowe, whose powerful and influential work was still developing at the time of his death in 2015. Leading philosophers present new essays on topics to do with ontology, necessity, existence, and mental causation.

The first obstacle that confronts the student of induction is that of defining the subject matter. One initial point is to note that much of the relevant subject matter goes under the description ‘the theory of confirmation’. The distinction is primarily that the study of induction concerns inference, i.e. cases where one takes the conclusion to be established by the evidence, whereas confirmation concerns the weight of evidence, which one may take to be something like the credibility of a hypothesis (...) in the light of the evidence. Discussions of confirmation often concern incremental confirmation, i.e. cases where the evidence is taken to increase the credibility of some hypothesis, even if not sufficiently to warrant inferring the truth of that hypothesis. However, some uses of ‘confirmation’ clearly refer to absolute confirmation, cases where the credibility of the hypothesis in the light of the evidence exceeds some (high) threshold. One may ask whether inductive inference corresponds to the case of absolute confirmation for some suitable threshold. I shall discuss inference and confirmation together, though it should be noted that some approaches eschew inference altogether. For example, the Bayesian takes scientific reasoning to be a matter of adjusting credences in propositions in the light of evidence, and says nothing about unqualified belief in a proposition. However, if we are interested in inductive knowledge then we must consider inference, since only then do we have a detached proposition that is the possible content of a mental state of knowing. A more pressing question concerns which inferences (or allegedly confirmatory relations) should be classed as inductive. A natural and straightforward approach is to define induction as encompassing any form of reasoning that extrapolates from one population to another, usually from a sample of a population to the whole population. For example, one might note that all observations of the position of some planet fall on an ellipse that has the Sun at one of its foci; from this one concludes that all the positions that planet takes fall on this ellipse (i.e.. (shrink)

One of the strongest objections to epiphenomenalism is that it precludes any kind of knowledge of qualia, since empirical knowledge has to include a causal relationship between the respective belief and the object of knowledge. It is argued that this objection works only if the causal relationship is understood in a very specific sense (as a 'direct' causal relationship). Epiphenomenalism can, however, live well with other kinds of causal relationships ('indirect' causal relationships) or even with a reliability account of knowledge (...) which does not invoke causation at all. Michael Pauen has argued extensively (this volume of Journal of Consciousness Studies), however, that this line of defence doesn't work because it presupposes the existence of psychophysical laws connecting qualia with physical phenomena which cannot be established under epiphenomenalist presuppositions. It is argued that Pauen's arguments lead to sceptical consequences which threaten not only interactionist alternatives to epiphenomenalism but finally his own account. (shrink)

Twentieth century philosophy of science has been dominated by a view of language with a strong prejudice against psychology, even while empirical psychology has moved away from the nineteenth century philosophical psychology against which the prejudice was originally directed. This legacy is shown to dominate even in recent Kripke‐inspired efforts toward new theories of meaning. Its influence is argued to undermine prospects for making sense of such phenomena as scientific progress. Avoiding this consequence requires that we pursue a psychologically informed (...) theory of meaning. (shrink)

The author considers the evolutionary approach to the development of the scientific knowledge in framework of the Niklas Luhmann's system-communicative theory and presents a thesis that in respect to the final evolutional state (state of stabilization of new form of knowledge) the organization of the Russian science has not yet achieved the world-level of sufficient autonomy because there was not yet been established the self-substitutive order of the knowledge accumulation which is inherent to the autopoiesis of the contemporary science i.e. (...) the process of continued change of some ones truths by some others. The factors impeding to establish such a self-substitutive order are to be connected by the author with the impact on the scientific discourse from some external communicative forms (the theological, financial, economical, political ones) and with the continuous change of some selective criterions that have to define what has to be accumulated as a memory of the science as a communicative system. (shrink)