Nicholaos Jones

Theology involves inquiry into God's nature, God's purposes, and whether certain experiences or pronouncements come From God. These inquiries are metaphysical, part of theology's concern with the veridicality of signs and realities that are independent from humans. Several research programs concerned with the relation between theology and science aim to secure theology's intellectual standing as a metaphysical discipline by showing that it satisfies criteria that make modern science reputable, on the grounds that modern science embodies contemporary canons of respectability for metaphysical disciplines. But, no matter the ways in which theology qua metaphysics is shown to resemble modern science, these research programs seem destined for failure. For, given the currently dominant approaches to understanding modern scientific epistemology, theological reasoning is crucially dissimilar to modern scientific reasoning in that it treats the existence of God as a certainty immune to refutation. Barring the development of an epistemology of modern science that is amenable to theology, theology as metaphysics is intellectually disreputable.

Mengzi 孟子 6A2 contains the famous water analogy for the innate goodness of human nature. Some evaluate Mengzi’s reasoning as strong and sophisticated; others, as weak or sophistical. I urge for more nuance in our evaluation. Mengzi’s reasoning fares poorly when judged by contemporary standards of analogical strength. However, if we evaluate the analogy as an instance of correlative thinking within a yin-yang 陰陽 cosmology, his reasoning fares well. That cosmology provides good reason to assert that water tends to flow downward, not because of available empirical evidence, but because water correlates to yin and yin correlates to naturally downward motion. Substantiating these contentions also gives occasion to better understand the nature of correlative reasoning in classical Chinese philosophy.

When do data provide good evidence for a hypothesis, evidence that warrants an inference to the hypothesis? Standard answers either reject the legitimacy of induction or else allow warranted inference from data to hypothesis when there are suitable relationships between and among the data and hypotheses. The severity account rejects all of these, maintaining instead that the good evidence relation concerns not only relations between data and hypotheses but also the methods for obtaining the data and the sensitivity of these methods to detecting falsehood. So, for example, the severity account allows two rival hypotheses to fit the data equally well, even to the point of having the same prior and posterior probabilities relative to those data, while the data nonetheless favour one hypothesis over the other by virtue of those data providing a severe test of one hypothesis and not the other. The contributions to Error and Inference variously trace the genesis of the severity account from statistics-oriented sciences, elaborate upon the account’s details, apply the account to various philosophical issues, and offer challenges to the account’s adequacy and replies to major criticisms. The editors have developed the severity account in detail elsewhere, and this anthology is an effort …

Life scientists increasingly rely upon abstraction-based modeling and reasoning strategies for understanding biological phenomena. We introduce the notion of constraint-based reasoning as a fruitful tool for conceptualizing some of these developments. One important role of mathematical abstractions is to impose formal constraints on a search space for possible hypotheses and thereby guide the search for plausible causal models. Formal constraints are, however, not only tools for biological explanations but can be explanatory by virtue of clarifying general dependency-relations and patterning between functions and structures. We describe such situations as constraint-based explanations and argue that these differ from mechanistic strategies in important respects. While mechanistic explanations emphasize change-relating causal features, constraint-based explanations emphasize formal dependencies and generic organizational features that are relatively independent of lower-level changes in causal details. Our distinction between mechanistic and constraint-based explanations is pragmatically motivated by the wish to understand scientific practice. We contend that delineating the affordances and assumptions of different explanatory questions and strategies helps to clarify tensions between diverging scientific practices and the innovative potentials in their combination. Moreover, we show how constraint-based explanation integrates several features shared by otherwise different philosophical accounts of abstract explanatory strategies in biology.

ABSTRACT There is a new argument form within theoretical biology. This form takes as input competing explanatory models; it yields as output the conclusion that one of these models is more plausible than the others. The driving force for this argument form is an analysis showing that one model exhibits more parametric robustness than its competitors. This article examines these inferences to the more robust explanation, analysing them as variants of inference to the best explanation. The article defines parametric robustness and distinguishes it from more familiar kinds of robustness. The article also argues that parametric robustness is an explanatory virtue not subsumed by more familiar explanatory virtues, and that the plausibility verdicts in the conclusions of inferences to the more robust explanations are best interpreted as guidance for research activity, rather than claims about likely truth. 1Introducing Inference to the More Robust Explanation 2Inference to the More Robust Explanation in the Study of Apoptosis 2.1Regulating apoptosis 2.2Competing models and evidential indecision 2.3Measuring robustness 2.4Robustness as a guide to plausibility 2.5Varieties of robustness 3Inference to the More Robust Explanation as Inference to the Best Explanation 3.1The structure of inference to the best explanation 3.2Parametric robustness as an explanatory virtue rather than an explanandum 3.3Relation of parametric robustness to other explanatory virtues 4Epistemological Significance of Inference to the More Robust Explanation 4.1Plausibility in practice 4.2Plausibility in principle 5Conclusion

Using as case studies two early diagrams that represent mechanisms of the cell division cycle, we aim to extend prior philosophical analyses of the roles of diagrams in scientific reasoning, and specifically their role in biological reasoning. The diagrams we discuss are, in practice, integral and indispensible elements of reasoning from experimental data about the cell division cycle to mathematical models of the cycle’s molecular mechanisms. In accordance with prior analyses, the diagrams provide functional explanations of the cell cycle and facilitate the construction of mathematical models of the cell cycle. But, extending beyond those analyses, we show how diagrams facilitate the construction of mathematical models, and we argue that the diagrams permit nomological explanations of the cell cycle. We further argue that what makes diagrams integral and indispensible for explanation and model construction is their nature as locality aids: they group together information that is to be used together in a way that sentential representations do not.

According to conciliatory views about the epistemology of disagreement, when epistemic peers have conflicting doxastic attitudes toward a proposition and fully disclose to one another the reasons for their attitudes toward that proposition (and neither has independent reason to believe the other to be mistaken), each peer should always change his attitude toward that proposition to one that is closer to the attitudes of those peers with which there is disagreement. According to pure higher-order evidence views, higher-order evidence for a proposition always suffices to determine the proper rational response to disagreement about that proposition within a group of epistemic peers. Using an analogue of Arrow's Impossibility Theorem, I shall argue that no conciliatory and pure higher-order evidence view about the epistemology of disagreement can provide a true and general answer to the question of what disagreeing epistemic peers should do after fully disclosing to each other the (first-order) reasons for their conflicting doxastic attitudes.

Can contradictions be meaningful? How can one assert 'P soku not-P' or 'P and yet not-P' without sacrificing intelligibility? Expanding on previous attempts, mainly by Dilworth and Heisig, to demystify the soku connective, a formal system is presented here for the logic of soku. Through a formal distinction between internal and external negation, grammatical features of the soku connective are shown to be logically irrelevant, and the principle of non-contradiction is preserved. Disparities with traditional logic are noted, with a focus on negation rather than 'soku'. The formal examination of the logic of soku is intended to present the logic in a way acceptable to more analytically minded philosophers and thereby enhance East-West and Japanese-Anglo-American interaction and criticism

General Relativity and the Standard Model often are touted as the most rigorously and extensively confirmed scientific hypotheses of all time. Nonetheless, these theories appear to have consequences that are inconsistent with evidence about phenomena for which, respectively, quantum effects and gravity matter. This paper suggests an explanation for why the theories are not disconfirmed by such evidence. The key to this explanation is an approach to scientific hypotheses that allows their actual content to differ from their apparent content. This approach does not appeal to ceteris-paribus qualifiers or counterfactuals or similarity relations. And it helps to explain why some highly idealized hypotheses are not treated in the way that a thoroughly refuted theory is treated but instead as hypotheses with limited domains of applicability.

The increasing application of network models to interpret biological systems raises a number of important methodological and epistemological questions. What novel insights can network analysis provide in biology? Are network approaches an extension of or in conflict with mechanistic research strategies? When and how can network and mechanistic approaches interact in productive ways? In this paper we address these questions by focusing on how biological networks are represented and analyzed in a diverse class of case studies. Our examples span from the investigation of organizational properties of biological networks using tools from graph theory to the application of dynamical systems theory to understand the behavior of complex biological systems. We show how network approaches support and extend traditional mechanistic strategies but also offer novel strategies for dealing with biological complexity.

This is an attempt to explain, in a way familiar to contemporary ways of thinking about mereology, why someone might accept some prima facie puzzling remarks by Fazang, such as his claims that the eye of a lion is its ear and that a rafter of a building is identical to the building itself. These claims are corollaries of the Huayan Buddhist thesis that everything is part of everything else, and it is intended here to show that there is a rational basis for this thesis that involves a nonstandard notion of parthood and, importantly, that does not violate the principle of noncontradiction.

Idealizing conditions are scapegoats for scientific hypotheses, too often blamed for falsehood better attributed to less obvious sources. But while the tendency to blame idealizations is common among both philosophers of science and scientists themselves, the blame is misplaced. Attention to the nature of idealizing conditions, the content of idealized hypotheses, and scientists’ attitudes toward those hypotheses shows that idealizing conditions are blameless when hypotheses misrepresent. These conditions help to determine the content of idealized hypotheses, and they do so in a way that prevents those hypotheses from being false by virtue of their constituent idealizations

When comparing alternative courses of action, modern military decision makers often must consider both the military effectiveness and the ethical consequences of the available alternatives. The basis, design, calibration, and performance of a principles-based computational model of ethical considerations in military decision making are reported in this article. The relative ethical violation (REV) model comparatively evaluates alternative military actions based upon the degree to which they violate contextually relevant ethical principles. It is based on a set of specific ethical principles deemed by philosophers and ethicists to be relevant to military courses of action. A survey of expert and non-expert human decision makers regarding the relative ethical violation of alternative actions for a set of specially designed calibration scenarios was conducted to collect data that was used to calibrate the REV model. Perhaps unsurprisingly, the survey showed that people, even experts, disagreed greatly amongst themselves regarding the scenarios’ ethical considerations. Despite this disagreement, two significant results emerged. First, after calibration the REV model performed very well in terms of replicating the ethical assessments of human experts for the calibration scenarios. The REV model outperformed an earlier model that was based on tangible consequences rather than ethical principles, that earlier model performed comparably to human experts, the experts outperformed human non-experts, and the non-experts outperformed random selection of actions. All of these performance comparisons were measured quantitatively and confirmed with suitable statistical tests. Second, although humans tended to value some principles over others, none of the ethical principles involved—even the principle of not harming civilians—completely overshadowed all of the other principles.