Nicholaos Jones

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.

One recent priority of the U.S. government is developing autonomous robotic systems. The U.S. Army has funded research to design a metric of evil to support military commanders with ethical decision-making and, in the future, allow robotic military systems to make autonomous ethical judgments. We use this particular project as a case study for efforts that seek to frame morality in quantitative terms. We report preliminary results from this research, describing the assumptions and limitations of a program that assesses the relative evil of two courses of action. We compare this program to other attempts to simulate ethical decision-making, assess possibilities for overcoming the trade-off between input simplification and output reliability, and discuss the responsibilities of users and designers in implementing such programs. We conclude by discussing the implications that this project highlights for the successes and challenges of developing automated mechanisms for ethical decision making.

While mechanistic explanation and, to a lesser extent, nomological explanation are well-explored topics in the philosophy of biology, topological explanation is not. Nor is the role of diagrams in topological explanations. These explanations do not appeal to the operation of mechanisms or laws, and extant accounts of the role of diagrams in biological science explain neither why scientists might prefer diagrammatic representations of topological information to sentential equivalents nor how such representations might facilitate important processes of explanatory reasoning unavailable to scientists who restrict themselves to sentential representations. Accordingly, relying upon a case study about immune system vulnerability to attacks on CD4+ T-cells, I argue that diagrams group together information in a way that avoids repetition in representing topological structure, facilitate identification of specific topological properties of those structures, and make available to controlled processing explanatorily salient counterfactual information about topological structures, all in ways that sentential counterparts of diagrams do not.

This paper elaborates upon various responses to the Problem of the One over the Many, in the service of two central goals. The first is to situate Huayan's mereology within the context of Buddhism's historical development, showing its continuity with a broader tradition of philosophizing about part-whole relations. The second goal is to highlight the way in which Huayan's mereology combines the virtues of the Nyāya-Vaisheshika and Indian Buddhist solutions to the Problem of the One over the Many while avoiding their vices.