In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...) we analyze the alternative role and meaning theory has in systems biology expressed as canonical template theories like Biochemical Systems Theory. (shrink)

The importation of computational methods into biology is generating novel methodological strategies for managing complexity which philosophers are only just starting to explore and elaborate. This paper aims to enrich our understanding of methodology in integrative systems biology, which is developing novel epistemic and cognitive strategies for managing complex problem-solving tasks. We illustrate this through developing a case study of a bimodal researcher from our ethnographic investigation of two systems biology research labs. The researcher constructed models of metabolic and cell-signaling (...) pathways by conducting her own wet-lab experimentation while building simulation models. We show how this coupling of experiment and simulation enabled her to build and validate her models and also triangulate and localize errors and uncertainties in them. This method can be contrasted with the unimodal modeling strategy in systems biology which relies more on mathematical or algorithmic methods to reduce complexity. We discuss the relative affordances and limitations of these strategies, which represent distinct opinions in the field about how to handle the investigation of complex biological systems. (shrink)

Integrative systems biology is among the most innovative fields of contemporary science, bringing together scientists from a range of diverse backgrounds and disciplines to tackle biological complexity through computational and mathematical modeling. The result is a plethora of problem-solving techniques, theoretical perspectives, lab-structures and organizations, and identity labels that have made it difficult for commentators to pin down precisely what systems biology is, philosophically or sociologically. In this paper, through the ethnographic investigation of two ISB laboratories, we explore the particular (...) structural features of ISB thinking and organization and its relations to other disciplines that necessitate cognitive innovation at all levels from lab PI’s to individual researchers. We find that systems biologists face numerous constraints that make the production of models far from straight-forward, while at the same time they inhabit largely unstructured task environments in comparison to other fields. We refer to these environments as adaptive problem spaces. These environments they handle by relying substantially on the flexibility and affordances of model-based reasoning to integrate these various constraints and find novel adaptive solutions. Ultimately what is driving this innovation is a determination to construct new cognitive niches in the form of functional model building frameworks that integrate systems biology within the biological sciences. The result is an industry of diverse and different innovative practices and solutions to the problem of modeling complex, large-scale biological systems. (shrink)

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not solve problems alone. Problem solving depends as ever on human cognitive resources. Current philosophical accounts hint at their importance, but it remains to be understood what roles human cognition plays in computational modeling. In this paper we focus on practices through which modelers in systems biology use computational simulation and other tools to (...) handle the cognitive complexity of their modeling problems so as to be able to make significant contributions to understanding, intervening in, and controlling complex biological systems. We thus show how cognition, especially processes of simulative mental modeling, is implicated centrally in processes of model-building. At the same time we suggest how the representational choices of what to model in systems biology are limited or constrained as a result. Such constraints help us both understand and rationalize the restricted form that problem solving takes in the field and why its results do not always measure up to expectations. (shrink)

Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices address the (...) challenges and constraints of interdisciplinary research in different contexts. In this paper we draw from our 5-year empirical ethnographic study of two systems biology labs and their collaborations with experimental biologists to analyze a significant problem-solving approach in ISB, which we call adaptive problem solving. ISB lacks much of the methodological and theoretical resources usually found in disciplines in the natural sciences, such as methodological frameworks that prescribe reliable model-building processes. Researchers in our labs compensate for the lack of these and for the complexity of their problems by using a range of heuristics and experimenting with multiple methods and concepts from the background fields available to them. Using these resources researchers search out good techniques and practices for transforming intractable problems into potentially solvable ones. The relative freedom lab directors grant their researchers to explore methodological options and find good practices that suit their problems is not only a response to the complex interdisciplinary nature of the specific problem, but also provides the field itself with an opportunity to discover more general methodological approaches and develop theories of biological systems. Such developments in turn can help to establish the field as an identifiably distinct and successful approach to understanding biological systems. (shrink)

We lay groundwork for applying ethnographic methods in philosophy of science. We frame our analysis in terms of two tasks: to identify the benefits of an ethnographic approach in philosophy of science and to structure an ethnographic approach for philosophical investigation best adapted to provide information relevant to philosophical interests and epistemic values. To this end, we advocate for a purpose-guided form of cognitive ethnography that mediates between the explanatory and normative interests of philosophy of science, while maintaining openness and (...) independence when framing such an investigation to achieve robust unbiased results. (shrink)

BackgroundThe ARRIVE (Animal Research: Reporting of In Vivo Experiments) guidelines are widely endorsed but compliance is limited. We sought to determine whether journal-requested completion of an ARRIVE checklist improves full compliance with the guidelines.MethodsIn a randomised controlled trial, manuscripts reporting in vivo animal research submitted to PLOS ONE (March–June 2015) were randomly allocated to either requested completion of an ARRIVE checklist or current standard practice. Authors, academic editors, and peer reviewers were blinded to group allocation. Trained reviewers performed outcome adjudication (...) in duplicate by assessing manuscripts against an operationalised version of the ARRIVE guidelines that consists 108 items. Our primary outcome was the between-group differences in the proportion of manuscripts meeting all ARRIVE guideline checklist subitems.ResultsWe randomised 1689 manuscripts (control: n = 844, intervention: n = 845), of which 1269 were sent for peer review and 762 (control: n = 340; intervention: n = 332) accepted for publication. No manuscript in either group achieved full compliance with the ARRIVE checklist. Details of animal husbandry (ARRIVE subitem 9b) was the only subitem to show improvements in reporting, with the proportion of compliant manuscripts rising from 52.1 to 74.1% (X2 = 34.0, df = 1, p = 2.1 × 10−7) in the control and intervention groups, respectively.ConclusionsThese results suggest that altering the editorial process to include requests for a completed ARRIVE checklist is not enough to improve compliance with the ARRIVE guidelines. Other approaches, such as more stringent editorial policies or a targeted approach on key quality items, may promote improvements in reporting. (shrink)

The book prescribes a way to educate ourselves and our young people how to disagree well and lays out a framework for flourishing together in society despite our radical differences.

Property and Practical Reason makes a moral argument for common law property institutions and norms, and challenges the prevailing dichotomy between individual rights and state interests and its assumption that individual preferences and the good of communities must be in conflict. One can understand competing intuitions about private property rights by considering how private property enables owners and their collaborators to exercise practical reason consistent with the requirements of reason, and thereby to become practically reasonable agents of deliberation and choice (...) who promote various aspects of the common good. The plural and mediated domains of property ownership, though imperfect, have moral benefits for all members of the community. They enable communities and institutions of private ordering to pursue plural and incommensurable good ends while specifying the boundaries of property rights consistent with basic moral requirements. (shrink)

This is a response to Macleod 2012's argument that the history of unjust property acquisitions requires rich libertarians to give away everything in excess of equality. At first, problematic questions are raised. How much property is usually inherited or illegitimate? Why should legitimate inheritance be affected? What of the burden of proof and court cases? A counterfactual problem is addressed. Three important cases are considered: great earned wealth; American slavery; land usurpation. All are argued to be problematic for (...) class='Hi'>Macleod 2012's thesis. Various problems are explained concerning using the Nozickian argument to decide the alleged excess that rich libertarians own. The essay's main error is the presupposition that free markets do not help the worst-off. The majority of unjust holdings today are not the result of historical injustices but arise through continuing transfers enabled by taxation and state-regulation. More study of libertarian contributions to the social sciences and philosophy would appear to be desirable "personal behavior" among socialists. (shrink)

Many of the current comparisons of taxic phylogenetic and biological homology in the context of morphology focus on what are seen as categorical distinctions between the two concepts. The first, it is claimed, identifies historical patterns of conservation and variation relating taxa; the second provides a causal framework for the explanation of this conservation and variation. This leads to the conclusion that the two need not be placed in conflict and are in fact compatible, having non-competing epistemic purposes or mapping (...) the same extensions in the form of monophyletic groupings (see Roth, The biological basis of homology 1–26, 1988; Sluys, J Zool Syst Evol Res 34:145–152, 1996; Abouheif, Trends Ecol Evol 12:405–408, 1997; Brigandt, J Exp Zool 299:9–17, 2003, Biol Philos 22:709–725, 2007; Assis and Brigandt, Evol Biol 36:248–255, 2009). This article argues that moves in this direction miss the essential disagreement between these concepts as they have been developed in the context of the debate concerning the best concept for evolutionary investigation. We should rather see these concepts employing a common fundamental methodological approach to homology, but disagreeing about how to apply the methodology effectively. Both concepts employ class reasoning, which pursues homologies as units of generalization—more precisely, as sources of reliable and relevant group-bound information in the form of shared underlying causes. The dispute can be better understood by two poles that structure such reasoning: the need for a reliable basis for projections about the causal history of shared structures, and the desire to identify homologous characters with more informative and specific causal information relevant to generalizing about evolutionary processes. Judgments in favor of one or the other in turn have affected the scope or extension of these competing homology concepts. (shrink)

Global Media Ethics is the first comprehensive cross-cultural exploration of the conceptual and practical issues facing media ethics in a global world. A team of leading journalism experts investigate the impact of major global trends on responsible journalism. The first full-length, truly global textbook on media ethics; Explores how current global changes in media promote and inhibit responsible journalism; Includes relevant and timely ethical discussions based on major trends in journalism and global media; Questions existing frameworks in media ethics in (...) light of the impact of global media; Contributors are leading experts in global journalism and communication. (shrink)

This chapter offers an account of the aspect of nineteenth‐century naturalism, by focusing on the work of J. S. Mill and Auguste Comte. Both philosophers have high ambitions for naturalism, aiming to offer a sweeping account of all of human knowledge in naturalistic terms. Mill argued that the metaphysical thinking must already have started to exert an influence in order for monotheistic approaches to take hold, and that Comte's account of the theological stage overstated the extent to which fetishistic or (...) polytheistic understanding of phenomena could exist independently of one another. But these are minor disagreements, framed in terms of a narrative that Mill basically accepts. Mill thought Comte's three stage theory important for understanding the rise our way of conceptualizing the world, and consistent with his own account of the rise of scientific induction. (shrink)

In 1925, A.J. Balfour, first Earl Balfour and author of the famous ‘Balfour Declaration’, attended the inauguration of the Hebrew University in Jerusalem. His education and experience of foreign policy equipped him to take a prominent role. However, the conditions of strife-torn Palestine weighed heavily upon him, and raised wider interests of imperial concern. This essay recounts the circumstances leading to his visit, and suggests that, whatever the region’s political destiny, Balfour’s vision of science-based economic development would play an essential (...) role in crafting its future. (shrink)

The late Colin Macleod's commentary on Iliad 24 has rightly received praise for its sensitivity to the nuances of Homeric language and its appreciation of the entire poem as a carefully constructed work of art. Although reluctant to accept the more radical solutions proposed by the ‘oral’ school, Macleod showed himself fully aware of the contribution made by the oral theory towards elucidating the history of the epic. Nevertheless, his commentary is concerned principally with the Iliad as we (...) have it: a poem which is at one level a masterly re-telling of saga but at another a sublime tragedy, commiserating the sorrows inseparable from human existence and holding up for our admiration the heroes who nobly confront pain and death. I believe that much, and probably most, of the Iliad can and should be viewed in this light. The last book of all, as Macleod himself has shown, offers especially rich rewards to an interpreter who keeps in the front of his mind the overriding aims of the great poet. Yet Macleod's method, like any other single method, will never yield a fully satisfactory answer on all occasions. However the ‘definitive’ or ‘monumental’ composition of the Iliad was brought about, it formed only one stage in the development of the Greek epic. Our Iliad cannot have been the first or the only treatment, on a large scale, of the matter of Troy. (shrink)

This book is a comprehensive introduction to media ethics and an exploration of how it must change to adapt to today's media revolution. Using an ethical framework for the new 'mixed media' ethics – taking in the global, interactive media produced by both citizens and professionals – Stephen J. A. Ward discusses the ethical issues which occur in both mainstream and non-mainstream media, from newspapers and broadcast to social media users and bloggers. He re-defines traditional conceptions of journalistic truth-seeking, objectivity (...) and minimizing harm, and examines the responsible use of images in an image-saturated public sphere. He also draws the contours of a future media ethics for the 'new mainstream media' and puts forward cosmopolitan principles for a global media ethics. His book will be invaluable for all students of media and for others who are interested in media ethics. (shrink)

Provides guiding principles and values for practising responsible global media ethics.