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)

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)

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)

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)

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)

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.

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)

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)

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)

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)

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)

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)

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)

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)

Adherents of traditional western Theism have espoused CONJUNCTION: God is essentially perfectly good and God is thankworthy for the good acts he performs. But suppose that (i) God’s essential perfect goodness prevents his good acts from being free, and that (ii) God is not thankworthy for an act that wasn’t freely performed. Together these entail the denial of CONJUNCTION. The most natural strategy for defenders of CONJUNCTION is to deny (i). We develop an argument for (i), and then identify two (...) ways for the defender of CONJUNCTION to respond. Next we turn to a considerably different, rather less obvious route toward defending CONJUNCTION that is compatible with (i)—one which instead denies (ii). Here too we identify two ways for the defender of CONJUNCTION to proceed, yielding a total of four ways for the theist to respond. Because the last of these represents an important and underappreciated alternative for the theist, we devote the second half of the paper to developing and defending it. We argue that divine responsibility is sufficient for divine thankworthiness and consistent with the absence of divine freedom. We do this while insisting on the view that both freedom and responsibility are incompatible with causal determinism. (shrink)

This chapter attempts to improve our conception of objectivity in general, especially in journalism and other media work. It defends the twin theses that: Global news media needs a new conception of objectivity and the conception of pragmatic objectivity is a viable candidate, and pragmatic objectivity is part of a radical rethinking of journalism and media ethics. It is an alternative to the professional objective model, a still-influential traditional idea of the objective journalist as a neutral stenographer of fact. Journalists (...) need to disrupt this model of good journalism. The chapter reconstructs objectivity as a natural evaluative capacity of humans that is situated and holistic. Then, it uses this naturalistic perspective to articulate pragmatic objectivity and apply it to journalism. (shrink)

The themes explored include political liberty, "legal tyranny," defences of influence in government, recognition of the Opposition, and the development of organic categories of political analysis - the latter in a chapter that explodes the association often presumed between organicism and conservative modes of thought. A chapter on the "Fourth Estate" examines the gradual process of legitimation of "interests," culminating in the influence of the press. Central to the account of new political forces and their recognition is the idea of (...) public opinion, which evolved during this period from the notion of public spirit. Chapters on the classical legacy of the century and on the High-Tories examine two backward-looking aspects of the political cultrure. Tracing the persistent influence of High-Toryism, Gunn questions the conventional wisdom about eighteenth-century ideological consensus in general and Whig solidarity in particular. He demonstrates that theories of government from the seventeenth century survived to a degree not previously admitted by modern scholarship. (shrink)

This chapter examines one class of public emotions – the “political emotions,” such as patriotism and promotion of the national interest and how they are, or are not, compatible with good journalism in a global media era. To what extent is journalism ethics, as we have known it, compatible with patriotism and love of nation? Can nation-based political emotions provide appropriate primary values for a global ethics and an emerging global media ethics? With regard to the first question, the chapter (...) argues that only a moderate patriotism is compatible with the principles of journalism ethics in a democracy. With regard to the second question, the chapter argues that a global ethics should not be based on nation-based values. It should be based on global emotions, or global political emotions. (shrink)

This chapter proposes a way to conceptualize journalism as both engaged and objective, called “democratically engaged journalism.” It is a “third way” between partisan and neutral journalism. The chapter argues that democratically engaged journalism is the moral ideology that journalism needs to respond to a toxic sphere of digital, global media.The chapter begins by defining engagement, disengagement, and democratically engaged journalism, using a continuum of kinds of journalism. Then it considers how democratically engaged journalism replies to a range of possible (...) objections concerning the role of facts, emotions, and neutrality. It concludes by identifying four duties for democratically engaged journalism. (shrink)

Any theory of information needs to comply with what we call the implementation, formalization, and representation constraints. These constraints are justified by basic considerations concerning scientific modelling and methodology. In the first part of this paper, we argue that the implementation and formalization constraints cannot be satisfied because the relation between Shannon information and IIT must be clarified. In the second part of the paper, we focus on the representation constraint. We argue that IIT cannot succeed in satisfying this constraint (...) for semantic contents without offering models for concepts, conceptual roles, and context sensitivity. In the final part of the paper, further complications are raised with respect to the distinction between consciousness and attention, which apply more specifically to the representation constraint. We conclude with some recommendations as to how IIT may succeed in solving these problems, highlighting the advantages and enormous potential of IIT as a scientific theory. (shrink)

In this paper we investigate a number of analytical solutions to the polynomial class of nonlinear Klein-Gordon equations in multidimensional spacetime. This is done in the context of classical φ4 and φ6 field theory, the former with and without the inclusion of an external force field conjugate to φ. Both massive (m≠0) and massless (m=0) cases are considered, as well as tachyonic solutions allowed (v>c). We first present a complete set of translationally invariant solutions for the φ4 model and demonstrate (...) the role of external force fields in altering the form of these solutions. Next, spherically symmetric solutions are discussed in both φ4 and φ6 cases since they provide the most realistic models of elementary particles. (shrink)

Julio A Andrade African Journal of Business Ethics 2013 7(1):40-42.

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)