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)

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)

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 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)

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)

It is often said that if free speech means anything it means freedom for the thought we hate. This core idea is generally referred to as “viewpoint neutrality” and is consistent with the liberal intuition that governments should remain neutral with regard to conceptions of the good life. None of the traditional defenses of free speech seem to secure viewpoint neutrality, however. Instead, each justification leaves room to censor some viewpoints. Ironically my defense of viewpoint neutrality does not come from (...) the liberal assumption that governments should remain neutral about the good life. I defend a version of the virtue argument for free speech that is explicitly perfectionist—-government does not have to remain neutral when promoting good lives for its citizens. Free speech is not just a means to promote virtue but is part and parcel of intellectual virtue—-a decidedly perfectionist value. (shrink)

This chapter contains sections titled: “I'm shocked, I tell you, shocked!” The Preacher and the Porn Star Picnic Sex and the Prudes “Don't look, Ethel!” Tease Me, Whip Me, Persuade Me Biting the Bullet Hard Cases If Porn Isn't Free Speech, What Is It? Notes.

We discuss the necessity of conscious thinking in the single-system propositional model of learning. Research from honeybees to humans suggests that associative learning can take place without the need for controlled reasoning or the development of beliefs of relationships between objects or events. We conclude that a single learning system is possible, but not if it depends on complex thinking.

In two important articles, Thomas Hurka applies his recursive account of value to virtue. Hurka’s contention is that being virtuous is merely a matter of having the proper pro-attitude toward what is objectively good. Hurka argues that the recursive framework honors much of our traditional conception of virtue, and even if it does not capture everything involved in virtue, it “describes at least part of what virtue involves.” I argue that the recursive account of virtue is not a partial description (...) of traditional virtue, however, but a reconception of virtue. Accepting the recursive account would require abandoning the most distinctive elements of traditional virtue ethics. (shrink)

_Practical Bioethics_ offers a mix of theory and readings, presented in a format that is succinct and approachable. Each chapter begins and ends with a case study, illustrating the core issues at play and emphasizing the practical nature of the dilemmas arising in medicine. Primary source texts are provided to flesh out the issues, and each of these is carefully edited and presented with interwoven explanatory comments to assist student readers. Throughout, J.K. Miles shows the importance of health-care ethics (...) to us all, whether we be medical providers, patients, or both. (shrink)

The current UN policy regarding free speech presents a philosophical dilemma between accepting the free speech provisions in the Universal Declaration of Human Rights and exceptions carved out for hatred, hostility, and religious defamation. The Declaration should be understood to imply viewpoint neutrality and the exceptions for defamation are not viewpoint neutral. If the UN were to adopt J. S. Mill’s crucial distinctions between expression and performative speech, content and context, and mental states and the acts motivated by them, it (...) would be clear that hatred, hostility, and defamation cannot be exceptions to viewpoint neutral free speech. If the heart of free speech is freedom especially for the thought we hate, then the UN should abandon its exceptions or abandon appeals to free speech. However, I will offer a strong reason that it should not do the latter. (shrink)

This chapter clarifies important component of alignment in character creation and development. It demonstrates an application of moral philosophy and introduces ethical dilemmas that allow players to make meaningful moral choices leads to a more rewarding gaming experience. The chapter highlights philosophy's most enduring and frustrating questions. According to Dungeons Dragons (DD), the alignment is an element of the player's character sheet that clarifies their worldview and moral outlook. It is also a category that can limit character class and an (...) aura that allows spells or abilities to detect a character's moral outlook – and if necessary “smite” that evil (or good) into oblivion. The DD attracts imaginative players. A party is likely be filled with virtuous paragons, nefarious knaves, and pragmatists. (shrink)

Virtue theory in philosophical bioethics has influenced clinical ethics with depictions of the virtuous doctor or nurse. Comparatively little has been done with the concept of the virtuous patient, however. Bioethicists should correct the asymmetry in virtue theory between physician virtues and patient virtues in a way that provides a practical theory for the new patient-centered medicine—something clinicians and administrators can take seriously.