Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecendented in its combination of biology with a ...

A semantics is presented for Storrs McCall's separate axiomatizations of Aristotle's accepted and rejected polysyllogisms. The polysyllogisms under discussion are made up of either assertoric or apodeictic propositions. The semantics is given by associating a property with a pair of sets: one set consists of things having the property essentially and the other of things having it accidentally. A completeness proof and a semantic decision procedure are given.

This volume covers a wide range of conceptual, epistemological and methodological issues in the philosophy of science raised by reflection upon medical science and practice.

This paper critically examines a particular strategy for resolving the central ethical dilemma associated with randomized clinical trials — the “community equipoise” strategy . The dilemma is that RCTs appear to violate a physician's duty to choose that therapy which there is most reason to believe is in the patient's best interest, randomizing patients even once evidence begins to favor one treatment. The community equipoise strategy involves the suggestion that our judgment that neither treatment is to be preferred is to (...) be assessed according to a community rather than an individual standard. Thus, though a physician may personally believe that there is some reason to prefer one treatment, patients can legitimately be randomized if there remains disagreement in the community of medical professionals. Rationales in favor of this conception include the following: medical knowledge is best understood as residing in the community, the judgments of others count as evidence, and so should change one's own opinion, subjects would not be better off outside the trial, and the point of any trial is the resolution of dispute in the medical community. I critically examine these rationales and argue that they are insufficient. Amongst the problems are tensions between various of these underlying rationales, and important ambiguities in just what the CE criterion is to amount to. Finally, I argue that even if use of CE was justified, it would not justify carrying out RCTs anywhere near long enough to discharge our duty to gain reliable knowledge on which to base safe and effective medical practice. Hence, we need some different justification for carrying out RCTs. (shrink)

The central dilemma concerning randomized clinical trials (RCTs) arises out of some simple facts about causal methodology (RCTs are the best way to generate the reliable causal knowledge necessary for optimally-informed action) and a prima facie plausible principle concerning how physicians should treat their patients (always do what it is most reasonable to believe will be best for the patient). A number of arguments related to this in the literature are considered. Attempts to avoid the dilemma fail. Appeals to informed (...) consent and mechanisms for minimizing the resulting harm are important for policy, but informed consent is problematic and mechanisms for minimization of harm do not address the dilemma. Appeals to some sort of contract model of justification are promising and illuminating. Keywords: randomized clinical trials, ethics CiteULike Connotea Del.icio.us What's this? (shrink)

In this article, I review and expand upon arguments showing that Freedman's so-called "clinical equipoise" criterion cannot serve as an appropriate guide and justification for the moral legitimacy of carrying out randomized clinical trials. At the same time, I try to explain why this approach has been given so much credence despite compelling arguments against it, including the fact that Freedman's original discussion framed the issues in a misleading way, making certain things invisible: Clinical equipoise is conflated with community equipoise, (...) and several versions of each are also conflated. But a misleading impression is given that, rather than distinct criteria being arbitrarily conflated, a puzzle is solved and a number of features unified. Various issues are pushed under the rug, hiding flaws of the "clinical equipoise" approach and thus deceiving us into thinking that we have a solution when we do not. Particularly significant is the ignoring of the crucial distinction between the individual patient decision and the policy decision. (shrink)

It is often claimed that a clinical investigator may ethically participate (e.g., enroll patients) in a trial only if she is in equipoise (if she has no way to ground a preference for one arm of the study). But this is a serious problem, for as data accumulate, it can be expected that there will be a discernible trend favoring one of the treatments prior to the point where we achieve the trial's objective. In this paper, I critically evaluate Benjamin (...) Freedman's 'clinical equipoise' solution to this dilemma. I argue that Freedman actually puts forth at least two distinct contrasts - one in terms of community vs. individual equipoise, and another concerning clinical vs. theoretical equipoise - and that neither of them resolves the dilemma. I then make a proposal for a more adequate account of how to think about the circumstances under which entering subjects in trials would be justified - a 'sliding-scale equipoise' that arises out of a discussion of patients' values. (shrink)

It is far from obvious that outside of highly specialized domains such as commercial agriculture, the methodology of biometrics—quantitative comparisons over groups of organisms—should be of any use in today’s bioinformatically informed biological sciences. The methods in our biometric textbooks, such as regressions and principal components analysis, make assumptions of homogeneity that are incompatible with current understandings of the origins of developmental or evolutionary data in historically contingent processes, processes that might have come out otherwise; the appropriate statistical methods are (...) those suited to random walks, not normal distributions. A valid methodology would further require that especially close attention be paid to the difference between aspects of processes that are plastic, those that encode their own histories or biographies, and the very small fraction of quantifications that can usefully and realistically be modeled as varying by colored noise around a central tendency that itself has some quantitative meaning. This point of view—that only a vanishingly small fraction of the quantitative information borne by any living organism is worth quantifying—is illustrated by some data on a human birth defect, namely, fetal alcohol syndrome. In a suggestive metaphor, the biometrician is like the pilgrim in Friedrich’s painting Der Wanderer über dem Nebelmeer, uncertain as to whether to measure the mountains or the clouds. The mountains stand for contingent history, the clouds for the subset of the data most closely matching controlled experiments suitable for quantitative biometric summary. Biometrics applies to the clouds, not the mountains. The success of statistical methods comes at the expense of all the theories that we simultaneously hold to be true about the biological materials to which they both pertain. Biometrics is thus complementary to all of the emerging reductionist sciences of biological structure. (shrink)

What is the relationship between ontology and modality - between what there is, and what there could be, must be, or might have been? Bob Hale interwove these two strands of metaphysics throughout his long and distinguished career, putting forward his theses in his book, Necessary Beings: An Essay on Ontology, Modality, and the Relations Between Them (OUP 2013). Hale addressed questions of ontology and modality on a number of fronts: through the development of a Fregean approach to ontology, an (...) essentialist theory of modality, and in his work on neo-logicism in the philosophy of mathematics. The essays in this volume engage with these themes in Hale's work in order to progress our understanding of ontology, modality, and the relations between them. Some directly address questions in modal metaphysics, drawing on ontological concerns, while others raise questions in modal epistemology and of its links to matters of ontology, such as the challenge to give an epistemology of essence. Several essays also engage with questions of what might be called 'modal ontology': the study of whether and what things exist necessarily or contingently. Such issues have an important bearing on the kinds of semantic commitments engendered in logic and mathematics (to the existence of sets, or numbers, or properties, and so on) and the extent to which one's ontology of necessary beings interacts with other plausible assumptions and commitments. (shrink)

Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...) models, identifying five constraints which guide the articulation of models in molecular systems biology. These constraints are not independent of one another, with the result that modeling becomes an iterative process. We illustrate the use of these constraints in the modeling of the mechanism for bistability in the lac operon. (shrink)

An elegant introduction to Bataille's major concepts and concerns, "Bataille: A Critical Reader" underlines the powerful impact his work has had, in different ...

One semantic and two syntactic decision procedures are given for determining the validity of Aristotelian assertoric and apodeictic syllogisms. Results are obtained by using the Aristotelian deductions that necessarily have an even number of premises.

A theorem due to Shoesmith and Smiley that axiomatizes two-valued multiple-conclusion logics is extended to partial logics.

Although Harry Woolf’s great collective volume Quantification mostly overlooked biology, Thomas Kuhn’s chapter there on the role of quantitative measurement within the physical sciences maps quite well onto the forms of reasoning that actually persuade us as biologists 50 years later. Kuhn distinguished between two contexts, that of producing quantitative anomalies and that of resolving them. The implied form of reasoning is actually C. S. Peirce’s abduction or inference to the best explanation: “The surprising fact C is observed; but if (...) A were true, C would be a matter of course; hence there is reason to suspect that A is true.” This article reviews abduction and the Kuhnian dichotomy in a range of classic examples where quantitative reasoning has ended arguments in the natural sciences. Included are John Snow’s discovery of the cause of cholera, Jean Perrin’s proof that atoms exist, the discovery of the double helix, the Alvarezes’ explanation of the extraterrestrial origin of the Cretaceous-Tertiary extinction, and current examples in passive smoking, ulcers, and the anthropogenicity of global warming. Modern biology is a quantitative science to the extent that we operate by “strong inference,” the insistence that our data are surprising on everybody else’s hypotheses but follow as a matter of course from our own, and that we demand numerical consilience whenever we infer across levels of analysis or across disciplines. (shrink)

Counting functions are shown to be complete by using a simpler argument than that used by Pelletier and Martin.

Parry discusses an extension of Aristotle's syllogistic that uses four nontraditional quantifiers. We show that his conjectured decision procedure for validity for the extended syllogistic is correct even if syllogisms have more than two premises. And we axiomatize this extension of the syllogistic.

The units of selection problem is an issue within evolutionary theory (or the philosophy thereof) and concerns the question of what units or objects are acted upon by natural selection -- for example, whether these are genes, organisms or groups of organisms. One of the central theses of Elliot Sober’s recent book,The Nature of Selection, is that the philosophical problem of what it means for something to be a unit of selection is to be understood by applying the correct account (...) of what it isin generalfor a factor to be a cause in a population.The account of population-causation that Sober utilizes for this purpose comes from the recent literature on probabilistic causality. This account requires that for C to cause E in a population, aunanimitycondition must be satisfied: C must raise the probability of E in each causal context. (shrink)

Although true in some aspects, the suggested characterization of today’s science as a dichotomy between traditional science and data-driven science misses some of the nuance, complexity, and possibility that exists between the two positions. Part of the problem is the claim that Data Science works without theories. There are many theories behind the data that are used in science. However, for data science, the only theories that matter are those in mathematics, statistics, and computer science. In this conceptual paper, we (...) add two other philosophy of science tenets, experiments and data, to the discussion to create a more nuanced view of how data science uses theories. Following Ihde’s concept of technoscience and the incessant quest for more precision, magnification, and resolution, we argue that technology-driven science created a need for more technology-driven science, culminating in data science. Further, we adapt Hacking and Galison’s views on physics to argue that data science is also an experimental science, which uses data objects in experiments. Drawing from Heelan, we called these objects “data-objects-for-knowing”. Finally, we conclude that data science is a science to study artificially created phenomena—a science to study the data manipulated by the equations and operations of AI. It disregards the connections between data and the real world that were carefully built by the theories from other sciences. In the experiments of data science, data are the world itself. The knowledge created by data science is purposely disconnected from any theory from other sciences; it is a knowledge for the sake of itself. (shrink)

The debate over encumbered versus unencumbered selves that characterized the dialogue between liberalism and republicanism did not end well. Neither side seemed enlightened by its encounter with the other, as it became increasingly difficult to pin down the differences between the sides, never more so than when Michael Sandel was violently agreeing with Richard Dagger. Drawing on the work of novelist and philosopher Iris Murdoch, this essay argues that Sandel could have made a much stronger argument for his view than (...) he did. Sandel need not have conceded or concluded that encumbered selves are unable to choose freely. Freedom is a more subtle and complicated concept that either Sandel or Dagger recognize. (shrink)

It is well known that if the nonempty player of the Banach–Mazur game has a winning strategy on a space, then that space is Baire in all powers even in the box product topology. The converse of this implication may also be true: We know of no consistency result to the contrary. In this paper we establish the consistency of the converse relative to the consistency of the existence of a proper class of measurable cardinals.

Investigations into inter-level relations in computer science, biology and psychology call for an *empirical* turn in the philosophy of mind. Rather than concentrate on *a priori* discussions of inter-level relations between 'completed' sciences, a case is made for the actual study of the way inter-level relations grow out of the developing sciences. Thus, philosophical inquiries will be made more relevant to the sciences, and, more importantly, philosophical accounts of inter-level relations will be testable by confronting them with what really happens (...) in science. Hence, close observation of the ever-changing reduction relations in the developing sciences, and revision of philosophical positions based on these empirical observations, may, in the long run, be more conducive to an adequate understanding of inter-level relations than a traditional *a priori* approach. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Disrupting Homelessness: Alternative Christian Approaches by Laura StiversFred GlennonDisrupting Homelessness: Alternative Christian Approaches Laura Stivers Minneapolis: Fortress Press, 2011. 187 pp. $18.00In this book Laura Stivers describes the limitations of traditional Christian approaches to homelessness that emphasize charity (rescue missions) or home ownership (Habitat for Humanity). While these approaches do, in fact, deal with some of the effects of homelessness, they not only fail to address the structural (...) causes of homelessness and poverty but they also reinforce certain ideological assumptions—such as individualism, a pattern of “blaming the victim,” and idyllic conceptions of home ownership—that keep us from addressing the [End Page 214] causes of homelessness in the first place. If we are really going to end homelessness, Stivers contends, we have to address the structural issues that keep people homeless, such as the inadequate availability of low-incoming rental housing, unemployment, low wages, and increasing inequality between rich and poor. If Christians and churches want to end homelessness, they must collaborate more fully and develop social movements that will address the full range of factors affecting homelessness, including causes and effects. In other words, they must embody in principle and in practice not only hospitality and compassion but also social justice. The place to begin, Stivers argues, is by listening to the homeless and the poor, allowing their experiential realities to set the agenda, and working in solidarity with them to disrupt the ideologies and to challenge the policies that perpetuate the problem.This requires an education in “disruption” that enables Christians to move beyond the behavioral manifestations of homelessness so that they can see the web of oppressive structures that have generated the bonds experienced by so many poor and homeless. Stivers provides a wealth of data that illustrate and document the full extent and complexity of homelessness in our society. Drawing upon Tracy West’s ethical methodology of “disruption,” Stivers then brings to light what she considers the dominant ideological assumptions that sustain homelessness. These include the assumptions that homeowners are responsible, autonomous citizens while the homeless are deviant, dependent, and criminal; and further that excessive wealth and inequality is justified. Stivers illustrates how these assumptions fail to consider certain factors—such as power, privilege, and racial and class disparities—that underlie and perpetuate the problems of homelessness and promote private over public policies to address them. To address these factors, Stivers argues for a different approach—modeled on such groups as the Industrial Areas Foundation and the PICO (People Improving Communities through Organizing) National Network—that embodies community organizing principles that engage the victims of homelessness in meaningful dialogue about the problems, actively listens to their stories and to their solutions, and works in solidarity with them to address the causes and the policies that perpetuate their homelessness.The audience for this book is Christians and churches seeking to address the issue of homelessness in our nation. Ethicists and Christians of like mind will have few problems with Stivers’s diagnosis of and remedy for homelessness, even if her remedy comes across as a bit utopian at places. Nonetheless, her rhetoric of empowerment, solidarity, social justice, and sustainability might drive away those of a more conservative theological bent. Since many involved in ministry to the homeless today presuppose precisely the assumptions she challenges, I am not sure she has done enough to convince them to change their approach, even though she attempts to ground her approach [End Page 215] biblically in the life and ministry of Jesus. Stivers is correct in asserting that substantive change will only come about as a result of a concerted social movement that involves churches of all theological stripes. The challenge is to find ways for us to set aside our differences for the sake of greater good: disrupting and ending homelessness.Fred GlennonLe Moyne CollegeCopyright © 2013 Society of Christian Ethics... (shrink)

Neural organization attempts to thwart, at least in part, modern neuroscientists' tendency to focus reductionistically on ever smaller microsystems. But although emphasizing higher levels of systems organization, the authors end up enforcing reductionisms of their own, principally the reduction of their domain to the study of invariable normal functioning, without explicit modeling of the deviations that constitute disease states or aging. This reductionism seriously weakens the authors' claims about the truth of their quantitative models.

Complexity in our universe, Herbert Simon once noted, generally takes a hierarchical, nearly decomposable form. If our purpose as biologists is to "carve Nature at the joints," then the quantitative biologist's pattern questions must embody some tentative claim of where the explanatory joints are—only after meaningful qualifications can notions of variance and covariance make sense. In morphometrics, specimens and variables alike can be "carved at the joints," with a correspondingly great gain in explanatory power in both versions. Simon's advice is (...) that the competent biologist's measurements should lie entirely within a single organismal component or else deal entirely with one of the joints. In either context, our best contemporary rhetorics of explanation in biology may resemble morphometrics in their frank combination of carefully supervised parallel quantifications that, taken together, result in new qualifications, leading in turn to new quantifications, and so on. In short, the relation between qualitative and quantitative in the organismal biological sciences is not an opposition but a complementarity, and the modern biometrical statistics of organismal form may be a particularly apposite praxis for exploring it. (shrink)

Back in 1987 the physicist/theoretical biologist Walter Elsasser reviewed a range of philosophical issues at the foundation of organismal biology above the molecular level. Two of these are particularly relevant to quantifications of form: the concept of ordered heterogeneity and the principle of nonstructural memory, the truism that typically the forms of organisms substantially resemble the forms of their ancestors. This essay attempts to weave Elsasser’s principles together with morphometrics for one prominent data type, the representation of animal forms by (...) positions of landmark points. I introduce a new spectrum of pattern descriptors of the shape variation of landmark configurations, ranging from the most homogeneous through growth gradients and focal features to a model of totally disordered heterogeneity incompatible with the rhetoric of functional explanation. An investigation may end up reporting its findings by one of these descriptors or by several. These descriptors all derive from one shared diagrammatic device: a log–log plot of sample variance against one standard formalism of today’s geometric morphometrics, the bending energies of the principal warps that represent all the scales of variability around the sample average shape. The new descriptors, which I demonstrate over a variety of contemporary morphometric examples, may help build the bridge we urgently need between the arithmetic of today’s burgeoning image-based data resources and the rhetoric of biological explanations aligned with the principles of Elsasser along with an even earlier philosopher of biology, the Viennese visionary Hans Przibram. (shrink)

Chow sets his version of statistical significance testing in an impoverished context of “theory corroboration” that explicitly excludes well-posed theories admitting of strong support by precise empirical evidence. He demonstrates no scientific usefulness for the problematic procedure he recommends instead. The important role played by significance testing in today's behavioral and brain sciences is wholly inconsistent with the rhetoric he would enforce.

This article interrogates postmodern and Levinasian conceptions of ethics with recourse to Quentin Tarantino's Reservoir Dogs and certain psychoanalytical concepts formulated in Jacques Lacan's Ethics of Psychoanalysis. Since Levinas, ethical thinking has, in some quarters, moved away from conventional questions about moral agency, rights and social justice, on to a concern towards the ultimate unknowability of `the other'. Ethics depends, for Levinas, on an unpredictable, accidental encounter with something Other, that, in its singularity, demands a response; it is precisely the (...) contingency of the encounter that constitutes the ethical difference from the realm of morality and law. Tarantino's movie narratives are also structured around accidents, disclosing the pain and jouissance of accidental expenditures that lie at the heart of any relation to the Other. In the midst of trauma, the Thing emerges, around which goods and signification circulate, that both delimits the identification of the Good and marks a space beyond moral law that becomes the site of radical ethical questioning. (shrink)

Excellence is everywhere. At the heart of the performance‐centred, technocratic language of business, sport and the university, the ubiquity of excellence is accompanied by a transparency of effects that mean nothing but nevertheless manage to transform practices within and between all cultural and corporate institutions. Tracing the notion of excellence associated, in the nineteenth century, with culture and humanity, this paper addresses the implications of its usage in recent decades for ideas concerning the contemporary role and status of the university (...) in order to theorise the upheavals in social and economic thinking that underlie recent cultural transformations. (shrink)