DNA‐based typing methods are increasingly important for the characterisation of bacteria. They are used to monitor the epidemiology of pathogens with public health significance and also to help understand the evolution and population biology of bacteria. However, these methods require accuracy and reproducibility and are often of a high‐throughput nature. Laboratory automation is therefore the key to the successful implementation of such methods. This review describes the impact of automation on DNA‐based typing methods, particularly multi‐locus sequence typing (MLST), and the (...) method components that can be automated. BioEssays 24:858–862, 2002. © 2002 Wiley Periodicals, Inc. (shrink)

We conduct an experiment with 459 nonprofessional investors to examine whether they evaluate companies differently based on management’s stated purpose for undertaking corporate social responsibility activities in the presence versus absence of a company-specific negative event. Specifically, we vary whether or not management intends to achieve financial returns from CSR activities in addition to promoting social good. We address investors’ decision processes by investigating whether their judgments are mediated by perceptions of future cash flows and/or the underlying ethical culture of (...) the company. Results show that absent a negative event, investment judgments are stronger when CSR activities are intended to achieve financial returns, through expectations of higher future cash flows. However, when a negative event occurs, we find a moderating effect of independent assurance of CSR disclosures. When disclosures are not assured, investors prefer CSR undertaken only for societal benefit, mediated by perceptions of a stronger ethical culture. However, when disclosures are assured, ethical culture is viewed similarly regardless of management’s intention to achieve financial returns from CSR activities. This suggests that management’s willingness to obtain independent assurance on disclosures is viewed as a positive ethical signal. Thus, assurance complements disclosure of CSR activities by contributing to protection against the impact of negative events. (shrink)

Through their transcript products genes regulate the rates at which an immense variety of transcripts and subsequent proteins occur. Understanding the mechanisms that determine which genes are expressed, and when they are expressed, is one of the keys to genetic manipulation for many purposes, including the development of new treatments for disease. Viewing each gene in a genome as a distinct variable that is either on or off, or more realistically as a continuous variable, the values of some of these (...) variables influence the values of others through the regulatory proteins they express, including, of course, the possibility that the rate of expression of a gene at one time may, in various circumstances, influence the rate of expression of that same gene at a later time. If we imagine an arrow drawn from each gene expression variable at a given time to a gene variable whose expression it influences a short while after, the result is a network, technically a directed acyclic graph. For example, the DAG in Figure 1 is a representation of a system in which the expression level of gene G1 at time 1 ) causes the expression level of G2, which in turn causes the expression level of G3. The arrows in Figure 1 which do not have a variable at their tails are “error terms” which represent all of the causes of a variable other than the ones explicitly represented in the DAG. The DAG describes more than associations—it describes causal connections among gene expression rates. A shock to a cell—by mutation, heating, chemical treatment, etc. may alter the DAG describing the relations among gene expressions, for example by activating a gene that was otherwise not expressed, producing a cascade of new expression effects. Although “knockout” experiments can reveal some of the underlying causal network of gene expression levels, unless guided by information from other sources, such experiments are limited in how much of the network structure they can reveal, due to the sheer number of possible combinations of experimental manipulations of genes necessary to reveal the complete causal network. Recent developments have made it possible to compare quantitatively the expression of tens of thousands of genes in cells from different sources in a single experiment, and to trace gene expression over time in thousands of genes simultaneously. cDNA microarrays are already producing extensive data, much of it available on the web. Thus there are calls for analytic software that can be applied to microarray and other data to help infer regulatory networks. In this paper we will review current techniques that are available for searching for the causal relations between variables, describe algorithmic and data gathering obstacles to applying these techniques to gene expression levels, and describe the prospects for overcoming these obstacles. (shrink)

Cambridge Texts in the History of Philosophy: Series Editors, Karl Ameriks and Desmond M. Clarke. Ren Descartes, Meditations on First Philosophy with Selections from the Objections and Replies . Translated and edited by John Cottingham. Cambridge, Cambridge University Press, 1996. Pp. xlvi + 120. 25., 7.95 pb. ISBN 0-521-55252-4 (hb.). ISBN 0-521-55818-2 (pb.). Ralph Cudworth, A Treatise Concerning Eternal and Immutable Morality with A Treatise of Freewill . Edited by Sarah Hutton. Cambridge, Cambridge University Press, 1996. Pp. xxxvi + 218. (...) 37.50 hb., 13.95 pb., ISBN 0-521-47362-4 (hb.). ISBN 0-521-47918-5 (pb.). Anne Conway: The Principles of the Most Ancient and Modern Philosophy . Translated and edited by Allison P. Coudert and Taylor Corse. Cambridge, Cambridge University Press, 1996. Pp. xxxix + 73. 35.00 hb., 12.95 pb. ISBN 0-521-47335-7 (hb.). ISBN 0-521-47904-5 (pb.). Julien Offray de La Mettrie: Machine Man and Other Writings . Translated and edited by Ann Thomson. Cambridge, Cambridge University Press, 1996. Pp. xxx + 179. 35.00 (hb.), 12.95. ISBN 0-521-47258-X (hb.). ISBN 0-521-47849-9 (pb.). (shrink)

Utilitarianism has had an unfortunate history. Its most influential exponents, Bentham and John Stuart Mill, set it out in such a way as to expose it to facile criticism and even to ridicule, and it has never fully recovered from this ill-omened start. In spite of the criticism and the ridicule, however, it still bulks large in ethical studies, and many people still have a hankering sympathy with it.

This essay critically comments on Contingent Future Persons (1997), an anthology of thirteen papers on the same topic as Obligations to Future Generations (1978), namely, the morality of decisions affecting the existence, number and identity of future persons. In my discussion, I identify the basic point of dispute between R. M. Hare and Michael Lockwood on potentiality; I criticize Nick Fotion's thesis that the Repugnant Conclusion is too far-fetched to be philosophically valuable; I object to Clark Wolf's "Impure Consequentialist Theory (...) of Obligation"; and I discuss the Non-Identity Problem in connection with essays by Robert Elliot and Ingmar Persson. (shrink)

The view from inside : gendered embodiment and the medical representation of sex / Shelley Wall -- The politics of medico-legal recognition : the terms of gendered subjectivity in the UK Gender Recognition Act / Sarah Burgess -- Journeys of choice? : abortion, travel, and women's autonomy / Christabelle Sethna and Marion Doull -- The code of ethics in medicine : intertextuality and meaning in Plato's Sophist and Hippocrates' oath / Twyla Gibson -- Sleeping ethics : gene, episteme, and the (...) body politic / Deborah Lynn Steinberg -- The last temptation of Marion Woodman : the anorexic remainder in bone : dying into life / David L. Clark. (shrink)

This paper uses readings of two classic autobiographies, Edmund Gosse's Father & Son and John Stuart Mill's Autobiography, to develop a distinctive answer to an old and central question in value theory: What role is played by pleasure in the most successful human life? A first section defends my method. The main body of the paper then defines and rejects voluntarist, stoic, and developmental hedonist lessons to be taken from central crises in my two subjects' autobiographies, and argues for (...) a fourth, diagnostic lesson: Gosse and Mill perceive their individual good through the medium of pleasure. Finally, I offer some speculative moral psychology of human development, as involving the waking, perception, management, and flowering of generic and individual capacities, which I suggest underlies Gosse and Mill's experiences. The acceptance of one's own unchosen nature, discovered by self-perceptive pleasure in the operation of one's nascent capacities, is the beginning of a flourishing adulthood in which that nature is fully developed and expressed. (shrink)

I argue for a perfectionist reading of Mill’s account of the good life, by using the failures of development recorded in his Autobiography as a way to understand his official account of happiness in Utilitarianism. This work offers both a new perspective on Mill’s thought, and a distinctive account of the role of aesthetic and emotional capacities in the most choiceworthy human life. I consider the philosophical purposes of autobiography, Mill’s disagreements with Bentham, and the nature of competent judges and (...) the pleasure they take in higher culture. I conclude that Millian perfectionism is an attractive and underappreciated option for contemporary value theory. (shrink)

This paper uses readings of two classic autobiographies, Edmund Gosse's Father & Son and John Stuart Mill's Autobiography, to develop a distinctive answer to an old and central question in value theory: What role is played by pleasure in the most successful human life? A first section defends my method. The main body of the paper then defines and rejects voluntarist, stoic, and developmental hedonist lessons to be taken from central crises in my two subjects' autobiographies, and argues for (...) a fourth, diagnostic lesson: Gosse and Mill perceive their individual good through the medium of pleasure. Finally, I offer some speculative moral psychology of human development, as involving the waking, perception, management, and flowering of generic and individual capacities, which I suggest underlies Gosse and Mill's experiences. The acceptance of one's own unchosen nature, discovered by self‐perceptive pleasure in the operation of one's nascent capacities, is the beginning of a flourishing adulthood in which that nature is fully developed and expressed. (shrink)

This chapter explores three answers to the question, What is it to take Mill's Autobiography “as literature”? First, it is to attempt to understand the Autobiography as an artefact, made in a context by an author with particular aims and secrets. Second, it is to place the Autobiography in a generic context, as a paradigm but not defining case. Third and most importantly, it is to pursue the idea that the Autobiography's form is necessary to what it does. In particular, (...) its diachronic, teleological, whole‐life self‐reflective form allows it to do a distinctive kind of ethics: arguing by example for a philosophy of ethical education; searching for a specification of the good life; and helping to educate its readers by developmental practice. (shrink)

In Supersizing the Mind, Andy Clark argues that the human mind is not bound inside the head but extends into body and environment.

From the Disney 'Teacher of the Year' and New York Times bestselling author comes a road map to enrich students' learning experiences, revised and updated for today's teachers and parents. After publishing the New York Times bestseller The Essential 55 (over 1 million copies sold), award-winning teacher Ron Clark took his rules on the road and traveled to schools and districts in 50 states. He met amazing teachers, administrators, students, parents, and all kinds of people involved in bringing up great (...) kids. These are the eleven qualities he describes in The Excellent 11: Enthusiasm, Adventure, Creativity, Reflection, Balance, Compassion, Confidence, Humor, Common Sense, Appreciation, and Resilience. Ron has filled this book with hundreds of suggestions, stories, and wonderfully funny anecdotes. You'll be smiling as you read--and finding the inspiration to change lives, one student at a time"--Back cover. (shrink)

In this book, Stuart Hampshire argues that no individual and no modern society can avoid conflicts between incompatible moral interests.

We might think that thought experiments are at their most powerful or most interesting when they produce new knowledge. This would be a mistake; thought experiments that seek understanding are just as powerful and interesting, and perhaps even more so. A growing number of epistemologists are emphasizing the importance of understanding for epistemology, arguing that it should supplant knowledge as the central notion. In this chapter, I bring the literature on understanding in epistemology to bear on explicating the different ways (...) that thought experiments increase three important kinds of understanding: explanatory, objectual and practical. (shrink)

In this book of essays, he argues that morality cannot be defined solely by rational and universal principles; instead, a major place must be found for changing and conflicting ideals, values peculiar to specific times and cultures.

In his précis of a recent book, Richard Joyce writes, “My contention…is that…any epistemological benefit-of-the-doubt that might have been extended to moral beliefs…will be neutralized by the availability of an empirically confirmed moral genealogy that nowhere…presupposes their truth.” Such reasoning – falling under the heading “Genealogical Debunking Arguments” – is now commonplace. But how might “the availability of an empirically confirmed moral genealogy that nowhere… presupposes” the truth of our moral beliefs “neutralize” whatever “epistemological benefit-of-the-doubt that might have been extended (...) to” them? In this article, I argue that there appears to be no satisfactory answer to this question. The problem is quite general, applying to all arguments with the structure of Genealogical Debunking Arguments aimed at realism about a domain meeting two conditions. The Benacerraf-Field Challenge for mathematical realism affords an important special case. (shrink)

What role does the imagination play in scientific progress? After examining several studies in cognitive science, I argue that one thing the imagination does is help to increase scientific understanding, which is itself indispensable for scientific progress. Then, I sketch a transcendental justification of the role of imagination in this process.

On 26 August 1974, Michel Foucault completed work on Discipline and Punish, and on that very same day began writing the first volume of The History of Sexuality. A little under ten years later, on 25 June 1984, shortly after the second and third volumes were published, he was dead. This decade is one of the most fascinating of his career. It begins with the initiation of the sexuality project, and ends with its enforced and premature closure. Yet in 1974 (...) he had something very different in mind for The History of Sexuality than the way things were left in 1984. Foucault originally planned a thematically organised series of six volumes, but wrote little of what he promised and published none of them. Instead over the course of the next decade he took his work in very different directions, studying, lecturing and writing about historical periods stretching back to antiquity. This book offers a detailed intellectual history of both the abandoned thematic project and the more properly historical version left incomplete at his death. It draws on all Foucault’s writings in this period, his courses at the Collège de France and lectures elsewhere, as well as material archived in France and California to provide a comprehensive overview and synthetic account of Foucault’s last decade. (shrink)

It is widely agreed that the intelligibility of modal metaphysics has been vindicated. Quine's arguments to the contrary supposedly confused analyticity with metaphysical necessity, and rigid with non-rigid designators.2 But even if modal metaphysics is intelligible, it could be misconceived. It could be that metaphysical necessity is not absolute necessity – the strictest real notion of necessity – and that no proposition of traditional metaphysical interest is necessary in every real sense. If there were nothing otherwise “uniquely metaphysically significant” about (...) metaphysical necessity, then paradigmatic metaphysical necessities would be necessary in one sense of “necessary”, not necessary in another, and that would be it. The question of whether they were necessary simpliciter would be like the question of whether the Parallel Postulate is true simpliciter – understood as a pure mathematical conjecture, rather than as a hypothesis about physical spacetime. In a sense, the latter question has no objective answer. In this article, I argue that paradigmatic questions of modal metaphysics are like the Parallel Postulate question. I then discuss the deflationary ramifications of this argument. I conclude with an alternative conception of the space of possibility. According to this conception, there is no objective boundary between possibility and impossibility. Along the way, I sketch an analogy between modal metaphysics and set theory. (shrink)

1. Animal Cruelty Industrial farming is appallingly abusive to animals. Pigs. In America, nine-tenths of pregnant sows live in “gestation crates. ” These pens are so small that the animals can barely move. When the sows are first crated, they may flail around, in an attempt to get out. But soon they give up. Crated pigs often show signs of depression: they engage meaningless, repetitive behavior, like chewing the air or biting the bars of the stall. The sows live like (...) this for four months. Gestation crates will be phased out in Europe by the end of 2012, but they will still be used in America.1 In nature, pigs nurse their young for about thirteen weeks. But in industrial farms, piglets are taken from their mothers after about ten days. Because the piglets are weaned prematurely, they develop a lifelong craving to suck and chew. But the farmers don’t want them sucking and chewing on other pigs’ tails. So the growers routinely snip off the tails of all their pigs. They do this with a pair of pliers and no anesthetic. However, the whole tail is not removed; a tender stump remains. The point is to render the area sensitive, so the pigs being chewed on will fight back. Which they do.2 Over 113 million pigs are slaughtered each year in America.3 Typically, these pigs are castrated, their needle teeth are clipped, and one of their ears is notched for identification —all without pain relief.4 In nature, pigs spend up to three quarters of their waking hours foraging and exploring their environment.5 But in the factory farms, “tens of thousands of hogs spend their entire lives ignorant of earth or straw or sunshine, crowded together beneath a metal roof standing on metal slats suspended over a septic tank. ”6 Bored, and in constant pain, the pigs must perpetually inhale the fumes of their own waste. These pigs often get sick, and their ill health is exacerbated by the overcrowding. In 2000, the U.S. Department of Agriculture compared hog farms containing over 10,000 pigs—which is the norm—with farms containing under 2,000 pigs. (shrink)

This paper examines three views of what an omission or an instance of refraining is. The view advanced is that in many cases, an omission is simply an absence of an action of some type. However, generally one’s not doing a certain thing counts as an omission only if there is some norm, standard, or ideal that calls for one’s doing that thing.

The distinction between perception and cognition frames countless debates in philosophy and cognitive science. But what, if anything, does this distinction actually amount to? In this introductory article, we summarize recent work on this question. We first briefly consider the possibility that a perception-cognition border should be eliminated from our scientific ontology, and then introduce and critically examine five positive approaches to marking a perception–cognition border, framed in terms of phenomenology, revisability, modularity, format, and stimulus-dependence.

John D. Norton is responsible for a number of influential views in contemporary philosophy of science. This paper will discuss two of them. The material theory of induction claims that inductive arguments are ultimately justified by their material features, not their formal features. Thus, while a deductive argument can be valid irrespective of the content of the propositions that make up the argument, an inductive argument about, say, apples, will be justified (or not) depending on facts about apples. The argument (...) view of thought experiments claims that thought experiments are arguments, and that they function epistemically however arguments do. These two views have generated a great deal of discussion, although there hasn’t been much written about their combination. I argue that despite some interesting harmonies, there is a serious tension between them. I consider several options for easing this tension, before suggesting a set of changes to the argument view that I take to be consistent with Norton’s fundamental philosophical commitments, and which retain what seems intuitively correct about the argument view. These changes require that we move away from a unitary epistemology of thought experiments and towards a more pluralist position. (shrink)

I claim that one way thought experiments contribute to scientific progress is by increasing scientific understanding. Understanding does not have a currently accepted characterization in the philosophical literature, but I argue that we already have ways to test for it. For instance, current pedagogical practice often requires that students demonstrate being in either or both of the following two states: 1) Having grasped the meaning of some relevant theory, concept, law or model, 2) Being able to apply that theory, concept, (...) law or model fruitfully to new instances. Three thought experiments are presented which have been important historically in helping us pass these tests, and two others that cause us to fail. Then I use this operationalization of understanding to clarify the relationships between scientific thought experiments, the understanding they produce, and the progress they enable. I conclude that while no specific instance of understanding (thus conceived) is necessary for scientific progress, understanding in general is. (shrink)

Logical monism is the view that there is ‘One True Logic’. This is the default position, against which pluralists react. If there were not ‘One True Logic’, it is hard to see how there could be one true theory of anything. A theory is closed under a logic! But what is logical monism? In this article, I consider semantic, logical, modal, scientific, and metaphysical proposals. I argue that, on no ‘factualist’ analysis (according to which ‘there is One True Logic’ expresses (...) a factual claim, rather than an attitude like approval), does the doctrine have both metaphysical and methodological import. Metaphysically, logics abound. Methodologically, what to infer from what is not settled by the facts, even the normative ones. I conclude that the only interesting sense in which there could be One True Logic is noncognitive. The same may be true of monism about normative areas, like moral, epistemic, and prudential ones, generally. (shrink)

This book analyses the concept of scientific explanation developed by French disciples of Descartes in the period 1660-1700. Clarke examines the views of authors such as Malebranche and Rohault, as well as those of less well-known authors such as Cordemoy, Gadroys, Poisson and R'egis. These Cartesian natural philosophers developed an understanding of scientific explanation as necessarily hypothetical, and, while they contributed little to new scientific discoveries, they made a lasting contribution to our concept of explanation--generations of scientists in subsequent centuries (...) followed their lead. (shrink)

Samuel Clarke was by far the most gifted and influential Newtonian philosopher of his generation, and A Demonstration of the Being and Attributes of God, which constituted the 1704 Boyle Lectures, was one of the most important works of the first half of the eighteenth century, generating a great deal of controversy about the relation between space and God, the nature of divine necessary existence, the adequacy of the Cosmological Argument, agent causation, and the immateriality of the soul. Together with (...) the other texts presented in this edition, it also provides the best introduction to Clarke's philosophical views, which, in addition to their intrinsic interest, are historically important for the light they shed both on the philosophical positions within the Newtonian circle and on the exchange between Clarke and Leibniz, the most famous philosophical controversy of the eighteenth century. (shrink)

The last three decades have witnessed a heated debate of the merits of intelligent design (ID) as a way to understand a number of observable natural phenomena. The present dispute has its roots in a much older discussion: that of natural theology, which has always had as its goal the discernment of design(s) attributable to God in the natural world. Despite its ongoing relevance, natural theology does not have a coherent scholarly history. Turning Points in Natural Theology from Bacon to (...) Darwin deftly fills that gap, analysing the argument of design during the period from Francis Bacon (1561-1626) to Charles Darwin (1809-82), with a specific focus on those moments at which the rhetorical terms changed significantly. (shrink)

This book, which inaugurates the Princeton Monographs in Philosophy series, starts from Plato's analogy in the Republic between conflict in the soul and conflict in the city. Plato's solution required reason to impose agreement and harmony on the warring passions, and this search for harmony and agreement constitutes the main tradition in political philosophy up to and including contemporary liberal theory. Hampshire undermines this tradition by developing a distinction between justice in procedures, which demands that both sides in a conflict (...) should be heard, and justice in matters of substance, which will always be disputed. Rationality in private thinking consists in adversary reasoning, and so it does in public affairs. Moral conflict is eternal, and institutionalized argument is its only universally acceptable restraint and the only alternative to tyranny. In the chapter "Against Monotheism," Hampshire argues that monotheistic beliefs are only with difficulty made compatible with pluralism in ethics. In "Conflict and Conflict Resolution," he argues that socialism, seen as the proposal of extended political solutions for natural human ills, is still a relevant, yet strongly contested, ideal. (shrink)

This is an amended version of material that first appeared in A. Clark, Microcognition: Philosophy, Cognitive Science, and Parallel Distributed Processing (MIT Press, Cambridge, MA, 1989), Ch. 1, 2, and 6. It appears in German translation in Metzinger,T (Ed) DAS LEIB-SEELE-PROBLEM IN DER ZWEITEN HELFTE DES 20 JAHRHUNDERTS (Frankfurt am Main: Suhrkamp. 1999).

Every action, touch, utterance, and look, every listening, taste, smell, and feel is a living question; but it is no ordinary propositional one-by-one question, rather it is a plenisentient sensing and probing non-propositional enquiry about how our world is, in its present continuous sense, and in relation to how we anticipate its becoming. I will take this assumption as my first premise and, by using the notion of enkinaesthesia, I will explore the ways in which an agent’s affectively-saturated co-engagement with (...) its world establishes patterns of co-articulation of meaning within the anticipatory affective dynamics and the experiential entanglement necessary for expedient action and adaptation. In advancing this thesis I will reject the minimalist notions of embodiment by amplifying and extending the claims made by the most radical of the embodied mind theories. Crucially, I will offer a new wave of embodiment theory which has at its core the radical extension of sensorimotor affect into the life and being of other agents where their experience is for us both direct and immediate. This I will present as an immanent intercorporeality. (shrink)