We present evidence of a potentially serious source of error intrinsic to all spotted cDNA microarrays that use IMAGE clones of expressed sequence tags (ESTs). We found that a high proportion of these EST sequences contain 5V-end poly(dT) sequences that are remnants from the oligo(dT)-primed reverse transcription of polyadenylated mRNA templates used to generate EST cDNA for sequence clone libraries. Analysis of expression data from two single-dye cDNA microarray experiments showed that ESTs whose sequences contain repeats of consecutive 5V- end (...) dT residues appeared to be strongly coexpressed, while expression data of all other sequences exhibited no such pattern. Our analysis suggests that expression data from sequences containing 5V poly(dT) tracts are more likely to be due to systematic cross-hybridization of these poly(dT) tracts than to true mRNA coexpression. This indicates that existing data generated by cDNA microarrays containing IMAGE clone ESTs should be filtered to remove expression data containing significant 5V poly(dT) tracts. D 2003 Elsevier Inc. All rights reserved. (shrink)

Conditioning can make imprecise probabilities uniformly more imprecise. We call this effect "dilation". In a previous paper (1993), Seidenfeld and Wasserman established some basic results about dilation. In this paper we further investigate dilation on several models. In particular, we consider conditions under which dilation persists under marginalization and we quantify the degree of dilation. We also show that dilation manifests itself asymptotically in certain robust Bayesian models and we characterize the rate at which dilation occurs.

We report two issues concerning diverging sets of Bayesian (conditional) probabilities-divergence of "posteriors"-that can result with increasing evidence. Consider a set P of probabilities typically, but not always, based on a set of Bayesian "priors." Fix E, an event of interest, and X, a random variable to be observed. With respect to P, when the set of conditional probabilities for E, given X, strictly contains the set of unconditional probabilities for E, for each possible outcome X = x, call this (...) phenomenon dilation of the set of probabilities (Seidenfeld and Wasserman 1993). Thus, dilation contrasts with the asymptotic merging of posterior probabilities reported by Savage (1954) and by Blackwell and Dubins (1962). (1) In a wide variety of models for Robust Bayesian inference the extent to which X dilates E is related to a model specific index of how far key elements of P are from a distribution that makes X and E independent. (2) At a fixed confidence level, (1-α), Classical interval estimates A n for, e.g., a Normal mean θ have length O(n -1/2 ) (for sample size n). Of course, the confidence level correctly reports the (prior) probability that θ ∈ A n ,P(A n )=1-α , independent of the prior for θ . However, as shown by Pericchi and Walley (1991), if an ε -contamination class is used for the prior on the parameter θ , there is asymptotic (posterior) dilation for the A n , given the data. If, however, the intervals A ′ n are chosen with length $O(\sqrt{\log (\text{n})/\text{n})}$ , then there is no asymptotic dilation. We discuss the asymptotic rates of dilation for ClassClassical and Bayesian interval estimates and relate these to Bayesian hypothesis testing. (shrink)

DNA microarrays are perfectly suited for comparing gene expression in different populations of cells. An important application of microarray techniques is identifying genes which are activated by a particular drug of interest. This process will allow biologists to identify therapies targeted to particular diseases, and, eventually, to gain more knowledge about the biological processes in organisms. Such an application is described in this paper. It is focused on diabetes and obesity, which is a genetically heterogeneous disease, meaning that multiple defective (...) genes are responsible for the diseases. The paper is divided in three parts, each dealing with a different problem addressed to our study. First we validate the data from our microarray experiment. We identified significant systematic sources of variability which are potentially issues for other microarray datasets. Second, we applied multiple hypothesis testing to identify differentially expressed genes. We found a set of genes which appear to change in expression level over time in response to a drug treatment. Third, we tried to address the problem of identification of co-expressed genes using cluster analysis. This last problem is still under discussion. (shrink)

James M. Robins, Richard Scheines, Peter Spirtes, and Larry Wasserman. The Limits of Causal Knowledge.

This volume concerns the status and ambitions of metaphysics as a discipline.

Ryan Wasserman explores a range of fascinating puzzles raised by the possibility of time travel, with entertaining examples from physics, science fiction, and popular culture, and he draws out their implications for our understanding of time, tense, freedom, fatalism, causation, counterfactuals, laws of nature, persistence, change, and mereology.

How should the well-off respond to the world's needy? Renowned ethicist Larry S. Temkin challenges common beliefs about philanthropy and Effective Altruism, exploring the complex ways that global aid may do more harm than good, and considers the alternatives available when neglecting the needy is morally impermissible.

What is the best question to ask an omniscient being? The question is intriguing; is it also paradoxical? We discuss several versions of what Ned Markosian calls the paradox of the question and suggest solutions to each of those puzzles. We then offer some practical advice about what do if you ever have the opportunity to query an omniscient being.

What is the relation between a clay statue andthe lump of clay from which it is made? According to the defender of the standardaccount, the statue and the lump are distinct,enduring objects that share the same spatiallocation whenever they both exist. Suchobjects also seem to share the samemicrophysical structure whenever they bothexist. This leads to the standard objection tothe standard account: if the statue and thelump of clay have the same microphysicalstructure whenever they both exist, how canthey differ in their (...) de re temporalproperties, de re modal properties and soon? In this paper I develop amereological answer to this question – thestatue and the lump differ with respect totheir parts and this explains theirdifference with respect to de re temporalproperties, de re modal properties andthe like. (shrink)

This paper critically engages ethical issues in the allocation of novel, and potentially costly, health care resources to patients with disorders of consciousness. First, we review potential benefits of novel health care resources for patients and their families and outline preliminary considerations to address concerns about cost. We then address two problems regarding the allocation of health care resources to patients with disorders of consciousness: (1) the problem of uncertain moral status; and (2) the problem of accurately measuring the welfare (...) burdens these resources would relieve. We conclude by suggesting that opportunity-based frameworks might complement standard approaches for justifying resources allocation to patients with disorders of consciousness. (shrink)

In The Responsive Environment, Larry D. Busbea takes up this concept of environment as an object and method of design at the height of its aesthetic, technical, and discursive elaboration. Exploring novel models of environmental perception, patterning, and control as developed by Gregory Bateson, Edward T. Hall, Wolf Hilbertz, György Kepes, Marshall McLuhan, Nicholas Negroponte, Paolo Soleri, and others, he shows how living space was reimagined as a domain capable of modification through input from its newly sensitized inhabitants.

There is extensive discussion in current Just War literature about the normative principles which should govern the initiation of war (jus ad bellum) and also the conduct of war (jus in bello), but this is the first book to treat the important and difficult issue of justice after the end of war. Larry May examines the normative principles which should govern post-war practices such as reparations, restitution, reconciliation, retribution, rebuilding, proportionality and the Responsibility to Protect. He discusses the emerging (...) international law literature on transitional justice and the problem of moving from a position of war and possible mass atrocity to a position of peace and reconciliation. He questions the Just War tradition, arguing that contingent pacifism is most in keeping with normative principles after war ends. His discussion is richly illustrated with contemporary examples and will be of interest to students of political and legal philosophy, law and military studies. (shrink)

This book interrogates the meaning and consequences of the unsettling parallel relationship between today’s critical theory and Right-wing political philosophy.

This chapter provides comments on some current longevity research. The ultimate aim of longevity research is to stop the aging process, so that none of us need die of old age. The chapter indicates the attitudes towards death and science. It discusses some worries about immortality raised by Leon Kass and Bernard Williams. In “Mortality and Morality: The Virtues of Finitude,” Leon Kass, raised many deep worries about immortality. One was that many of our greatest creations resulted from the recognition (...) of our own mortality. Bernard Williams notes that if our lives persisted unendingly through time, then there would either be significant alterations in a person's deepest projects, commitments, and character, or there would not. The author suggests that we should favor living well over living longer, and ongoing reproduction over immortality, and we should think long and hard before proceeding with certain lines of longevity research. (shrink)

African American distrust of medicine has consequences for treatment seeking and healthcare behaviour. Much work has been done to examine acute events that have contributed to this phenomenon and a sophisticated bioethics discipline keeps watch on current practices by medicine. But physicians and clinicians are not the only actors in the medical arena, particularly when it comes to health beliefs and distrust of medicine. The purpose of this paper is to call attention not just to ethical shortcomings of the past, (...) but to the structural contexts of those events and the contributions and responsibilities of popular media and academic disciplines in the production of knowledge. We argue that ignoring context and producing inaccurate work has real impacts on health and healthcare, particularly for African Americans, and thus engenders ethical obligations incumbent on disciplines traditionally recognised as purely academic. (shrink)

Assume that, even with a time machine, Tim does not have the ability to travel to the past and kill Grandfather. Why would that be? And what are the implications for traditional debates about freedom? We argue that there are at least two satisfactory explanations for why Tim cannot kill Grandfather. First, if an agent’s behavior at time _t_ is causally dependent on fact _F_, then the agent cannot perform an action (at _t_) that would require _F_ to have not (...) obtained. Second, if an agent’s behavior at time _t_ is causally dependent on fact _F_, then the agent cannot perform an action (at _t_) that would prevent _F_ from obtaining. These two explanations have distinct upshots for more traditional debates over freedom. The first implies that causal determinism is incompatible with the ability to do otherwise and also raises questions about the traditional arguments for the incompatibility of divine foreknowledge and the ability to do otherwise; the second does neither. However, both explanations imply that the Molinist account of divine providence renders agents unable to do otherwise, at least in certain circumstances. (shrink)

This book, the result of cooperation between the Center for Dewey Studies at Southern Illinois University Carbondale, and the Dewey Center at the University of ...

What would happen if you made your business decisions by the book? By the Bible that is. This updated version of the best-selling Business by the Book offers radical principles of business management that go beyond the Ten Commandments and other biblical maxims. Business by the Book is a step-by-step presentation of how businesses should be run according to the Creator of all management rules: God. Larry Burkett, founder and president of Christian Financial Concepts, provides business principles from his (...) own experience as well as what God’s Word says on topics such as: Hiring and Firing Decisions Pay Increases and Promotions Management Selection Employee Pay Decisions Borrowing and/or Lending Decisions Forming Corporations and Partnerships Business Tithing Retirement Whether you are the owner of a business, a corporate executive, or a manager, this best-selling classic is for you. (shrink)

This chapter wades into the growing discussion surrounding embodied cognition and predictive processing. After surveying a recent debate between Jakob Hohwy and Andy Clark, it articulates two outstanding issues facing discussions of compatibility. It argues that headway on these issues can be made by drawing on the resources of philosophy of science.

Temkin's book is a very original and deeply unsettling work of skeptical philosophy that mounts an important new challenge to contemporary ethics.

Diplomatic theory and practice -- International funding for animal protection -- International conferences and delegation management -- The media as a tool for diplomacy -- Important associations and international organizations -- Epilogue.

INTRODUCTION The appeal to teleological principles of explanation within the body of natural science has had an unfortunate history. ...

The problem of the relation between mind and brain has been among the most persistent in modern Western thought, one that even recent advances in neuroscience haven't been able to put to rest. Historian Larry McGrath's Making Spirit Matter is about how a particularly productive and influential generation of late nineteenth- and early twentieth-century French thinkers attempted to answer this puzzle by showing the mutual dependence of spirit and matter. The veritable revolution taking place across disciplines, from philosophy to (...) psychology, located our spiritual powers in the brain and offered a radical reformulation of the meaning of science, spirit, and the self. Pulling out connections between thinkers such as Bergson, Blondel, and Fouille̹e, among others, McGrath plots the intellectual movements that brought back to life themes of agency, time, and experience by putting into action the very sciences that seemed to undermine metaphysics and theology. In so doing, Making Spirit Matter lays bare the long legacy of this moment in the history of ideas and how it might renew our understanding of the relationship between mind and brain. (shrink)

Preface -- The mood elevator -- What drives the mood elevator? -- Up the mood elevator : the big payoffs -- Escaping unhealthy normal -- Braking your mood elevator : the power of curiosity -- Interrupting your pattern -- Feeding the thoughts you favor -- Living in mild preference -- Shifting your set point : the wellness equation -- Quieting your mind -- Cultivating gratitude -- Honoring our separate realities -- Nurturing faith and optimism -- Dealing with your down days (...) -- Relationships and the mood elevator -- Pointers for riding the mood elevator -- Notes -- How this book came to be -- Bibliography -- Acknowledgments -- Index -- About the author. (shrink)