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.

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)

Our purpose in this article is to identify and suggest resolution for two core problematics of grounded theory. First, while grounded theory provides transparency to one part of the conceptualization process, where codes emerge directly from the data, it provides no such systematic or transparent way for gaining insight into the conceptual relationships between discovered codes. Producing a grounded theory depends not only on the definition of conceptual pieces, but the delineation of a relationship between at least two of those (...) pieces. Second, the conceptualization process of grounded theory is done in hierarchical fashion, where individual codes emerge from the data but then are used to generate insight into more general concepts and thematic statements. But various works on grounded theory have failed to provide any systematic way of using data specific levels of scale (the codes) to gain insight into more macro levels of scale (concepts and themes). We offer fractal concept analysis as a means of resolving both of these issues. By using a logic structure generator, fractal concept analysis delineates self-similar conceptual frameworks at various levels of abstraction, yielding a method for linking concepts together within and between levels of scale encountered in the grounded theory coding and categorization process. We conclude that this fractal analytic technique can bolster the aims of grounded theory as a formalized and systematic process for generating theory from empirical data. (shrink)

Being a patient and living a life -- Clinical space and traits of healing -- False starts and frequent failures -- Three journeys : A.'Ibuprofen and love', B. 'Staying tuned up', C. 'We all want the same things' -- Being a patient : the moral field -- Rethinking healthcare ethics : the patient's moral authority.

The Eleatic philosophers argued that it was impossible for anything to change, since that would require something to differ from itself. Although this line of reasoning is unpersuasive, it challenges us to provide an account of temporal predication, which is the focus of much recent work on change. This paper surveys various approaches to change and temporal predication and addresses related questions about identity, persistence, properties, time, tense, and temporal logic.

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.

Rabbi Simcha Wasserman was a rosh yeshivah; kiruv pioneer; advisor; foster father; storyteller; transmitter of tradition; founder of yeshivos; hatzalah activist. This book captures him speaking with patience, simplicity, and intellect, about burning topics such as Holocaust, Kabbalah, Providence, and child-rearing. Includes a biographical sketch.

EDITORS' INTRODUCTION B he Vedas tell of a conversation between a young man, Shvetaketu, and his father concerning what the son had learned in his education ...

This book from award winning author Dr. Larry Crabb seeks to think through a model of counseling which can be integrated into the functioning of the local church. It contains a chart appendix.

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

(This insularity was further promoted by the guileless duplicity of scholars in other fields, who were all too prepared to bequeath "the problem of ...

This essay contains a partial exploration of some key concepts associated with the epistemology of realist philosophies of science. It shows that neither reference nor approximate truth will do the explanatory jobs that realists expect of them. Equally, several widely-held realist theses about the nature of inter-theoretic relations and scientific progress are scrutinized and found wanting. Finally, it is argued that the history of science, far from confirming scientific realism, decisively confutes several extant versions of avowedly 'naturalistic' forms of scientific (...) realism. (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)

In De veritate I.2, Thomas Aquinas claims that “to every true act of understanding there must correspond some being and likewise to every being there corresponds a true act of understanding.” For Aquinas, the ratio of truth consists in a conformity between intellect and being. This account of truth, however, doesnot appear to allow for a certain class of truths, namely those that are about nonbeings. Many think that it is true that ‘no chimeras exist,’ that ‘blindness can becaused by (...) exposure to bright lights,’ and that ‘evil should be avoided.’ Yet, in each of these cases of truth, there does not appear to be a being to which the intellectconforms. In this paper, I will explore the ways in which Aquinas’s notion of truth as “conformity to being” is able to accommodate truths about nonbeings. (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)

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

Laudan constructs a fresh approach to a longtime problem for the philosopher of science: how to explain the simultaneous and widespread presence of both agreement and disagreement in science. Laudan critiques the logical empiricists and the post-positivists as he stresses the need for centrality and values and the interdependence of values, methods, and facts as prerequisites to solving the problems of consensus and dissent in science.

Previous theories of the relationship between dispositions and conditionals are unable to account for the fact that dispositions come in degrees. We propose a fix for this problem that has the added benefit of avoiding the classic problems of finks and masks.

Analyses of dispositional ascriptions in terms of conditional statements famously confront the problems of finks and masks. We argue that conditional analyses of dispositions, even those tailored to avoid finks and masks, face five further problems. These are the problems of: (i) Achilles' heels, (ii) accidental closeness, (iii) comparatives, (iv) explaining context sensitivity, and (v) absent stimulus conditions. We conclude by offering a proposal that avoids all seven of these problems.

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.

While procreation is ubiquitous, attention to the ethical issues involved in creating children is relatively rare. In Debating Procreation, David Benatar and David Wasserman take opposing views on this important question. David Benatar argues for the anti-natalist view that it is always wrong to bring new people into existence. He argues that coming into existence is always a serious harm and that even if it were not always so, the risk of serious harm is sufficiently great to make procreation (...) wrong. In addition to these "philanthropic" arguments, he advances the "misanthropic" one that because humans are so defective and cause vast amounts of harm, it is wrong to create more of them.David Wasserman defends procreation against the anti-natalist challenge. He outlines a variety of moderate pro-natalist positions, which all see procreation as often permissible but never required. After criticizing the main anti-natalist arguments, he reviews those pronatalist positions. He argues that constraints on procreation are best understood in terms of the role morality of prospective parents, considers different views of that role morality, and argues for one that imposes only limited constraints based on the well-being of the future child. He then argues that the expected good of a future child and of the parent-child relationship can provide a strong justification for procreation in the face of expected adversities without giving individuals any moral reason to procreate. (shrink)

Disability and enhancement are often treated as opposing concepts. To become disabled in some respect is to move away from those who are enhanced in that same respect; to become enhanced is to move away from the corresponding state of disability. This chapter examines how best to understand the concepts of disability and enhancement in this symmetrical way. After considering various candidates, two types of accounts are identified as the most promising: welfarist accounts and typical-functioning accounts. The authors ultimately defend (...) a complex typical-functioning account as the best way to achieve a symmetrical understanding of disability and enhancement. (shrink)

Unethical conduct has reached crisis proportions in business :A1–A10, 2011) and on today’s college campuses :58–65, 2007). Despite the evidence that suggests that more than half of business students admit to dishonest practices, only about 5 % of business school deans surveyed believe that dishonesty is a problem at their schools :299–308, 2010). In addition, the AACSB which establishes standards for accredited business schools has resisted the urging of deans and business experts to require business schools to teach an ethics (...) class, and fewer than one-third of businesses schools now teach a business ethics course at the graduate or undergraduate levels. In this paper we briefly introduce the status of business ethics education and report the results of a survey of business students, deans of the top business schools, and business ethics subject matter experts about ten ethical outcomes. We then offer five specific recommendations to encourage business ethics faculty and decision makers to improve the teaching of business ethics. (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)