Selection operates at many levels. Some of the most obvious cases are organismic, such as changes in coloration under the influence of predation (cf. Kettlewell 1973; also Endler 1986). It also operates at other levels. Meiotic drive involves selection for a gene, independently of its effect on the organism. At a higher level, there may also be selection for patterns of colony growth in social insects, again under the influence of predation (cf. Wilson 1971). The appropriate level of selection is (...) a matter of the causal patterns exhibited, or the target of selection. It can also be understood as a question of the appropriate level at which to seek explanatory laws.Robert Brandon (1982, 1990) first clearly distinguished the question of the level of selection from debates over the units of selection. In doing so, he argued that the phenotype is commonly the target of selection, whatever the unit of selection might be. (shrink)

Selection operates at many levels. Robert Brandon has distinguished the question of the level of selection from the unit of selection, arguing that the phenotype is commonly the target of selection, whatever the unit of selection might be. He uses "screening off" as a criterion for distinguishing the level of selection. Cave animals show a common morphological pattern which includes hypertrophy of some structures and reduction or loss of others. In a study of a cave dwelling crustacean, Gammarus minus, we (...) find evidence for selection for both increased antennal size and reduction of eyes. The genetic structure of the population does not support the view that the phenotype screens off the genotype in explaining the differences in fitness. Nonetheless, the results do indicate that the level of selection is at least at the level of the phenotype in both cases. (shrink)

If there is a movement or school that epitomizes analytic philosophy in the middle of the twentieth century, it is logical empiricism. Logical empiricists created a scientifically and technically informed philosophy of science, established mathematical logic as a topic in and tool for philosophy, and initiated the project of formal semantics. Accounts of analytic philosophy written in the middle of the twentieth century gave logical empiricism a central place in the project. The second wave of interpretative accounts was constructed to (...) show how philosophy should progress, or had progressed, beyond logical empiricism. The essays survey the formative stages of logical empiricism in central Europe and its acculturation in North America, discussing its main topics, and achievements and failures, in different areas of philosophy of science, and assessing its influence on philosophy, past, present, and future. (shrink)

Whenever the use of non-experimental data for discovering causal relations or predicting the outcomes of experiments or interventions is contemplated, two difficulties are routinely faced. One is the problem of latent variables, or confounders: factors influencing two or more measured variables may not themselves have been measured or recorded. The other is the problem of sample selection bias: values of the variables or features under study may themselves influence whether a unit is included in the data sample.

This paper introduces a class of graphical independence models that is closed under marginalization and conditioning but that contains all DAG independence models. This class of graphs, called maximal ancestral graphs, has two attractive features: there is at most one edge between each pair of vertices; every missing edge corresponds to an independence relation. These features lead to a simple parameterization of the corresponding set of distributions in the Gaussian case.

It is well known that there may be many causal explanations that are consistent with a given set of data. Recent work has been done to represent the common aspects of these explanations into one representation. In this paper, we address what is less well known: how do the relationships common to every causal explanation among the observed variables of some DAG process change in the presence of latent variables? Ancestral graphs provide a class of graphs that can encode conditional (...) independence relations that arise in DAG models with latent and selection variables. In this paper we present a set of orientation rules that construct the Markov equivalence class representative for ancestral graphs, given a member of the equivalence class. These rules are sound and complete. We also show that when the equivalence class includes a DAG, the equivalence class representative is the essential graph for the said DAG. (shrink)

The introduction of statistical models represented by directed acyclic graphs (DAGs) has proved fruitful in the construction of expert systems, in allowing efficient updating algorithms that take advantage of conditional independence relations (Pearl, 1988, Lauritzen et al. 1993), and in inferring causal structure from conditional independence relations (Spirtes and Glymour, 1991, Spirtes, Glymour and Scheines, 1993, Pearl and Verma, 1991, Cooper, 1992). As a framework for representing the combination of causal and statistical hypotheses, DAG models have shed light on a (...) number of issues in statistics ranging from Simpson’s Paradox to experimental design (Spirtes, Glymour and Scheines, 1993). The relations of DAGs with statistical constraints, and the equivalence and distinguishability properties of DAG models, are now well understood, and their characterization and computation involves three properties connecting graphical structure and probability distributions: (i) a local directed Markov property, (ii) a global directed Markov property, (iii) and factorizations of joint densities according to the structure of a graph (Lauritizen, et al., 1990). (shrink)

Linear structural equation models (SEMs) are widely used in sociology, econometrics, biology, and other sciences. A SEM (without free parameters) has two parts: a probability distribution (in the Normal case specified by a set of linear structural equations and a covariance matrix among the “error” or “disturbance” terms), and an associated path diagram corresponding to the functional composition of variables specified by the structural equations and the correlations among the error terms. It is often thought that the path diagram is (...) nothing more than a heuristic device for illustrating the assumptions of the model. However, in this paper, we will show how path diagrams can be used to solve a number of important problems in structural equation modelling. (shrink)

The integrins are receptors for proteins of the extracellular matrix, both providing a physical link to the cytoskeleton and transducing signals from the extracellular matrix. Activation of integrins leads to tyrosine and serine phosphorylation of a number of proteins, elevation of cytosolic calcium levels, cytoplasmic alkalinization, changes in phospholipid metabolism and, ultimately, changes in gene expression. The recently discovered focal adhesion kinase localizes to focal contacts, which are sites of integrin clustering, and focal adhesion kinase can physically associate with integrins (...) in vitro. As integrins lack intrinsic catalytic activity, focal adhesion kinase is a candidate for a signaling molecule that is recruited by integrins in order to trigger the generation of intracellular second messengers. Thus, focal adhesion kinase may play a central role in signal transduction through integrins. (shrink)

It has been shown in Spirtes(1995) that X and Y are d-separated given Z in a directed graph associated with a recursive or non-recursive linear model without correlated errors if and only if the model entails that ρXY.Z = 0. This result cannot be directly applied to a linear model with correlated errors, however, because the standard graphical representation of a linear model with correlated errors is not a directed graph. The main result of this paper is to show how (...) to associate a directed graph with a linear model L with correlated errors, and then use d-separation in the associated directed graph to determine whether L entails that a particular partial correlation is zero. (shrink)

Thomas Richardson and Peter Spirtes. Parameterizing and Scoring Mixed Ancestral Graphs.

Thomas Richardson and Peter Spirtes. Scoring Ancestral Graph Models.

[Alan W. Richardson] This essay explores the uses that Michael Friedman and Bas van Fraassen have recently made of the work of Hans Reichenbach. It uses Friedman's work to complicate van Fraassen's invocation of Reichenbach's voluntarism in support of empiricism. It uses van Fraassen's work to motivate a concern with Friedman's neo-Kantian reading of Reichenbach. We are, finally, left with questions about the status and content of the account of the epistemic subject available to an epistemological voluntarist. /// [ (...) class='Hi'>Thomas E. Uebel] This response considers the question whether empiricists are condemned to silence about the epistemic agency their theories attribute or presuppose. It is argued that, unlike Reichenbach or Carnap, Neurath allowed for and indeed provided specifications of the role of epistemic agency in scientific inquiry. If this is correct, it underscores once more the need to distinguish between the various strands of logical positivism which show different strengths and weaknesses. (shrink)

[ Alan W. Richardson] This essay explores the uses that Michael Friedman and Bas van Fraassen have recently made of the work of Hans Reichenbach. It uses Friedman's work to complicate van Fraassen's invocation of Reichenbach's voluntarism in support of empiricism. It uses van Fraassen's work to motivate a concern with Friedman's neo-Kantian reading of Reichenbach. We are, finally, left with questions about the status and content of the account of the epistemic subject available to an epistemological voluntarist. /// (...) [Thomas E. Uebel] This response considers the question whether empiricists are condemned to silence about the epistemic agency their theories attribute or presuppose. It is argued that, unlike Reichenbach or Carnap, Neurath allowed for and indeed provided specifications of the role of epistemic agency in scientific inquiry. If this is correct, it underscores once more the need to distinguish between the various strands of logical positivism which show different strengths and weaknesses. (shrink)

Logical Empiricism is commonly regarded as uninterested in, if not hostile to sociological investigations of science. This paper reconstructs the views of Otto Neurath and Philipp Frank on the legitimacy and relevance of sociological investigations of theory choice. It is argued that while there obtains a surprising degree of convergence between their programmatic pronouncements and the Strong Programme, the two types of project nevertheless remain distinct. The key to this difference lies in the different assessment of a supposed dilemma facing (...) post-Mertonian sociologists of science. (shrink)

This paper describes the application of eight statistical and machine-learning methods to derive computer models for predicting mortality of hospital patients with pneumonia from their findings at initial presentation. The eight models were each constructed based on 9847 patient cases and they were each evaluated on 4352 additional cases. The primary evaluation metric was the error in predicted survival as a function of the fraction of patients predicted to survive. This metric is useful in assessing a model’s potential to assist (...) a clinician in deciding whether to treat a given patient in the hospital or at home. We examined the error rates of the models when predicting that a given fraction of patients will survive. We examined survival fractions between 0.1 and 0.6. Over this range, each model’s predictive error rate was within 1% of the error rate of every other model. When predicting that approximately 30°K of the patients will survive, all the models have an error rate of less than 1.5%. The models are distinguished more by the number of variables and parameters that they contain than by their error rates; these differences suggest which models may be the most amenable to future implementation as paper-based guidelines. (shrink)

Peter Abelard (1079–1142 ce) was the most wide‐ranging philosopher of the twelfth century. He quickly established himself as a leading teacher of logic in and near Paris shortly after 1100. After his affair with Heloise, and his subsequent castration, Abelard became a monk, but he returned to teaching in the Paris schools until 1140, when his work was condemned by a Church Council at Sens. His logical writings were based around discussion of the “Old Logic”: Porphyry's Isagoge, aristotle'S Categories and (...) On Interpretation and boethius'S textbook on topical inference. They comprise a freestanding Dialectica (“Logic”; probably c.1116), a set of commentaries (known as the Logica [Ingredientibus], c. 1119) and a later (c. 1125) commentary on the Isagoge (Logica Nostrorum Petititoni Sociorum or Glossulae). In a work Abelard called his Theologia, issued in three main versions (between 1120 and c.1134), he attempted a logical analysis of trinitarian relations and explored the philosophical problems surrounding God's claims to omnipotence and omniscience. The Collationes (“Debates,” also known as “Dialogue between a Christian, a Philosopher and a Jew”; probably c.1130) present a rational investigation into the nature of the highest good, in which the Christian and the Philosopher (who seems to be modeled on a philosopher of pagan antiquity) are remarkably in agreement. The unfinished Scito teipsum (“Know thyself,” also known as the “Ethics”; c.1138) analyses moral action. (shrink)

: This essay explores some themes in use of a relativized Kantian a priori in the work of Thomas Kuhn and Michael Friedman. It teases out some shared and some divergent beliefs and attitudes in these two philosophers by comparing their characteristic questions and problems to the questions and problems that seem most appropriately to attend to an adequate understanding of games and their histories. It argues for a way forward within a relativized Kantian framework that is suggested but (...) not argued for in Friedman (2001): philosophers of science should move from a concern with unreason as meaninglessness to a concern with unreason as argumentative coercion. It ends with a few suggestions regarding a place for philosophy in the history of reason. (shrink)

This paper draws upon contemporary feminist philosophy in order to consider the changing meaning of privacy and its relationship to identity, both online and offline. For example, privacy is now viewed by European Court of Human Rights (ECtHR) as a right, which when breached can harm us by undermining our ability to maintain social relations. I briefly outline the meaning of privacy in common law and under the European Convention on Human Rights (ECHR) in order to show the relevance of (...) contemporary feminist thought, in particular the image of selfhood that stresses its relationality. I argue that the meaning of privacy is in the process of altering as a result of a number of contingent factors including both changes in technology, particularly computer mediated communication (CMC), and changes in the status of women. This latter point can be illustrated by the feminist critique of the traditional reluctance of the liberal state to interfere with violence and injustice within the “privacy” of the home. In asking the question: “how is the meaning of “privacy” changing?” I consider not only contemporary legal case law but also Thomas Nagel’s influential philosophical analysis of privacy. Nagel’s position is useful because of the detail with which he outlines what privacy used to mean, whilst bemoaning its passing. I agree with his view that its meaning is changing but am critical of his perspective. In particular, I challenge his claim regarding the traditional “neutrality of language” and consider it in the context of online identity. (shrink)

_"Clarissa" on the Continent _defines and explores two strategies of literary translation—creative vs. preservative and strong vs. weak—as they transform one of the most influential English novels. Thomas Beebee compares the two opposing strategies as they influence the French translation of _Clarissa_ by the novelist Antione François de Prévost and the German translation by the Göttingen Orientalist Johann David Michaelis, and in doing so he demonstrates that each translator found authority for his procedure within the text itself. Each translation (...) is also examined in light of Richardson's other writings and placed in its literary and cultural context. This study uses translations in order to interpret _Clarissa_, to show how the basis for the novel's reception on the Continent was laid, and to explore the differences and interactions among three literary and cultural systems of the eighteenth century. The close examination of these two important translations enable the formulation of not only a theory of creative vs. preservative translation but also the interconnections between literary theory and translation theory. Beebee also looks at later translations of _Clarissa_ as products of literary and historical change and at Prévostian strategies of the novel. (shrink)

_"Clarissa" on the Continent _defines and explores two strategies of literary translation—creative vs. preservative and strong vs. weak—as they transform one of the most influential English novels. Thomas Beebee compares the two opposing strategies as they influence the French translation of _Clarissa_ by the novelist Antione François de Prévost and the German translation by the Göttingen Orientalist Johann David Michaelis, and in doing so he demonstrates that each translator found authority for his procedure within the text itself. Each translation (...) is also examined in light of Richardson's other writings and placed in its literary and cultural context. This study uses translations in order to interpret _Clarissa_, to show how the basis for the novel's reception on the Continent was laid, and to explore the differences and interactions among three literary and cultural systems of the eighteenth century. The close examination of these two important translations enable the formulation of not only a theory of creative vs. preservative translation but also the interconnections between literary theory and translation theory. Beebee also looks at later translations of _Clarissa_ as products of literary and historical change and at Prévostian strategies of the novel. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Buddhist-Christian Studies 20 (2000) 247-248 [Access article in PDF] Christ and Buddha: Weaving a Path for the New Millennium Thomas G. Hand, S.J.Mercy Center, Burlingame, CAThis dialogue conference/retreat was held at Mercy Center, Burlingame, CA, August 10-15, 1999. Well over the stated limit of 150 people joined a faculty of ten in presentations, discussions, sharing, meditation, and rituals. The conference was born primarily out of the personal and (...) social need for dialogue felt by Sandi Peters, who joined the program staff of Mercy Center after three years spent at Insight Meditation East, Barre, Massachusetts.Besides Peters as presider, the faculty members were: representing the Buddhist side--Nigel Edmonds (Mahayana and Christianity), Chris Phillips (Theravada), Ven. Thubten Chodron (Vajrayana), Rev. Heng Sure (Chinese Mahayana), and Patrick Thornton (Theravada and Christianity); representing the Christian side--Thomas G. Hand, S. J. (Catholic), Kevin Hunt, OCSO (Cistercian monk), Roshi Jinne Richardson (Zen and Christianity), and Rev. Shari Young (Episcopal and Zen).In a well-received keynote talk, Thomas Hand offered as the basis for the whole dialogue "The Primacy of Experience" in both traditions. The major themes were: (1st day) "The Challenges of Buddhist-Christian Dialogue," (2nd day) "The Language and Symbols of the Traditions," (4th day) "Weaving a Path for the New Millennium" as a joint venture of the two traditions together. On the third day, participants engaged in "Practice--East and West," including presentations geared toward practice both then and there and in the future.One marked difference between this conference and those that Mercy Center put on from 1985 to 1988 was the quality of the participants. In the earlier conferences, many were seekers and intellectual questioners. This year, besides such qualities, the participants were sincere practitioners. In fact, a great many were practicing in both traditions. They often classified themselves as Buddhist Christians or as Christian-root Buddhists. The greater depth of dialogue that has developed in less than fifteen years was clearly apparent. What is more, the sharing and insights of both Buddhist and Christian presenters seemed to have become increasingly relaxed, articulate, and vital. Their presentations were met with much deeper understanding and enthusiasm by all the participants. [End Page 247]Besides the presentations, participants deeply appreciated the chi kong and tai chi sessions, the daily meditation together, the day of practice, the tea ceremony, and the closing ritual. In a word, the conference was holistic dialogue.Those of dual practice were especially happy to find that they are not alone, that many are coming together to weave a new Path for the new millennium.Tapes are available. Contact Sandi Peters at (650) 340-7486.... (shrink)

These days, a number of philosophers of science indulge in lamenting about a crisis of their discipline. They complain about its loss of relevance, and bemoan the mar gi na lization of their dis cipline in the philosophical community and in the wider academia , Hardcastle and Richardson ). The Munich take on the philosophy of science does not succumb to this temptation. According to it, philosophy of science is well and alive. In Carlos Ulises Moulines’s Die Entwicklung der (...) modernen Wissen schaftstheorie Eine historische Einführung the word “crisis” is used only in reference to the 1940s when clas sical logical positivism encountered some dif fi culties in dealing with problems concerning veri fi cation, the ana ly tic/synthetic distinction, and similar conundrums. For Moulines, “crisis” is not a word that applies to contemporary philosophy of science. (shrink)

This review essay on three recent books on John Rawls’s theory of justice, by Catherine Audard, Samuel Freeman, and Thomas Pogge, describes the great boon they offer serious students of Rawls. They form a united front in firmly and definitively rebuffing Robert Nozick’s libertarian critique, Michael Sandel’s communitarian critique, and more generally critiques of “neutralist liberalism,” as well as in affirming the basic unity of Rawls’s position. At a deeper level, however, they diverge, and in ways that, this essay (...) suggests, go astray on subtle questions of interpretation: Freeman overemphasizes reciprocity, Pogge miscasts Rawls as a consequentialist, and Audard exaggerates the Kantian aspect of Rawls’s core, continuing commitment to “doctrinal autonomy.”. (shrink)

For much of the second half of the 20th Century, the primary role logical empiricism played was that of the argumentative foil. The 'received view' on a given topic (especially in philosophy of science, logic, or language) was frequently identified with some supposedly dogmatic tenet of logical empiricism. However, during the last twenty-five years, scholars have paid serious, sustained attention to what the logical positivists, individually and collectively, actually said. Early scholarship on logical empiricism had to engage in heavy-duty PR (...) work: why should anyone study the now-discarded mixture of blunders and implausibilities collected under the label 'logical empiricism'? However, thanks to the efforts of the pioneers, people studying the logical empiricists today need not articulate an extended apologia for their chosen subject of study -- rather, they can simply get on with their work. Many of the best fruits of these recent labors are on display in The Cambridge Companion to Logical Empiricism (CCLE), edited by Alan Richardson and Thomas Uebel. (shrink)

Ten years after the Human Genome Project’s completion the life sciences stand in a moment of uncertainty, transition, and contestation. The postgenomic era has seen rapid shifts in research methodology, funding, scientific labor, and disciplinary structures. Postgenomics is transforming our understanding of disease and health, our environment, and the categories of race, class, and gender. At the same time, the gene retains its centrality and power in biological and popular discourse. The contributors to Postgenomics analyze these ruptures and continuities and (...) place them in historical, social, and political context. Postgenomics, they argue, forces a rethinking of the genome itself, and opens new territory for conversations between the social sciences, humanities, and life sciences. Contributors. Russ Altman, Rachel A. Ankeny, Catherine Bliss, John Dupré, Michael Fortun, Evelyn Fox Keller, Sabina Leonelli, Adrian Mackenzie, Margot Moinester, Aaron Panofsky, Sarah S. Richardson, Sara Shostak, Hallam Stevens. (shrink)

There is a mental geography that may find its explorers, but never its cartographers.Annie Le BrunThe nature of the relationship between surrealism and anthropology has been a focus of recent anthropological debate. This relation has not been considered at the level of methodology and the aim of this article is to consider surrealism in specific methodological relation with anthropology, particularly about how the idea of travel has been conceptualized.

Ever since it was first published 1930, William Empson's "Seven Types of Ambiguity" has been perceived as a milestone in literary criticism - far from being an impediment to communication, ambiguity now seemed an index of poetic richness and expressive power. Little, however, has been written on the broader trajectory of Western thought about ambiguity before Empson; as a result, the nature of his innovation has been poorly understood. This book remedies this omission. Starting with classical grammar and rhetoric, and (...) moving on to moral theology, law, biblical exegesis, German philosophy, and literary criticism, the author explores the many ways in which readers and theorists posited, denied, conceptualized, and argued over the existence of multiple meanings in texts between antiquity and the twentieth century. This process took on a variety of interconnected forms, from the Renaissance delight in the "elegance" of ambiguities in Horace, through the extraordinary Catholic claim that Scripture could contain multiple literal - and not just allegorical - senses, to the theory of dramatic irony developed int he nineteenth century, a theory intertwined with discoveries of the double meanings in Greek tragedy. Such narratives are not merely of antiquarian interest: rather, they provide an insight into the foundations of modern criticism, revealing deep resonances between acts of interpretation in disparate eras and contexts. This book lays bare the long tradition of efforts to liberate language, and even a poet's intention, from the strictures of a single meaning. (shrink)

Moral reasoning is individual or collective practical reasoning about what, morally, one ought to do. Philosophical examination of moral reasoning faces both distinctive puzzles — about how we recognize moral considerations and cope with conflicts among them and about how they move us to act — and distinctive opportunities for gleaning insight about what we ought to do from how we reason about what we ought to do.