We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

We have argued that Lehrer's definitions of coherence and justification have serious technical defects. As a result, the definition of justification is both too weak and too strong. We have suggested solutions for some of the problems, but others seem irremediable. We would also argue more generally that if coherence is anything like what Lehrer's theory says it is, then coherence is neither necessary nor sufficient for justification. While our current objections are directed at the ‘letter’ of Lehrer's theory, other (...) criticisms can be aimed at its very ‘spirit’. We would argue that coherence is unnecessary for justification because of the existence of ‘basic beliefs’, those about self-presenting states (‘I have a tingling sensation in my leg’) or self-evident truths (‘All men are men’). Such beliefs may be justified even though there are no other propositions in the subject's acceptance system that makes them more probable than competitors. Coherence is, moreover, insufficient for justification, because it ignores the inferential structure of the subject's acceptance system, and requires no justification of any kind for the subject's acceptance system itself. But we must develop these more fundamental objections on another occasion. (shrink)

Time belongs to a handful of categories (like form, symbol, cause) that are genuinely transdisciplinary. Time touches every dimension of our being, every object of our attention - including attention itself. It therefore can belong to no single field of study. Of course, this universalist view of time is not itself universal but rather is a product of the modern age, an age that conceived of itself as the 'new' time. Time has thus gained new importance as a theme of (...) general research with the 'post-modern turn' now manifest in many areas of intellectual endeavor, especially in the humanities and social sciences. 'Chronotypes' are models or patterns through which time assumes practical or conceptual significance. Time is not given but (as the subtitle indicates) fabricated in an ongoing process. Chronotypes are themselves temporal and plural, constantly being made and remade at multiple individual, social, and cultural levels. They interact, they change over time, and they have histories, whose construal is itself an act of temporal construction. This book - an interdisciplinary collaboration of philosophers, historians, literary critics, and anthropologists - examines the ways individuals, societies, and cultures make sense of time by constructing it in diverse patterns. Its title intentionally echoes a concept of narrative theory, Mikhail Bakhtin's 'chronotype', because narrative recurs as a chief form within which we build temporality. The topics treated by these essays range from story-telling to cross-cultural communication, from epistemological debates to concepts of historical periodization, from the construction of life stories to the stratification of social time. (shrink)

An anthology of contemporary readings in analytic aesthetics, this reference reflects the relationships among the central aesthetic concerns of recent years. Providing a new perspective on the contemporary philosophy of art, this volume examines the challenge of Postmodernism and how it may or may not affect the future of analytic aesthetics... offers a case study of the progress that has been made in handling the problem of expression in the arts... reconceptualizes the concepts of the art work, its properties, and (...) our experience and evaluation of it -- to take into account an expanding cultural, sociological contextualization, i.e., art as a culturally emergent product of social institutions and conventions... features several readings organized around clusters of writers discussing each other's ideas and proposals, including: Beardsley, Dickie, and Blizek -- Wolterstorff, Levinson, and Bender -- Stolnitz and Dickie -- Beardsley, Margolis, and Novitz -- and Sibley and Dickie. Suitable for professionals in the art industry and anyone interested in the philosophy or aesthetics of art. (shrink)

As a group, the essays in this volume pose that question as a first attempt to write the archaeology of the nature and history of description in the digital age.

Phillips and colleagues claim that the representation of knowledge is more basic than the representation of belief, presupposing them to be categorically distinct mental states with distinct evolutionary purposes. We argue that the relationship between the two is much more complex, is further shaped by culture and language, and leaves its mark on manifestations of theory of mind and teaching.

According to Keith Lehrer’s coherence theory, knowledge is true acceptance whose justification is undefeated by a falsehood. It has recently become clear that Lehrer’s handling of important Gettier-inspired problems depends upon his position that only falsehoods accepted by the subject can act as defeaters of knowledge. I argue against this and present an example in which an unreckoned truth---one neither believed nor believed to be false by the subject---defeats knowledge. I trace the negative implications of this matter for the coherence (...) theory. (shrink)

Although by the middle of the book beauty has been defined as a real, though general, property of things and phenomena when they are viewed through our cognitive desire to organize the world, and although beauty is referred to throughout, with great emphasis placed on the beauty of theories, this book is not a discursus on the nature of beauty in the traditional sense established in the Enlightenment and the nineteenth century, as the book’s title might imply to some. Instead, (...) in typical Zemachean fashion, hard-headed analytic techniques from logic, metaphysics, and the philosophy of language are applied to an array of aesthetic issues ranging from the ontology of aesthetic properties and the nature of aesthetic judgments to the fearing of fictional entities and the place of truth in aesthetics. The books defends a pervasively realistic view on these and many other matters, and does so with clear and provocative argumentation of real metaphysical sophistication. The book is a tour de force of analytic aesthetics and a welcome and courageous antidote to the current trends of relativism and deconstruction. (shrink)

A survey of professional foresters in the northeastern United States was conducted to determine whether professional forest resource managers viewed forest ecosystem management and other "new" forestry language as representing practical constructs, and whether there is a difference between USDA Forest Service foresters and private-sector foresters in the degree to which they have applied "new" forestry. Results suggested that the forest management behaviors of most foresters in the region may be influenced more by traditional forestry concepts and language than by (...) "new" forestry. (shrink)

This book re-examines the roles of causation and cognition in early modern philosophy. The standard historical narrative suggests that early modern thinkers abandoned Aristotelian models of formal causation in favor of doctrines that appealed to relations of efficient causation between material objects and cognizers. This narrative has been criticized in recent scholarship from at least two directions. Scholars have emphasized that we should not think of the Aristotelian tradition in such monolithic terms, and that many early modern thinkers did not (...) unequivocally reduce all causation to efficient causation. -/- In line with this general approach, this book features original essays written by leading experts in early modern philosophy. It is organized around five guiding questions: -/- What are the entities involved in causal processes leading to cognition? What type(s) or kind(s) of causality are at stake? Are early modern thinkers confined to efficient causation or do other types of causation play a role? What is God's role in causal processes leading to cognition? How do cognitive causal processes relate to other, non-cognitive causal processes? Is the causal process in the case of human cognition in any way special? How does it relate to processes involved in the case of non-human cognition? -/- The essays explore how fifteen early modern thinkers answered these questions: Francisco Suárez, René Descartes, Louis de la Forge, Géraud de Cordemoy, Nicolas Malebranche, Thomas Hobbes, Baruch de Spinoza, Gottfried Wilhelm Leibniz, Ralph Cudworth, Margaret Cavendish, John Locke, John Sergeant, George Berkeley, David Hume, and Thomas Reid. The volume is unique in that it explores both well-known and understudied historical figures, and in that it emphasizes the intimate relationship between causation and cognition to open up new perspectives on early modern philosophy of mind and metaphysics. (shrink)

ABSTRACTIn this essay, I will argue for an understanding of justice that is grounded in our imperfect world by drawing upon the works of John Dewey and the Classical Daoist philosophers. It will require a reconstructed understanding of persons as a field/continuum of interrelations and an updated understanding of human action and agency. This understanding of justice takes the form of non-coercive action, interaction that respects the particularity of each lived situation. The practice culminates in an ability to respond (...) to the environment considered to be ziran or ‘self-so’ by the Daoist Philosophers. As described in the Dao De Jing, it is the cultivation of the ‘Three Jewels of the Dao’, the most central of them being compassion making, this practice of justice as non-coercive action also understandable as the practice of compassion as described by the Classical Daoist philosophers. (shrink)

This study argues that Dōgen’s “Leaving Home Life” fascicle is not simply about leaving home/lay life to become a practicing monk. At first glance, the fascicle might not appear philosophically significant. To help bring the themes of that work into greater focus, I juxtapose Dōgen’s Shōbōgenzō and John Dewey’s later works on aesthetic experience and education. Both the teachings of Dōgen and the later Deweyan works on aesthetic experience are similar in the sense that both describe nature as a (...) radically plural and interdependent world without recourse to an underlying substance ontology or reality antecedent to and outside of experience. Both Dōgen and Dewey also claim that the experience of nature as... (shrink)

Is Hume a liberal or a conservative? Hume scholars are divided over this question. This paper rejects the widespread reading of Hume as a conservative and argues that Hume is a liberal, even though his version of liberalism is fundamentally different from Lockean liberalism. Hume differs from Locke in that he attempts to justify a liberal political order without appealing to natural rights or a social contract. Instead, his liberalism is deeply rooted in his empiricist epistemology and in his sentimentalist (...) ethics. Because the starting point of Hume’s political theory is his analysis of the nature of human beings as they actually are, he ends up with a liberal theory that is less idealizing than Lockean liberalism. He thus defends what I call a non-ideal liberalism. The paper also argues that Hume’s non-ideal liberalism does not rule out political ideals altogether. Such ideals, however, must be derived in such a way that they do not violate his empiricist principles. (shrink)

John McKnight's The Careless Society tellingly exposes the ways the professionalized welfare state creates dependency. But McKnight is too quick to condemn this result as the product of professional self‐interest, and to posit as the alternative a selfless, republican model of community. He overlooks the more realistic possibility that the pursuit of their interests by social groups empowered to take care of themselves would better serve those interests, and would simultaneously create a feeling of interdependence and civic responsibility.

A pioneering look at the fundamental role of logic in optimizationand constraint satisfaction While recent efforts to combine optimization and constraintsatisfaction have received considerable attention, little has beensaid about using logic in optimization as the key to unifying thetwo fields. Logic-Based Methods for Optimization develops for thefirst time a comprehensive conceptual framework for integratingoptimization and constraint satisfaction, then goes a step furtherand shows how extending logical inference to optimization allowsfor more powerful as well as flexible modeling and solutiontechniques. Designed to (...) be easily accessible to industryprofessionals and academics in both operations research andartificial intelligence, the book provides a wealth of examples aswell as elegant techniques and modeling frameworks ready forimplementation. Timely, original, and thought-provoking,Logic-Based Methods for Optimization: * Demonstrates the advantages of combining the techniques inproblem solving * Offers tutorials in constraint satisfaction/constraintprogramming and logical inference * Clearly explains such concepts as relaxation, cutting planes,nonserial dynamic programming, and Bender's decomposition * Reviews the necessary technologies for software developersseeking to combine the two techniques * Features extensive references to important computationalstudies * And much more. (shrink)