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)

William James’ Principles of Psychology, in which he made famous the ‘specious present’ doctrine of temporal experience, and Edmund Husserl’s Zur Phänomenologie des inneren Zeitbewusstseins, were giant strides in the philosophical investigation of the temporality of experience. However, an important set of precursors to these works has not been adequately investigated. In this article, we undertake this investigation. Beginning with Reid’s essay ‘Memory’ in Essays on the Intellectual Powers of Man, we trace out a line of development of ideas about (...) the temporality of experience that runs through Dugald Stewart, Thomas Brown, William Hamilton, and finally the work of Shadworth Hodgson and Robert Kelly, both of whom were immediate influences on James (though James pseudonymously cites the latter as ‘E.R. Clay’). Furthermore, we argue that Hodgson, especially his Metaphysic of Experience (1898), was a significant influence on Husserl. (shrink)

'Alain Badiou: Between Theology and Anti-theology' provides one of the first comprehensive analyses of the relationship between Badiou's philosophy and theology. Examining the full range of Badiou's writings, this provocative study explores how Badiou's philosophy relies on theology even if he claims otherwise and actively attempts to work against theology. Despite the complex questions discussed - ranging across ontology, the theory of truth and the subject, philosophy and its conditions, and anti-philosophy - this book presents a clear and accessible overview (...) of the theological, religious and biblical themes which animate Badiou's philosophy. (shrink)

Economics is probably the most subtle, precise and powerful of the social sciences and its theories have deep philosophical import. Yet the dominant alliance between economics and philosophy has long been cheerfully simple. This is the textbook alliance of neo-Classicism and Positivism, so crucial to the defence of orthodox economics against by now familiar objections. This is an unusual book and a deliberately controversial one. The authors cast doubt on assumptions which neo-Classicists often find too obvious to defend or, indeed, (...) to mention. They set out to disturb an influential concensus and to champion an unpopular cause. Although they go deeper into both philosophy and economics than is usual in interdisciplinary works, they start from first principles and the text is provokingly clear. This will be a stimulating book for all economic theorists and philosophers interested in the philosophy of science and social science. (shrink)

I highlight a metaphysical concern that stands in the way of more widespread adoption of causal modeling techniques such as causal Bayes nets. Researchers in some fields may resist adoption due to concerns that they don't 'really' understand what they are saying about a system when they apply such techniques. Students in these fields are repeated exhorted to be cautious about application of statistical techniques to their data without a clear understanding of the conditions required for those techniques to yield (...) genuine insight into the data. They are acutely aware that anyone can chuck some data into a software package and get what looks like an answer, even though these tests may not be well-defined for the data on which they can apparently be run. This is thus a healthy skepticism for uptake of causal modeling methods, which points directly to the need for a metaphysical understanding of causation in order to successfully use the modeling methods. Without a clear understanding of what the methods are committing to, including what it means to say that there exists a causal relationship, researchers have limited ability to identify potentially bad output, or to independently verify results. (shrink)

Even in areas of philosophy of science that don’t involve formal treatments of truth, one’s background view of truth still centrally shapes views on other issues. I offer an informal way to think about truth as trueing, like trueing a bicycle wheel. This holist approach to truth provides a way to discuss knowledge products like models in terms of how well-trued they are to their target. Trueing emphasizes: the process by which models are brought into true; how the idealizations in (...) models are not false but rather like spokes in appropriate tension to achieve a better-trued fit to target; and that this process is not accomplished once and done forever, but instead requires upkeep and ongoing fine-tuning. I conclude by emphasizing the social importance of being a pragmatist about truth in order to accurately answer questions about science such as, “but do we really know that…”. (shrink)

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Losing an arm to rescue a child from a burning building is supererogatory. But is losing an arm to save two children more supererogatory than losing two arms to save a single child? What factors make one act more supererogatory than another? I provide an innovative account of how to compare which of two acts is more supererogatory, and show the superiority of this account to its chief rival.

This chapter contains sections titled: Introduction What Are the Biological Sciences (Not)? Systematics Ecology and Evolution Levels of Selection Conclusion References.

Contributing to the naturalistic virtue ethics tradition, Natural Citizens applies recent work in the life sciences to develop a form of ethical naturalism that aspires to be non-reductive yet empirically responsible.

This chapter examines the relationship between laws and mechanisms as approaches to characterising generalizations and explanations in science. I give an overview of recent historical discussions where laws failed to satisfy stringent logical criteria, opening the way for mechanisms to be investigated as a way to explain regularities in nature. This followed by a critical discussion of contemporary debates about the role of laws versus mechanisms in describing versus explaining regularities. I conclude by offering new arguments for two roles for (...) laws that mechanisms cannot subsume, one epistemically optimistic and one pessimistic, both broadly Humean. Do note that this piece is not primarily Hume exegesis; it is more of a riff in the key of Hume. (shrink)

Does it make sense to refer to bird song - a complex vocalization, full of repetitive and transformative patterns that are carefully calculated to woo a mate - as art? What about a pack of wolves howling in unison or the cacophony made by an entire rain forest? Redefining music as "the art of possibly animate things," Musical Vitalities charts a new path for music studies that blends musicological methods with perspectives drawn from the life sciences. In opposition to humanist (...) approaches that insist on a separation between culture and nature--approaches that appear increasingly untenable in an era defined by human-generated climate change--Musical Vitalities treats music as one example of the cultural practices and biotic arts of the animal kingdom rather than as a phenomenon categorically distinct from nonhuman forms of sonic expression. The book challenges the human exceptionalism that has allowed musicologists to overlook music's structural resemblances to the songs of nonhuman species, the intricacies of music's physiological impact on listeners, and the many analogues between music's formal processes and those of the dynamic natural world. Through close readings of Austro-German music and aesthetic writings that suggest wide-ranging analogies between music and nature, Musical Vitalities seeks to both rekindle the critical potential of nineteenth-century music and rejoin the humans at the center of the humanities with the nonhumans whose evolutionary endowments and planetary fates they share. (shrink)

This chapter examines the philosophical discussion concerning the relationship between time, memory, attention, and consciousness, from Locke through the Scottish Common Sense tradition, in terms of its influence on James' development of the specious present doctrine. The specious present doctrine is the view that the present moment in experience is non punctate, but instead comprises some nonzero amount of time; it contrasts with the mathematical view of the present, in which the divide between past and future is merely a point (...) or a line with no thickness. The anonymous source for the term 'specious present' is revealed as a retired businessman-turned-amateur philosopher. The more likely source for the idea itself is a little-known philosopher, Shadworth Hollway Hodgson, who was not merely a significant influence on James but also on Husserl's development of the tripartite account of internal time consciousness. I conclude by demonstrating how James' changing views on the relationship between concepts and experience meant that by the later period of his writings, including those in which he develops his own views on pragmatism, James would have not merely noted the contrast between a mathematical conception of the present and our actual experience of it, he would have taken a further step and condoned the thick experience of the present as demonstrating the inadequacy of the intellectualized mathematical characterization. (shrink)

This book approaches Hobbes's philosophy from a completely new perspective: his creativity. Creativity is the production of something which experts consider to be original, valuable and of high quality. James Hamilton explores Hobbes's creativity by focusing on his development, personality, and motivation in the context of his culture and environment, and on the ways in which he thought creatively, as inferred from his writings. Identification of the ideas which Hobbes drew upon is an important part of the study for (...) two reasons. First, they are necessary to determine which of Hobbes's ideas and theories are original and which are not. Second, analysis of his creativity requires an understanding of the ideas from which he drew. Hamilton concludes that Hobbes became a great philosopher because of his creative virtuosity. (shrink)

Alexander Hamilton presents his early formative years, sharing the way his engagement with the cyanotype process has informed his art practice, from his time at Edinburgh College of Art, to his program of exhibitions and residencies, through to his work within the field of public arts. This personal history is combined with essays by academics, scholars and curators who engage with the intellectual roots of his work and practice. A comprehensive selection of Hamilton’s photography, including his unique plant-based (...) cyanotypes, completes this beautiful book. (shrink)

Twentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of what is best for an agent to do in light of the actual circumstances in which she acts and what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who may be (...) uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance. (shrink)

We use Homer and Sun Tzu as a background to better understand and reformulate confrontation, anger and violence in medicine, contrasting an unproductive ‘love of war’ with a productive ‘art of war’ or ‘art of strategy’. At first glance, it is a paradox that the healing art is not pacific, but riddled with militaristic language and practices. On closer inspection, we find good reasons for this cultural paradox yet regret its presence. Drawing on insights from Homer's The Iliad and The (...) Odyssey, we argue for better understanding of confrontation, anger, bullying, intimidation and violence in medicine in order to change the culture. For example, equating medicine with war is not a given condition of medicine but a convenient metaphor with historical origins and a historical trajectory. Other, non-martial metaphors, such as medicine as collaboration, may be more appropriate in an age of team-based care. Taking lessons from Homer, we suggest three key ways in which cold-hearted confrontation and anger in medicine can be transformed into productive, warm-hearted engagement: the transformation of angry impulse into reflection, moral courage and empathy. Thinking with Homer can offer an aesthetically and morally charged alternative to the current body of literature on topics, such as anger in doctors, and how this may be ‘managed’, without recourse to an instrumental economy where emotions are viewed as commodities, and emotional responses can be ‘trained’ through communication skills courses. (shrink)

Michel Foucault's analysis of "the birth of the clinic" describes the genesis of a unified discourse that, in retrospect, has shaped western medicine for two centuries. However, in looking prospectively toward a 21st century medicine, Foucault's analysis is necessary but not sufficient. To better critically address medicine and medical education in the era of simulation, we could draw on frameworks developed by futurists such as Jean Baudrillard. Foucault's analysis does not account for contemporary, complex developments of the clinical gaze as (...) the gaze is distributed across practitioners in increasing use of sophisticated, representational diagnostic imaging. Further, Foucault's antihumanist rhetoric sometimes strays into the antihumane, and this is disturbing for those who support the development of patient-centered medicine. Yet we are increasingly teaching aspects of medicine, such as communication, in simulated learning environments in which complex reality is absent, perhaps inadvertently creating an "inhumanity" in medical education. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

This chapter contains sections titled: Of Jerks and “Nice” Guys Gurus of The Game Aristotle: My Wingman After The Game.

An exploration of YouTube as a platform for remix, reuse, and sampling.

In the operating theater, the micro-politics of practice, such as interpersonal communications, are central to patient safety and are intimately tied with values as well as knowledge and skills. Team communication is a shared and distributed work activity. In an era of "professionalism," that must now encompass "interprofessionalism," a virtue ethics framework is often invoked to inform practice choices, with reference to phronesis or practical wisdom. However, such a framework is typically cast in individualistic terms as a character trait, rather (...) than in terms of a distributed quality that may be constituted through intentionally collaborative practice, or is an emerging property of a complex, adaptive system. A virtue ethics approach is a necessary but not sufficient condition for a collaborative bioethics within the operating theater. There is also an ecological imperative - the patient's entry into the household (oikos) of the operating theater invokes the need for "hospitality" as a form of ethical practice. (shrink)

It's commonly understood within the academy that the terms "man," "woman," and "other" are socially constructed, and that their meanings are maintained by the current political order. But few thinkers have attempted to reconcile that knowledge - which is rooted in Marxism - with queer theory. The few who have, meanwhile, usually attempt to do so through issues of libidinal desire and sexual expression. In the Politics of Everybody, Holly Lewis argues powerfully that the emphasis on desire, though seemingly (...) innocuous, is actually symptomatic of neoliberal habits of thought, and consequently, is responsible for a continued focus on the limited politics of identity. Instead, Lewis shows, we should look to the arena of body production, categorization, and exclusion; only through such a reorientation can we create a politics of liberation that is truly inclusive and grounded in lived experience."-- Provided by publisher. (shrink)

Inclusion of the humanities in undergraduate medicine curricula remains controversial. Skeptics have placed the burden of proof of effectiveness upon the shoulders of advocates, but this may lead to pursuing measurement of the immeasurable, deflecting attention away from the more pressing task of defining what we mean by the humanities in medicine. While humanities input can offer a fundamental critical counterweight to a potentially reductive biomedical science education, a new wave of thinking suggests that the kinds of arts and humanities (...) currently used in medical education are neither radical nor critical enough to have a deep effect on students’ learning and may need to be reformulated. The humanities can certainly educate for tolerance of ambiguity as a basis to learning democratic habits for contemporary team-based clinical work. William Empson’s ‘seven types of ambiguity’ model for analyzing poetry is transposed to medical education to: (a) formulate seven values proffered by the humanities for improving medical education; (b) offer seven ways of measuring impact of medical humanities provision, thereby reducing ambiguity; and (c) --as a counterweight to (b) – celebrate seven types of ambiguity in contemporary medical humanities that critically reconsider issues of proof of impact. (shrink)

Even though the evidence‐based medicine movement (EBM) labels mechanisms a low quality form of evidence, consideration of the mechanisms on which medicine relies, and the distinct roles that mechanisms might play in clinical practice, offers a number of insights into EBM itself. In this paper, I examine the connections between EBM and mechanisms from several angles. I diagnose what went wrong in two examples where mechanistic reasoning failed to generate accurate predictions for how a dysfunctional mechanism would respond to intervention. (...) I then use these examples to explain why we should expect this kind of mechanistic reasoning to fail in systematic ways, by situating these failures in terms of evolved complexity of the causal system(s) in question. I argue that there is still a different role in which mechanisms continue to figure as evidence in EBM: namely, in guiding the application of population‐level recommendations to individual patients. Thus, even though the evidence‐based movement rejects one role in which mechanistic reasoning serves as evidence, there are other evidentiary roles for mechanistic reasoning. This renders plausible the claims of some critics of evidencebased medicine who point to the ineliminable role of clinical experience. Clearly specifying the ways in which mechanisms and mechanistic reasoning can be involved in clinical practice frames the discussion about EBM and clinical experience in more fruitful terms. (shrink)

In this field guide, I distinguish five separate senses with which the term ‘mechanism’ is used in contemporary philosophy of science. Many of these senses have overlapping areas of application but involve distinct philosophical claims and characterize the target mechanisms in relevantly different ways. This field guide will clarify the key features of each sense and introduce some main debates, distinguishing those that transpire within a given sense from those that are best understood as concerning distinct senses. The ‘new mechanisms’ (...) sense is at the center of most of these contemporary debates and will be treated at greater length; subsequent senses of mechanism will be primarily distinguished from this one. In part I of this paper, I distinguish two senses of the term ‘mechanism’, both of which are explicitly hierarchical and nested in character, such that any given mechanism is comprised of smaller sub-mechanisms, in turn comprised of yet smaller sub-sub-mechanisms and so on. While both of the senses discussed here are anti-reductive, they differ in their focus on scientific practice versus metaphysics, in the degree of regularity they attribute to mechanisms, and in terms of their relationships to the discussions of mechanisms in the history of philosophy and science. (shrink)

A finer-grained delineation of a given explanandum reveals a nexus of closely related causal and non- causal explanations, complementing one another in ways that yield further explanatory traction on the phenomenon in question. By taking a narrower construal of what counts as a causal explanation, a new class of distinctively mathematical explanations pops into focus; Lange’s characterization of distinctively mathematical explanations can be extended to cover these. This new class of distinctively mathematical explanations is illustrated with the Lotka-Volterra equations. There (...) are at least two distinct ways those equations might hold of a system, one of which yields straightforwardly causal explanations, but the other of which yields explanations that are distinctively mathematical in terms of nomological strength. In the first, one first picks out a system or class of systems, finds that the equations hold in a causal -explanatory way; in the second, one starts with the equations and explanations that must apply to any system of which the equations hold, and only then turns to the world to see of what, if any, systems it does in fact hold. Using this new way in which a model might hold of a system, I highlight four specific avenues by which causal and non- causal explanations can complement one another. (shrink)

Twentieth century philosophers introduced the distinction between “objective rightness” and “subjective rightness” to achieve two primary goals. The first goal is to reduce the paradoxical tension between our judgments of (i) what is best for an agent to do in light of the actual circumstances in which she acts and (ii) what is wisest for her to do in light of her mistaken or uncertain beliefs about her circumstances. The second goal is to provide moral guidance to an agent who (...) may be uncertain about the circumstances in which she acts, and hence is unable to use her standard moral principle directly in deciding what to do. This paper distinguishes two important senses of “moral guidance”; proposes criteria of adequacy for accounts of subjective rightness; canvasses existing definitions for “subjective rightness”; finds them all deficient; and proposes a new and more successful account. It argues that each comprehensive moral theory must include multiple principles of subjective rightness to address the epistemic situations of the full range of moral decision-makers, and shows that accounts of subjective rightness formulated in terms of what it would reasonable for the agent to believe cannot provide that guidance. -/- . (shrink)

Millions of us increasingly seek happiness in fads and self-help books, reaching upward every day toward some enlightened state that we wish to attain. Surfing icon Laird Hamilton is more intent on looking inward and appreciating the brilliant creatures we already are. In Liferider, Laird uses five key pillars-Death & Fear, Heart, Body, Soul, and Everything Is Connected-to illustrate his unique worldview and life practices, offering inspiration to anyone who wants to elevate their ordinary, landlocked lives to do extraordinary (...) things. This is Laird Hamilton in his own words--raw, honest, and unvarnished--on topics he has rarely explored before. Based on extensive interviews and conversations between Laird and his coauthor, Julian Borra, with additional insights from Laird's wife, pro-volleyball player Gabby Reece, Liferider takes on human resilience, relationships, business, technology, risk-taking, and the importance of respecting the natural world, all through the lens of Laird's extraordinary life both in and beyond the ocean. (shrink)

What is it like to experience rapture? For philosopher Christopher Hamilton, it is a loss of self that is also a return to self—an overflowing and emptying out of the self that also nourishes and fills the self. In this inviting book, he reflects on the nature of rapture and its crucial yet unacknowledged place in our lives. Hamilton explores moments of rapture in everyday existence and aesthetic experience, tracing its disruptive power and illuminating its philosophical significance. Rapture (...) is found in sexual love and other forms of intense physical experience, such as Philippe Petit’s nerve-defying wire walk between the Twin Towers. Hamilton also locates it in quieter but equally joyous moments, such as contemplating a work of art or the natural world. He considers a range of examples in philosophy and culture—Nietzsche and Weil, Woolf and Chekhov, the extremes of experience in Werner Herzog’s films—as well as aspects of ordinary life, from illness to gardening. Conversational and evocative, this book calls on us to ask how we might make ourselves more open to experiences of rapturous joy and freedom. (shrink)

"Yoga and life are journeys, and this book is a wonderful guide along the path!"—Greg Louganis, four-time Olympic gold medalist Holistic wisdom for sustained peace Ally Hamilton changed her life with the eight limbs of yoga, a spiritual tradition first recorded in the Yoga Sutras 1,600 years ago. Join Ally as she shows you how to apply the wisdom of this honored tradition to your modern-day life. Physical poses—asanas—are the best-known aspects of yoga, but in the eight limbs practice, (...) healing comes through exploring your relationship to the world and to yourself while learning to recognize the obstacles that block your path. Yoga's Healing Power shows how to create the life you want from the inside out, working with your mind and emotions, your body and breath, your memories and your pain. With hands-on exercises, meditations, journaling prompts, and stories of healing, this book helps you uncover your particular gifts and begin to feel joy. Praise: "Ally is really onto something fantastic with Yoga's Healing Power...We're not talking just physical yoga; this is yoga as a way of life."—Kathryn Budig, author of Aim True "I was deeply humbled and greatly inspired by Ally Hamilton's courageous take on life, love, loss, and surrender."—Claire Bidwell Smith, author of The Rules of Inheritance. (shrink)

This paper articulates an account of causation as a collection of information-theoretic relationships between patterns instantiated in the causal nexus. I draw on Dennett’s account of real patterns to characterize potential causal relata as patterns with specific identification criteria and noise tolerance levels, and actual causal relata as those patterns instantiated at some spatiotemporal location in the rich causal nexus as originally developed by Salmon. I develop a representation framework using phase space to precisely characterize causal relata, including their degree (...) of counterfactual robustness, causal profiles, causal connectivity, and privileged grain size. By doing so, I show how the philosophical notion of causation can be rendered in a format that is amenable for direct application of mathematical techniques from information theory such that the resulting informational measures are causal informational measures. This account provides a metaphysics of causation that supports interventionist semantics and causal modeling and discovery techniques. (shrink)

The requirement that moral theories be usable for making decisions runs afoul of the fact that decision makers often lack sufficient information about their options to derive any accurate prescriptions from the standard theories. Many theorists attempt to solve this problem by adopting subjective moral theories—ones that ground obligations on the agent’s beliefs about the features of her options, rather than on the options’ actual features. I argue that subjective deontological theories suffer a fatal flaw, since they cannot appropriately require (...) agents to gather information before acting. (shrink)