Some central ideas associated with developmental systems theory are outlined for non-specialists. These ideas concern the nature of biological development, the alleged distinction between “genetic” and “environmental” traits, the relations between organism and environment, and evolutionary processes. I also discuss some criticisms of the DST approach.

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Michael A. PetersBeijing Normal UniversityMy deepest condolences to Pepe, Dom and Marcus and to Jim’s grandchildren. Tina and I spent a lot of time at the Marshall family home, often attending dinn...

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

Abstract:Adam Smith argues that virtue falls into two broad categories: “justice,” which he calls a “negative” virtue because it principally comprises restraint from harming or injuring others; and “beneficence,” which he calls “positive” because it comprises the actions we ought to take to improve others’ situations. Smith’s conception of justice is thus quite “thin,” and some critics argue that it is indeed too thin, since it fails to incorporate substantive concerns for the well-being of others. In this essay, (...) I lay out Smith’s conception of justice and offer a way to understand it that attempts to comprehend the various things he says about it. I then offer a cluster of objections drawing on criticisms that might fall under the heading of “social justice.” Finally, I suggest how Smith might respond to the criticisms by outlining a Smithian conception of what I call “ultimate justice.”. (shrink)

David Hume has traditionally been assumed to be a soft determinist or compatibilist, at least in the ‘reconciling project’ that he presents in Section 8 of the first Enquiry, entitled ‘Of liberty and necessity.’ Indeed, in encyclopedias and textbooks of Philosophy he is standardly taken to be one of the paradigm compatibilists, rivalled in significance only by Hobbes within the tradition passed down through Locke, Mill, Schlick and Ayer to recent writers such as Dennett and Frankfurt. Many Hume scholars also (...) concur in viewing him as a determinist, for example Norman Kemp Smith, Barry Stroud, A. J. Ayer, Paul Russell Don Garrett, Terence Penelhum, George Botterill, John Bricke, and John Wright. My main purpose in this paper will be to provide the evidence to substantiate this traditional interpretation, which has hitherto been widely assumed rather than defended. In the absence of such a defence, the consensus has been left open to challenge, most notably in a recent paper and a subsequent book by James Harris, who boldly claims that Hume ‘does not subscribe to determinism of any kind, whether Hobbesian or merely nomological.’. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Evolution of the Society for the Advancement of American PhilosophyJames Campbelldespite my increasingly decrepit appearance, I can lay no claim to being one of the founders of SAAP. When I joined the Society in the mid-1970s, it was already a well-functioning organization—if a much smaller one than today. After a few years of attending meetings, I began to submit papers, and I first appeared on the program at (...) our sixth annual meeting at John Carroll University in 1979. (See Fig. 1, the complete program, below.) While I was not one of the founders of SAAP, I did know them all. Presiding at the early meetings were, in the order of their presidencies, such elders as John Lachs, John J. McDermott, Darnell Rucker, James Gouinlock, Beth J. Singer, Peter H. Hare, Sandra B. Rosenthal, Thelma Z. Lavine, Joseph Betz, Charlene Haddock Seigfried, and Andrew J. Reck. Serving in the background at the same time were such patron saints as Justus Buchler, Douglas Greenlee, Abraham Edel, Max Harold Fisch, Elizabeth Flower, Edward H. Madden, David L. Miller, Frank M. Oppenheim, Evelyn Shirk, John E. Smith, and H. S. Thayer. It was a good time to be coming to American Philosophy, under the guidance of a Society that respected the fundamentals of pluralism and "fallibilism."1IThe brief discussion of the evolution of SAAP that I offer here initially emphasizes what the Society has meant to me over nearly five decades.2 As I was entering graduate school in 1974, I was drawn by the American philosophical tradition. It was, as William James writes, my "dumb conviction" that the best answers were to be found in this philosophical direction and not in the others, and that my job was to pursue these answers.3 What I found in this tradition was a refuge from both the analytic style of philosophy then dominant in America, with what I saw as its obsession with truth4 and its [End Page 1] confusion of cleverness with wisdom, and the alternatives of the various continental traditions that, although they pursued wisdom, seemed to me to rely too strongly on the mysterious or the untranslatable. My own sense of the American philosophical tradition at the time was an amalgam of Puritanism, Deism, Transcendentalism, Pragmatism in its various forms, and a large dose of Columbia Naturalism. Through further study and especially through my interactions at SAAP meetings, I became more grounded in these approaches and more open to other strands within the tradition.5 For me, cooperative interaction with others was essential to further understanding. Just as for Josiah Royce, the secret was "the community."6Among the lessons that I drew from the American philosophical tradition were the following. I knew that it was necessary to resist the human tendency to believe that what works for me will work for everyone else. As George Santayana reminds us, all philosophy is "personal."7 Thus, certain thinkers and certain thoughts will benefit from their initial plausibility to us, and other thoughts and thinkers will be initially suspect. To counter this personal prejudice, we need to partake in careful, long-term study. On a related point, Ralph Waldo Emerson urges us to seek insight from others, to accept what he calls "provocation" while not accepting their answers.8 At the same time, we live among these other individuals, marry them, teach their children, and benefit from their contributions to our social existence. In other words, American Philosophy teaches us that people are social creatures—a point which both Emerson and James were wary of, but not blind to—and that our thinking should focus on the world of shared experience. As Benjamin Franklin writes, our efforts in "Philosophy" make sense only when our pursuit of wisdom is related to human well-being.9 This point is so important that we need to wonder how our efforts were ever allowed to narrow and separate from a broad sense of human welfare to focus upon supposedly more important minutiae. With John Dewey, I saw the job of philosophers to be helping individuals to understand and deal with their philosophical "problems" of living.10 And, perhaps more... (shrink)

These volumes conclude a series initiated in 1974, marking almost fifty years of effort by a huge cohort of scholars. This review is thus a valedictory for the whole series as well as an account of what we have learned from the most recent volumes about Darwin's final years (1879–82). The project was begun by Frederick Burckhardt, who shared the editorial role for the early volumes with Sydney Smith and a rolling sequence of assistant editors and advisers who eventually (...) comprised a significant fraction of the leading members of what used to be called the ‘Darwin industry’. Smith passed away in 1988 (volume 7 notes his legacy). Burkardt too left this world in 2007 – volume 16, part 1 includes an obituary, but his name has been retained and Cambridge University Press still ask that the series be cited as ‘Burkhardt et al.’ Duncan Porter took over for volumes 8–15, again with a sequence of fellow editors and assistants, after which James Secord became head of the project through its final years. The dedications of successive volumes record the efforts of individual scholars who have aided the teams and the involvement of the many institutions and foundations that have leant moral and material support over the years. For those of us with Cambridge connections, the University Library will not seem the same without the presence of the team it supported. (shrink)

This article examines Bentham's contribution to anti-colonial thought in the context of the development of the British radical movement that attacked colonialism on the grounds that it advantaged what Bentham called the at the expense of the . It shows that Bentham was influenced as much by Josiah Tucker and James Anderson as by Adam Smith. Bentham's early economic critique is examined, and the sharp changes in his arguments after 1800 assessed, in the context of the American and (...) French Revolutions and the effects of British industrialization. The article also highlights the importance of Bentham's writings inspired by the Spanish colonial crisis of the early 1820s. They show developments in his economic analysis and include some very acute discussions of the psychological satisfactions that elites could gain from colonialism. The article ends with a brief comparison between Bentham and later radical thinkers to put his ideas in context. (shrink)

James K.A. Smith argues that the ontology of participation associated with Radical Orthodoxy is incompatible with a Christian affirmation of the intrinsic being and goodness of creatures. In response, he proposes a Leibnizian view in which things are endowed with the innate dynamism of ‘force’. Creatures have a certain depth of being, and are intrinsically good, just because they each have an inner virtuality that they bring into expression. Such force is said to be a metaphysical component of (...) the agent. In this paper it is asked whether John Milbank's ontology of participation can be defended by distinguishing between two senses of being a subject. Perhaps it is possible for a creature to bring into expression what is an infused ‘alien’ gift rather than a metaphysical component – to be expressive subject, but not ontic subject, for divine power. However, while this distinction promises to make sense of the reception of an indwelling ‘other’ in grace, knowledge and love, neither proper substance nor proper existence can be received in this way. A creature must be the ontic subject for its being, after all. Still, divine being might proceed from God as radical indwelling gift, as non-ontic ground for ontic being. (shrink)

This volume seeks to bring the concepts and doctrines of property law into the philosophy of property. It offers contributions from leading theorists of property law. The papers serve as introductions to many facets of philosophical work grounded in the law of property and as cutting edge contributions to the scholarly literature.

Collection of articles concerning methods of inerpreting Plato's works.

Prologue.--Some characteristics of the Cambridge Platonists.--Benjamin Whichcote (1609-1683)--John Smith (1616-1652)--Ralph Cudworth (1617-1685)--Nathaniel Culverwel (1618?-1651)--Henry More (1614-1687)--Peter Sterry (d. 1672)--Epilogue.

Examines the relationship between sport and education from both social and moral points of view. The text argues that sport has such a vital role to play in society that it should be an integral part of the curriculum. It presents guidelines for an effective teaching of sports in schools.

In May 2010, philosophers, family and friends gathered at the University of Notre Dame to celebrate the career and retirement of Alvin Plantinga, widely recognized as one of the world's leading figures in metaphysics, epistemology, and the philosophy of religion. Plantinga has earned particular respect within the community of Christian philosophers for the pivotal role that he played in the recent renewal and development of philosophy of religion and philosophical theology. Each of the essays in this volume engages with some (...) particular aspect of Plantinga's views on metaphysics, epistemology, or philosophy of religion. Contributors include Michael Bergman, Ernest Sosa, Trenton Merricks, Richard Otte, Peter VanInwagen, Thomas P. Flint, Eleonore Stump, Dean Zimmerman and Nicholas Wolterstorff. The volume also includes responses to each essay by Bas van Fraassen, Stephen Wykstra, David VanderLaan, Robin Collins, Raymond VanArragon, E. J. Coffman, Thomas Crisp, and Donald Smith. (shrink)

Politics and the Environment includes chapters on environmental philosophy and ideology, environmental movements, collective action, environment and economics. Each chapter includes real- life examples of pressing problems.

The domains of quantum theory and general relativity overlap in situations where quantum mechanical effects cannot be ignored. In order to deal with this overlap of theoretical domains, there has been a tendency to apply the rules of quantum field theory to the classical gravitational field equations and without much regard for the implications of the whole enterprise. The gravitational version of the asymmetric ageing of identical biological specimens shows that curved spacetime is not dispensable. This result is used to (...) conclude that the particle-based interpretations of quantum gravity are not acceptable. (shrink)

The Pinocchio paradox, devised by Veronique Eldridge-Smith in February 2001, is a counter-example to solutions to the Liar that restrict the use or definition of semantic predicates. Pinocchio’s nose grows if and only if what he is stating is false, and Pinocchio says ‘My nose is growing’. In this statement, ‘is growing’ has its normal meaning and is not a semantic predicate. If Pinocchio’s nose is growing it is because he is saying something false; otherwise, it is not growing. (...) ‘Because’ stands here for a non-semantic relation; it might be supposed to be causal or of some other nature, but it is not semantic. The paradox is discussed in relation to Tarski’s and Kripke’s theories of truth. Although the paradox is not necessarily a counter-example to a theory of a truth predicate, it is a problem for a theory of truth of the kind preserved by validity. (shrink)

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – (...) and this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

A number of recent discussions have argued that George Price's equationfor representing evolutionary change is a powerful and illuminatingtool, especially in the context of debates about multiple levels ofselection. Our paper dissects Price's equation in detail, and comparesit to another statistical tool: the calculation and comparison ofaverage fitnesses. The relations between Price's equation and equationsfor evolutionary change using average fitness are closer than issometimes supposed. The two approaches achieve a similar kind ofstatistical summary of one generation of change, and they (...) achieve thisvia a similar loss of information about the underlying fitnessstructure. (shrink)

Robert Frost is by far the most celebrated major American poet of the twentieth century. In part, this is because his poetry seems, on the surface, to be so accessible, even homey. But Frost was not just a powerful writer of popular lyric and narrative verse, argues Peter J. Stanlis in this major contribution to American literary study and philosophy. Rather, his work is deeply rooted in a complex philosophical dualism that opposes both idealistic monism, centered in spirit, and (...) scientific positivism, which posits that the universe can be understood as nothing but matter. In _Robert Frost: The Poet as Philosopher,_ Stanlis shows how Frost’s philosophical dualism of spirit and matter is perceived through metaphors and applied to science, religion, art, education, and society. He further argues that Frost’s dualism provides a critique of the monistic forces that were instrumental in the triumph of twentieth-century totalitarianism. Thoroughly informed by his twenty-three year friendship and correspondence with Frost, Stanlis’s landmark volume is the first attempt to deal with the poet’s philosophy in a systematic manner. It will appeal not only to fans of Frost but to all who understand poetry as a form of revelation for understanding human nature. (shrink)

Robert Frost is by far the most celebrated major American poet of the twentieth century. In part, this is because his poetry seems, on the surface, to be so accessible, even homey. But Frost was not just a powerful writer of popular lyric and narrative verse, argues Peter J. Stanlis in this major contribution to American literary study and philosophy. Rather, his work is deeply rooted in a complex philosophical dualism that opposes both idealistic monism, centered in spirit, and (...) scientific positivism, which posits that the universe can be understood as nothing but matter. In _Robert Frost: The Poet as Philosopher_, Stanlis shows how Frost’s philosophical dualism of spirit and matter is perceived through metaphors and applied to science, religion, art, education, and society. He further argues that Frost’s dualism provides a critique of the monistic forces that were instrumental in the triumph of twentieth-century totalitarianism. Thoroughly informed by his twenty-three year friendship and correspondence with Frost, Stanlis's landmark volume is the first attempt to deal with the poet’s philosophy in a systematic manner. It will appeal not only to fans of Frost but to all who understand poetry as a form of revelation for understanding human nature. (shrink)

The paradox in Inquiry in Plato's Meno raises the fundamental epistemological problem of how one can come to know the basic and primary criteria of philosophical reasoning. Two key tenets of the Socratic search for definitions underlie the paradox. First, Socrates argues in both the Euthyphro and Hippias Major, that knowledge of particular instances of a given Form presupposes knowledge of the universal Form. Secondly, Socrates insists in the Meno that knowledge of essence logically preceeds knowledge of a Form's other (...) properties. Taken together, these two principles entail that one cannot gain knowledge of essence either by inductive or by deductive reasoning. Thus when Socrates seeks to determine the correct definition of the essence of virtue, he faces the apparently insuperable problem of having no rational method for establishing the proper definition. The paradox of inquiry states in effect that Socratic elenchus is absurd because it posits an essence both as the goal and the necessary starting point of rational argumentation. ;It is in the face of this serious skeptical dilemma that Plato articulates a profoundly original conception of reasoning. According to Plato, the solution to the paradox is that reasoning toward a definition of essences involves raising to explicit consciousness one's implicit knowledge of the very essence being sought. The description of this process as a recalling of knowledge actually acquired in an earlier life is intended only as a metaphor: it illuminates the process of bringing to full awareness what one already implicitly knows. Both the problem and the solution presented in the Meno exhibit the characteristic Platonic interrelationship of metaphysicis and epistemology. When Socrates asks for a definition of virtue in the Meno, he means to uncover the nature of a Form which exists separately from its examples. Socratic definition is neither a form of conceptual analysis nor an analysis of immanent characteristics in particulars. The failure of many commentators to appreciate the recollection theory often derives from a failure to comprehend these metaphysical dimensions of Plato's solution. (shrink)

A commentary on Richard Joyce's The Evolution of Morality.

The brain displays both the anatomical features of a vast amount of interconnected topological mappings as well as the functional features of a nonlinear, metastable system at the edge of chaos, equipped with a phase space where mental random walks tend towards lower energetic basins. Nevertheless, with the exception of some advanced neuro-anatomic descriptions and present-day connectomic research, very few studies have been addressing the topological path of a brain embedded or embodied in its external and internal environment. Herein, by (...) using new formal tools derived from algebraic topology, we provide an account of the metastable brain, based on the neuro-scientific model of Operational Architectonics of brain-mind functioning. We introduce a “topodynamic” description that shows how the relationships among the countless intertwined spatio-temporal levels of brain functioning can be assessed in terms of projections and mappings that take place on abstract structures, equipped with different dimensions, curvatures and energetic constraints. Such a topodynamical approach, apart from providing a biologically plausible model of brain function that can be operationalized, is also able to tackle the issue of a long-standing dichotomy: it throws indeed a bridge between the subjective, immediate datum of the naïve complex of sensations and mentations and the objective, quantitative, data extracted from experimental neuro-scientific procedures. Importantly, it opens the door to a series of new predictions and future directions of advancement for neuroscientific research. (shrink)