REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (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)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

The authors of this collection fail to make clear the distinction between naturalistic and purely logical/methodological approaches to the philosophy of science. I also criticise Thomas Nickles's attempt to devise an explanatory method for discovery in science using programs that produce trial and error explorations of a domain, which he thinks replaces the need for a conjecture a refutation approach (cf. Popper and Campbell). Such programs embody undeclared conjectures in the way they are set up.

Defences of inference to the best explanation (IBE) frequently associate IBE with scientific realism, the idea that it is reasonable to believe our best scientific theories. I argue that this linkage is unfortunate. IBE does not warrant belief, since the fact that a theory is the best available explanation does not show it to be (even probably) true. What IBE does warrant is acceptance: taking a proposition as a premise in theoretical and/or practical reasoning. We ought to accept our best (...) scientific theories since they are the theories that are most likely to lead to the goal of science, which is that of knowledge. In support of this claim I invoke Bill Lycan's Panglossian reflections regarding Mother Nature.1. (shrink)

History and the modern sciences are characterized by what is sometimes called a methodological naturalism that disregards talk of divine agency. Some religious thinkers argue that this reflects a dogmatic materialism: a non-negotiable and a priori commitment to a materialist metaphysics. In response to this charge, I make a sharp distinction between procedural requirements and metaphysical commitments. The procedural requirement of history and the sciences—that proposed explanations appeal to publicly-accessible bodies of evidence—is non-negotiable, but has no metaphysical implications. The metaphysical (...) commitment is naturalistic, but is both a posteriori and provisional, arising from the fact that for more than 400 years no proposed theistic explanation has been shown capable of meeting the procedural requirement. I argue that there is nothing to prevent religious thinkers from seeking to overturn this metaphysically naturalistic stance. But in order to do so they would need to show that their proposed theistic explanations are the best available explanations of a range of phenomena. Until this has been done, the metaphysical naturalism of history and the sciences remains defensible. (shrink)

While a great deal of abuse has been directed at intelligent design theory (ID), its starting point is a fact about biological organisms that cries out for explanation, namely "specified complexity" (SC). Advocates of ID deploy three kind of argument from specified complexity to the existence of a designer: an eliminative argument, an inductive argument, and an inference to the best explanation. Only the first of these merits the abuse directed at it; the other two arguments are worthy of respect. (...) If they fail, it is only because we have a better explanation of SC, namely Darwin's theory of evolution by natural selection. (shrink)

It is sometimes said that permitting, say, voluntary euthanasia would erode the motivations and inhibitions supporting other, legitimate prohibitions on killing to the point where widespread disregard for the moral law would result. this paper discusses the relevance of such "slippery slope" arguments for the rule-utilitarian who claims that we can assess moral rules by asking whether their acceptance would maximize utility. first it is argued that any normative theory of this type cannot recognize slope arguments as legitimate considerations in (...) this assessment. second, it is suggested that a theory based on the very different notion of choosing a moral code can permit slope arguments to weigh as relevant considerations. (shrink)

A number of recent historians claim to have defeated what they call the ‘conflict thesis’, the idea that there exists some inevitable conflict between Darwinism and Christianity. This is often thought to be part of a broader ‘warfare thesis’, which posits an inevitable conflict between science and religion. But, all they have defeated is one, relatively uninteresting form of this thesis. There remain other forms of the conflict theses that remain entirely plausible, even in light of the historical record.

Theistic evolutionists often suggest that one can reconcile evolutionary theory with biblical teaching. But in fact Christians have accepted Darwinian theory only after reinterpreting the opening chapters of Genesis. Is such a reinterpretation justified? Within Western Christian thought, there exists a hermeneutical tradition that dates back to St Augustine and which offers guidelines regarding apparent conflicts between biblical teaching and natural philosophy (or “science”). These state that the literal meaning of the text may be abandoned only if the natural-philosophical conclusions (...) are established beyond doubt. But no large-scale scientific theory, such as Darwin’s, can claim this degree of certainty. It follows that to justify their reinterpretation of Genesis 1–3, Christians must either argue that the literal sense of the biblical text can be maintained or accept that the Augustinian view of biblical authority is untenable. Three alternative views are discussed: a first that attempts to limit the scope of biblical authority, a second that distinguishes between the Bible and the Word of God, and a third that abandons the idea that religious faith offers certain knowledge. While the third view seems the most defensible, it comes at a cost: the recognition that, as John Locke put it, “reason must be our last judge and guide in everything.”. (shrink)

In his 1615 letter to the Grand Duchess Christina of Lorraine, Galileo argues for a “principle of limitation”: the authority of Scripture should not be invoked in scientific matters. In doing so, he claims to be following the example of St Augustine. But Augustine’s position would be better described as a “principle of differing purpose”: although the Scriptures were not written in order to reveal scientific truths, such matters may still be covered by biblical authority. The Roman Catholic Church has (...) rejected Galileo’s principle, opting rather for Augustine’s, leaving open the possibility of future conflicts between scientists and Church authority. (shrink)

Colin Cheyne has argued that under certain circumstances an internalist or deontological theory of epistemic justification will give rise to a paradox. The paradox, he argues, arises when a principle of epistemic justification is both justifiably believed (in terms of the theory) and false. To avoid this paradox, Cheyne recommends abandoning the principle of justification-transference, which states that acts of believing made on the basis of a justifiably-believed principle are themselves justified. Since such a principle seems essential to any internalist (...) theory of justified believing, internalist theories may also need to be abandoned. I argue that while some theories of epistemic justification may indeed give rise to this paradox, an internalist or deontological theory of subjective justification will avoid it. The reason for this is that a false principle of justified believing does not render acts of believing subjectively unjustified, provided that the agent does not realize that the principle is false. (shrink)

David Friedrich Strauss is best known for his mythical interpretation of the Gospel narratives. He opposed both the supernaturalists (who regarded the Gospel stories as reliable) and the rationalists (who offered natural explanations of purportedly supernatural events). His mythical interpretation suggests that many of the stories about Jesus were woven out of pre-existing messianic beliefs and expectations. Picking up this suggestion, I argue that the Gospel writers thought paradigmatically rather than historically. A paradigmatic explanation assimilates the event-to-be- explained to what (...) is thought to be a prototypical instance of divine action. It differs from a historical or scientific explanation insofar as it does not specify the conditions under which it should be applied. It is, therefore, a wonderfully flexible way to understand the present in the light of the past. (shrink)

In accordance with Leo Strauss’s ingenious suggestion, the Athenian Stranger of Plato’s Laws is best understood as an alternative ‘Socrates’, fleeing from the hemlock to Crete. Situated between Crito and Phaedo, Laws effectively tests the reader’s loyalty to the real Socrates who obeys Athenian law and dies cheerfully in Athens. Having separated Plato from the Stranger, a nuanced defence of Karl Popper’s suspicions about Laws confronts the apologetic readings of both Strauss and Christopher Bobonich. As hinted by his preference for (...) wine, the antidote for hemlock, the Athenian Stranger repeatedly proves himself the opposite of Socrates, particularly with respect to piety. Once the Stranger is recognized as ‘an unreliable narrator’, this apparently ponderous product of Plato’s senility becomes the taut thriller of an innovative teacher at the peak of his powers. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Although Gilles Deleuze never explicitly developed what might be considered a ‘philosophy of technology’, this article nonetheless attempts to outline the rudiments of a Deleuzian approach to technology by proposing a series of interrelated concepts: (1) prosthesis (technological artefacts are externalised organs); (2) proto-technicity, or originary technicity (but this technicity already exists in Nature, all the way down, and precedes any ‘theory’); (3) exodarwinism (the fact that evolutionary time has bifurcated, and technology evolves in a faster and accelerating time scale); (...) (4) de-specialisation or de-differentiation (what conditions the externalisation of organs is their deterritorialisation); (5) motricity (the link between the brain and the hand/mouth is primarily one of movement); (6) inscription, or graphism (the link between mouth and hand takes place through phonetic writing, when the hand reproduces speech in graphic inscriptions); (7) maker's knowledge (we know the organisations of matter found in nature through the organisations of matter that we ourselves have created); and finally, (8) totipotence (like a stem cell, the body is capable of externalising an almost unlimited number of forms and functions; it is itself an abstract and the source of abstractions). (shrink)

This book is a translation of W.V. Quine's Kant Lectures, given as a series at Stanford University in 1980. It provide a short and useful summary of Quine's philosophy. There are four lectures altogether: I. Prolegomena: Mind and its Place in Nature; II. Endolegomena: From Ostension to Quantification; III. Endolegomena loipa: The forked animal; and IV. Epilegomena: What's It all About? The Kant Lectures have been published to date only in Italian and German translation. The present book is filled out (...) with the translator's critical Introduction, "The esoteric Quine?" a bibliography based on Quine's sources, and an Index for the volume. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)

What is the concept of sense developed by Deleuze in his 1969 Logic of Sense? This paper attempts to answer this question analysing the three dimensions of language that Deleuze isolates: the primary order of noises and intensities ; the secondary order of sense ; and the tertiary organisation of propositions. What renders language possible is that which separates sounds from bodies and organises them into propositions, freeing them for the expressive function. Deleuze argues that it is the dimension of (...) sense that brings about this genesis of language, and he analyses in detail the three syntheses that bring about the production of this surface of sense. Yet Deleuze also distinguishes between two types of non-sense: the nonsense of Lewis Carroll's portmanteau words, which remain ensconced in the dimension of sense, and the more profound nonsense of Antonin Artaud's psychotic scream-breaths, which penetrate the almost unbearable world of the primary order of noise and intensities. In the end, the focus of Logic of Sense is less the surface domain of sense than the primary depth of corporeal intensities. What Deleuze calls a ‘minor’ use of language is nothing other than an intensive use of language that constitutes a principle of metamorphosis. (shrink)

Deleuze argued that a fundamental mutation in the concept of time occurred in Kant. In antiquity, the concept of time was subordinated to the concept of movement: time was a ‘measure’ of movement. In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an autonomy of its own: time becomes "the pure and empty form" of everything that moves and changes. What is essential in the theory of time is not the distinction between objective ‘clock (...) time’ (or physical time) and the subjective experience of ‘time consciousness,’ since both of them measure movements, whether the movement of extensive objects or intensive states. What is fundamental is rather the relation between time and movement, since time can only assume its own concept when it ceases to be subordinate to movement, whether that movement is objective or subjective. This article examines how Kant inverted the relation between time and movement, and how Deleuze’s own theory of time builds on Kant’s revolution and extends it further. (shrink)

What is the fundamental purpose that justifies the existence of the modern university? The answer proposed in this essay is the promotion of social freedom. The essay begins by distinguishing social freedom from negative freedom and reflective freedom along the lines proposed by other theorists of social freedom, such as Frederick Neuhouser and Axel Honneth. After noting the need for a more developed account of the university than has so far been provided by these other theorists, the essay analyses the (...) various dimensions in which universities have, at their best, promoted social freedom. The essay then explains why it is through the promotion of social, as distinct from negative or reflective freedom, that universities fulfil their purpose. It concludes with some reflections on how this understanding of the purpose of the university fits an “immanent” model of social criticism. (shrink)

The current study is a pilot trial to examine the effects of a nonelective, classroom-based, teacher-implemented, mindfulness meditation intervention on standard clinical measures of mental health and affect in middle school children. A total of 101 healthy sixth-grade students (55 boys, 46 girls) were randomized to either an Asian history course with daily mindfulness meditation practice (intervention group) or an African history course with a matched experiential activity (active control group). Self-reported measures included the Youth Self Report (YSR), a modified (...) Spielberger State-Trait Anxiety Inventory, and the Cognitive and Affective Mindfulness Measure –Revised. Both groups decreased significantly on clinical syndrome subscales and affect but did not differ in the extent of their improvements. Meditators were significantly less likely to develop suicidal ideation or thoughts of self-harm than controls. These results suggest that mindfulness training may yield both unique and non-specific benefits that are shared by other novel activities. (shrink)

Difference and Repetition might be said to have brought about a Deleuzian Revolution in philosophy comparable to Kant’s Copernican Revolution. Kant had denounced the three great terminal points of traditional metaphysics – self, world and God – as transcendent illusions, and Deleuze pushes Kant’s revolution to its limit by positing a transcendental field that excludes the coherence of the self, world and God in favour of an immanent and differential plane of impersonal individuations and pre-individual singularities. In the process, he (...) introduces numerous conceptual innovations into philosophy: the becoming of concepts; a transformation of the form of the question; an insistence that philosophy must start in the middle; an attempt to think in terms of multiplicities; the development of a new logic and a new metaphysics based on a concept of difference; a new conception of space as intensive rather than extensive; a conception of time as a pure and empty form; and an understanding of philosophy as a system in heterogenesis – that is, a system that entails a perpetual genesis of the heterogeneous, an incessant production of the new. -/- Keywords: concepts, becoming, multiplicity, singularity, the middle [au milieu], difference, intensity, time, system, the new. (shrink)

This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...) to which the introduction of an UBI would meet these criteria is then examined, with a focus on the social role that stands to be most affected by an UBI, namely that of the worker-earner. It is argued that while an UBI is likely to be only partially effective as an instrument of specifically social freedom, its main justification lies not here, but in securing a basis for the subjective freedom that social freedom presupposes. (shrink)

This paper explores the relation of the theory of time and the theory of truth in Deleuze’s philosophy. According to Deleuze, a mutation in our conception of time occurred with Kant. In antiquity, time had been subordinated to movement, it was the measure or the “number of movement” (Aristotle). In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an independence and autonomy of its own for the first time. In Deleuze’s phrasing, time becomes the (...) pure and empty form of everything that moves and changes — not an eternal form (as in Plato), but precisely the form of what is not eternal. In turn, the theory of time is inextricably linked to the concept of truth, since to say that a proposition is true means that it is true “in all times and in all places.” Truth, in other words, is timeless, eternal, non-temporal. When the form of the true is confronted with the form of time, the concept of truth is necessarily put into crisis, and Deleuze’s argument is that time allows the power of the false to assume an autonomy of its own. The analysis will attempt to show how the liberation of time from movement (the pure and empty form of time) leads to a liberation of the false from the true (the power of the false). (shrink)

This article examines Gilles Deleuze’s concept of the simulacrum, which Deleuze formulated in the context of his reading of Nietzsche’s project of “overturning Platonism.” The essential Platonic distinction, Deleuze argues, is more profound than the speculative distinction between model and copy, original and image. The deeper, practical distinction moves between two kinds of images or eidolon, for which the Platonic Idea is meant to provide a concrete criterion of selection “Copies” or icons (eikones) are well-grounded claimants to the transcendent Idea, (...) authenticated by their internal resemblance to the Idea, whereas “simulacra” (phantasmata) are like false claimants, built on a dissimilarity and implying an essential perversion or deviation from the Idea. If the goal of Platonism is the triumph of icons over simulacra, the inversion of Platonism would entail an affirmation of the simulacrum as such, which must thus be given its own concept. Deleuze consequently defines the simulacrum in terms of an internal dissimilitude or “disparateness,” which in turn implies a new conception of Ideas, no longer as self-identical qualities (the auto kath’hauto), but rather as constituting a pure concept of difference. An inverted Platonism would necessarily be based on a purely immanent and differential conception of Ideas. Starting from this new conception of the Idea, Deleuze proposes to take up the Platonic project anew, rethinking the fundamental figures of Platonism (selection, repetition, ungrounding, the question-problem complex) on a purely differential basis. In this sense, Deleuze’s inverted Platonism can at the same time be seen as a rejuvenated Platonism and even a completed Platonism. (shrink)

This paper was presented as the keynote address at the 2005 Philosophy Graduate Student Conference at the University of Memphis on “Limitations of Subjectivity.”.

The “Treatise on Nomadology: The War Machine" is one of the most important and innovative chapters in Gilles Deleuze and Felix Guattari's book, A Thousand Plateaus. It is a highly original text in political philosophy whose implications have yet to be fully mined—or even partially mined, for that matter. This short text analyzes the "noumenal" status that Deleuze assigns to the nomadic war machine, and analyzes the fundamental role that the nomadology plays in Deleuze and Guattari's political philosophy.