Openness and transparency are becoming hallmarks of responsible data practice in science and governance. Concerns about data falsification, erroneous analysis, and misleading presentation of research results have recently strengthened the call for new procedures that ensure public accountability for data-driven decisions. Though we generally count ourselves in favor of increased transparency in data practice, this Commentary highlights a caveat. We suggest that legislative efforts that invoke the language of data transparency can sometimes function as “Trojan Horses” through which other political (...) goals are pursued. Framing these maneuvers in the language of transparency can be strategic, because approaches that emphasize open access to data carry tremendous appeal, particularly in current political and technological contexts. We illustrate our argument through two examples of pro-transparency policy efforts, one historical and one current: industry-backed “sound science” initiatives in the 1990s, and contemporary legislative efforts to open environmental data to public inspection. Rules that exist mainly to impede science-based policy processes weaponize the concept of data transparency. The discussion illustrates that, much as Big Data itself requires critical assessment, the processes and principles that attend it—like transparency—also carry political valence, and, as such, warrant careful analysis. (shrink)

We address three fundamental questions: What does it mean for an entity to be living? What is the role of inter-organismic collaboration in evolution? What is a biological individual? Our central argument is that life arises when lineage-forming entities collaborate in metabolism. By conceiving of metabolism as a collaborative process performed by functional wholes, which are associations of a variety of lineage-forming entities, we avoid the standard tension between reproduction and metabolism in discussions of life – a tension particularly evident (...) in discussions of whether viruses are alive. Our perspective assumes no sharp distinction between life and non-life, and does not equate life exclusively with cellular or organismal status. We reach this conclusion through an analysis of the capabilities of a spectrum of biological entities, in which we include the pivotal case of viruses as well as prions, plasmids, organelles, intracellular and extracellular symbionts, unicellular and multicellular life-forms. The usual criterion for classifying many of the entities of our continuum as non-living is autonomy. This emphasis on autonomy is problematic, however, because even paradigmatic biological individuals, such as large animals, are dependent on symbiotic associations with many other organisms. These composite individuals constitute the metabolic wholes on which selection acts. Finally, our account treats cooperation and competition not as polar opposites but as points on a continuum of collaboration. We suggest that competitive relations are a transitional state, with multi-lineage metabolic wholes eventually outcompeting selfish competitors, and that this process sometimes leads to the emergence of new types or levels of wholes. Our view of life as a continuum of variably structured collaborative systems leaves open the possibility that a variety of forms of organized matter – from chemical systems to ecosystems – might be usefully understood as living entities. (shrink)

Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...) sense and philosophical understandings of multicellularity, individuality and organism. We show how metagenomics requires us to think in different ways about what human beings are and what their relation to the microbial world is. Metagenomics could also transform the way in which evolutionary processes are understood, with the most basic relationship between cells from both similar and different organisms being far more cooperative and less antagonistic than is widely assumed. In addition to raising fundamental questions about biological ontology, metagenomics generates possibilities for powerful technologies addressed to issues of climate, health and conservation. We conclude with reflections about process-oriented versus entity-oriented analysis in light of current trends towards systems approaches. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:347 THE ROLE OF PART XII IN HUME'S DIALOGUES CONCERNING NATURAL RELIGION Anyone appreciative of Hume's greatness as a philosopher will want to suppose that the Dialogues both form a coherent whole and express Hume's own views on natural religion or religion based on reason (as opposed to religion based on revelation). In the last connection, given what we know of Hume's epistemology, life, and correspondence, one would be (...) inclined to suppose that he would reject out of hand the claims of revealed religion and contend that if there existed an acceptable religion it would have to be some form of natural religion. But insofar as natural religion claimed to establish scientifically the existence and nature of God one would envisage Hume dissenting. Now as long as we restrict our gaze to Parts I-XI of the Dialogues we seem to be able, easily enough, to satisfy all these suppositions. In Part IV, under the name of 'mysticism, ' revealed religion is summarily and facetiously dismissed as 2 indistinguishable from atheism. Demea's apparently permanent departure from the discussion at the conclusion of Part XI as much as says, symbolically, that revealed religion is not a serious contender for one's belief. Its a priori arguments -- the argument from sufficient reason and the ontological argument -- are almost as shortly attacked and dismissed (D 188-192). Also quite in keeping with Hume's philosophical view on knowledge of matters of fact is, on the other hand, the lengthy and detailed examination he bestows on the empiricist argument from design. That Philo, ostensibly his spokesman, is however able to uncover all kinds of logical short-comings in its claims to scientifically 348 establish the existence and nature of God does not surprise us; it coheres perfectly with our preconceived picture of Hume the skeptic, and his system as restricting science to numbers and quantities or, in the term's looser sense, to human nature and its more immediate surroundings. In short, Parts I-XI seem to be all of one Humean whole. But at first and even second glance Part XII notoriously seems to tear our hopes to find coherence and a plausible representation of Hume to tatters. There are, for one thing, those mocking sentences that seem to paint Hume in the colors of a devout, believing Christian, 'avid' for revelation. Thus, at the end of Part XII, apparently expressing Hume's deepest convictions, Philo says that "a person, seasoned with a just sense of the imperfections of natural reason, will fly to revealed truth with the greatest avidity" and immediately afterwards, "To be a philosophical sceptic is, in a man of letters, the first and most essential step towards being a sound, believing Christian" (D 227, 228). For another thing, in Part XII Hume seems to be completely reversing his refutations in Parts I-XI of the argument from design's claims to establish the existence and nature of God. Thus, where in Part II he had Philo reject the use of causal reasoning in the establishment of a Mind as the first cause of the universe on the relevantly Humean grounds that, to do so, "it were requisite, that we had experience of the origin of worlds" (D 150), in Part XII he has Philo, apparently speaking for himself (Hume), argue that "as there are also considerable differences, we have reason to suppose a proportional difference in the causes; and in particular ought to attribute a much higher degree of power and energy to the supreme cause than any we have ever observed in mankind. 349 Here then the existence of a DEITY is plainly ascertained by reason" (D 217). Indeed, all forms of the argument of design, purely analogical as well as causal, seem resurrected in Part XII, although they were one and all hanged and buried in Parts I-XI. Moreover, it seems that in Part XII Hume via Philo is saying that science itself leads us "to acknowledge a first intelligent Author" (D 214-215). Before proceeding to deal with certain other incoherencies with which Part XII seems to confront us let us address ourselves to the two that I have so far... (shrink)

My final aim in this paper is to show that Descartes is not guilty, as is so often maintained, of circular argumentation in the Meditations. But first it is important to uncover and remove certain tenacious misconceptions and confusions concerning what goes on in the Meditations which lend credence to the charge of circular argumentation. In this connection Mr. Harry Frankfurt's recent article, “Memory and the Cartesian Circle,” is peculiarly instructive; for it presents not only a completely untenable defence of (...) Descartes but one that, implicitly at least, rests on the very misconceptions that give substance to the notion of a Cartesian Circle. With the intention, then, of clearing the ground for the construction of my own defence of Descartes, I shall spend the first part of this paper examining Frankfurt's central thesis, the errors contained in it, and their sources. This thesis is contained in his statement, which I shall henceforth designate by the letter “J,” “Descartes did not attempt to justify present clear and distinct perceptions.”. (shrink)

Let me first explain what I am not attacking in this paper. I am not attacking, for instance, the right of free speech or any of the other specific rights listed in the U.S. Constitution's Bill of Rights or the United Nations' Charter. I am, rather, attacking any specific right's being called a ‘human right’. I mean to show that any such designation is not only fraudulent but, in case anyone might want to say that there can be noble lies, (...) grossly wicked, amounting indeed to genocide. (shrink)

The absence of self in Classical litera­ture and the emergence in the eigh­teenth century of the concept of the unique and individual self asserting its existence and seeking its truth in pri­vate experience and feeling is often touched upon in cultural histories but little explained. Seeking the reasons for and the effects of the change of attitude toward one’s concept of one’s self in the “new” eighteenth-century attitude to­ward history, biography, travel litera­ture, pornography, and the novel, Lyons finds, first, that (...) the term _self _is deceptively vague. It evolved, he notes, to fill the vacuum created by doubt about the existence of the soul. Second, Lyons finds that without a concept of the self—that ineffable something in a human being that to its inventors and their followers was an abstract of pure and intuited natural laws—the revolution and romanticism of the modern age would have been very different from what it has been. More importantly, Lyons concludes that the concept led to monumental error and to bitter disappointments rooted, as his il­luminating history shows, in the im­possibility of defining that which never was. (shrink)

Footnotes to the Synthesis? Content Type Journal Article Pages 1-4 DOI 10.1007/s11016-011-9569-6 Authors John O. Reiss, Department of Biological Sciences, Humboldt State University, 1 Harpst St., Arcata, CA 95521, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

WHEN, CONTROVERSIALLY, IT IS MAINTAINED that Aristotle was a functionalist, what is meant by "functionalist" cannot have the sense of "teleological functionalist," for in that sense there can be no doubt that Aristotle was a functionalist. The sense of "functionalism" that is patently being exploited is that which appears in contemporary philosophies of mind with affinities to logical behaviorism but also with some important divergencies and which Paul Churchland describes as the view that "psychological states are functional states in the (...) sense that for any being to have a psychology is for it to instance or embody a certain functional organization among its sensory inputs, internal states, and motor outputs." It is in this philosophical-psychological sense that the title of this paper controversially asks, Was Aristotle a functionalist? and to which I mean to give a negative answer. Thus, unless otherwise stated, it shall henceforth be this sense of the term that occurs in what follows. In order, however, to avoid ambiguity I shall call such functionalism "mind-functionalism.". (shrink)

In September 2008, 10 years after the untimely death of Pere Alberch (1954–1998), the 20th Altenberg Workshop in Theoretical Biology gathered a group of Pere’s students, col- laborators, and colleagues (Figure 1) to celebrate his contribu- tions to the origins of EvoDevo. Hosted by the Konrad Lorenz Institute for Evolution and Cognition Research (KLI) outside Vienna, the group met for two days of discussion. The meeting was organized in tandem with a congress held in May 2008 at the Cavanilles Institute (...) for Biodiversity and Evolutionary Biology (ICBiBE) in Valencia, Spain. The talks at the KLI were equal parts: nostalgic remembrance, excitement over new ways of thinking about old problems, and an unrepressed vitriol against the resurgence of reductionist thinking in EvoDevo. Here we highlight some of the key aspects of Pere’s life and work that informed and infused the talks. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Hume's Missing Shade of Blue Re-viewed John 0. Nelson It is obviously important for Hume's purposes in the Treatise to maintain that simple ideas are always founded in precedent, resembling impressions;1 andhe explicitly, overandover, doesso, evensometimes being so carried away by this first principle ofhis science of man (T 7) or so careless as to say that not just all simple ideas but all ideas are founded in (...) precedent, resembling impressions. At the same time, as often noted, Hume explicitly maintains that it is possible for there to be a simple idea having no precedent, corresponding impression. He argues: There is however one contradictory phaenomenon, which may prove, that 'tis not absolutely impossible for ideas to go before their correspondent impressions... Suppose... a person to have enjoyed his sight for thirty years, and to have become perfectly well acquainted with colours of all kinds, excepting one particular shade of blue... Let all the different shades of that colour, except that single one, beplac'd before him... Now Iask, whether 'tis possible for him, from his own imagination, to supply this deficiency, and raise up to himselfthe idea ofthat particular shade, tho' it had never been conveyed to him by his senses? I believe there arefew but will be ofopinion that he can; and this may serve as a proof, that the simple ideas are not always derived from the correspondent impressions. (T 5) Nowjust prior to this concession (as Cummins calls it ), Hume has said that the full examination ofthis question [the causal relationship between ideas and impression] is the subject of the present treatise; and therefore we shall here content ourselves with establishing one general proposition, That all our simple ideas in their first appearance are deriv'd from simple impressions, which are correspondent to them, and which they exactly represent. (T 4) Volume XV Number 2 353 JOHN O. NELSON And just after the same concession, that a simple idea may be raised up which does not have a prior, correspondent impression, Hume says that it still remains true, that all our simple ideas proceed either mediately or immediately, from their correspondent impressions (T 7). Thus we have Hume explicitly asserting, it seems, both that all simple ideas have precedent correspondent impressions and that they do not. But this, on the face ofit, is an arrant contradiction! Can Hume have Homerically nodded? We have been quoting from the Treatise, but Hume makes the very same contradictory-seeming claims in the Enquiryl A thinker of Hume's acumen might nod for a page or two's quarter hour but not for all of nine years! Moreover, in both places Hume refers to the phenomenon of the impression-less idea ofblue as a contradictory phenomenon, indicating clearly enough that he was himself aware of there seeming to be an inconsistency here in his contentions. What can possibly be going on? Is Hume deliberately being paradoxical? Perhaps trying, for sensation's sake, to shock the reader and so increase sales of his work, as some commentators in the past might have wished to say? But this would be at the expense ofhis own contentions and principles and not the reader's, and not even Hume's bitterest foes and most malicious critics — so far as I know — have ever proposed that Hume would, figuratively speaking, like Oedipus, gouge out his own eyes, even in order to increase sales of the Treatise, nor does it make the slightest sense to think he would. The mystery deepens when we remember that Hume has said, in defining the program of the Treatise, that his intention is to establish the one general proposition that all our simple ideas in their first appearance are deriv'd from simple impressions, which are correspondentto them (T4). What astrange way, we want to exclaim, to show that all our simple ideas are derived from correspondent simple impressions by almost immediately afterwards arguing that it is possible to have an idea that has had no correspondent, precedent impression! Such an egregious nonsequitur mightbe expected ofan absolutely incompetent beginner in philosophy, but we are speaking of David Hume, generally recognized as the profoundest and most acute of... (shrink)

Now it cannot be denied, I think, that this argument has the appearance of being sound, that is, both true in its premises and valid in its conclusion. But one surely ought to harbor suspicions concerning an argument which establishes the most momentous of all conclusions upon nothing more than a few propositions. In this paper I shall attempt to show that these suspicions are well-founded by pointing out that the above "proof" derives whatever force it has from an equivocation.

In this essay I try, first, to show that Lockean passages in Book I can be given a Berkeleian interpretation. I take two passages that have, in particular, been cited as allowing only a Lockean interpretation and show how they can be more coherently construed as Berkeleian in their intended meaning. In the process of this demonstration I show that only a Berkeleian interpretation is tenable for Book I. Second, I defend the Berkeleian interpretation against several charges; for instance, a (...) charge of textual inconsistency. I do, however, acknowledge in the process that in the Enquiry and subsequently Hume abandons Berkeley for Locke. I then offer an explanation of why he did and lastly I try to show that though Hume is thereby committed to an inconsistency he provides a way for justifying his (and our) conversational commitment to that inconsistency. (shrink)

A r anderson and n d belnap, Jr., Maintained in their 1962 article, "the pure calculus of entailment," that necessary propositions can be entailed only by necessary propositions, And not by contingent ones. Against this r w ashby offered an apparently conclusive counterexample in "entailment and modality" (1963). In support of anderson and belnap, The author of the present paper develops a definition of entailment and argues that contingent propositions never entail necessary ones. However, Psychological factors may intervene in our (...) logical perceptions to produce an appearance or illusion of entailment between a contingent and a necessary proposition. (staff). (shrink)