Bayesian pseudo-confirmation,use-novelty,and genuine confirmation

According to the comparative Bayesian concept of confirmation, rationalized versions of creationism come out as empirically confirmed. From a scientific viewpoint, however, they are pseudo-explanations because with their help all kinds of experiences are explainable in an ex-post fashion, by way of ad-hoc fitting of an empirically empty theoretical framework to the given evidence. An alternative concept of confirmation that attempts to capture this intuition is the use novelty (UN) criterion of confirmation. Serious objections have been raised against this criterion. In this paper I suggest solutions to these objections. Based on them, I develop an account of genuine confirmation that unifies the UN-criterion with a refined probabilistic confirmation concept that is explicated in terms of the confirmation of evidence-transcending content parts of the hypothesis.     

Negotiating history: Contingency,canonicity, and case studies

Objections to the use of historical case studies for philosophical ends fall into two categories. Methodological objections claim that historical accounts and their uses by philosophers are subject to various biases. We argue that these challenges are not special; they also apply to other epistemic practices. Metaphysical objections, on the other hand, claim that historical case studies are intrinsically unsuited to serve as evidence for philosophical claims, even when carefully constructed and used, and so constitute a distinct class of challenge. We show that attention to what makes for a canonical case can address these problems. A case study is canonical with respect to a particular philosophical aim when the features relevant to that aim provide a reasonably complete causal account of the results of the historical process under investigation. We show how to establish canonicity by evaluating relevant contingencies using two prominent examples from the history of science: Eddington’s confirmation of Einstein’s theory of general relativity using his data from the 1919 eclipse and Watson and Crick’s determination of the structure of DNA.     

The rhetorical strategy of William Paley’s Natural theology (1802): Part 1, William Paley’s Natural theology in context

This article reconstructs the historical and philosophical contexts of William Paley’s Natural theology (1802). In the wake of the French Revolution, widely believed to be the embodiment of an atheistic political credo, the refutation of the transmutational biological theories of Buffon and Erasmus Darwin was naturally high on Paley’s agenda. But he was also responding to challenges arising from his own moral philosophy, principally the psychological quandary of how men were to be kept in mind of the Creator. It is argued here that Natural theology was the culmination of a complex rhetorical scheme for instilling religious impressions that would increase both the virtue and happiness of mankind. Philosophy formed an integral part of this strategy, but it did not comprise the whole of it. Equally vital were those purely rhetorical aspects of the discourse which, according to Paley, were more concerned with creating ‘impression’. This facet of his writing is explored in part one of this two-part article. Turning to the argumentative side of the scheme, part two examines Paley’s responses to David Hume and Erasmus Darwin in the light of the wider strategy of inculcation at work throughout all his writings.     

Scientists and their cultural heritage: Knowledge,politics and ambivalent relationships

For many years, scientific heritage has received attention from multiple actors from different spheres of activity—archives, museums, scientific institutions. Beyond the heterogeneity revealed when examining the place of scientific heritage in different places, an authentic patrimonial configuration emerges and takes the form of a nebula of claims and of accomplishments that result, in some cases, in institutional and political recognition at the national level, in various country all around the world. At the international level, the creation of the international committee dedicated to University Museums and Collections (UMAC) within the International Council of Museums (ICOM) certainly testified from this raising interest in academic heritage and the existence of a specific community concern with it.This article presents numerous initiatives for the preservation of scientific heritage in France, with the goal of analysing the relationship scientists have with their heritage. We argue that scientific communities have a special relationship with heritage, which is characterized by a number of ambiguities. We show that such ambivalences allow analysis of identity, discipline, professional, and social issues operative in defining heritage and being redefined by heritage. To explore these dimensions, we have chosen to present three different case studies. The first traces the institutional uses of heritage by a scientific institution, the Commissariat à l’énergie atomique (CEA), through the transformation of the first French atomic reactor (ZOE) into a museum. The second example describes the initiatives of French astronomers from the mid-1990s to construct a national programme for the protection of astronomy heritage. Lastly, we recount the case of universities, with the example of the Université de Strasbourg.     

On the viability of the No Alternatives Argument

If we cannot directly empirically test the claims of a particular scientific theory directly, then it would be nice to have some other criteria with which to assess its viability. In his 2013 book, String Theory and the Scientific Method, Richard Dawid aims to develop such criteria, with an eye to vindicating research programmess in disciplines where direct empirical data is scant or non-existent. In an accompanying paper, Dawid, Hartmann and Sprenger formalise Dawid's so-called ‘No Alternatives Argument’ (NAA) using a generalised Bayesian framework, as a first step towards formalising Dawid's entire research programme (which itself relies on two further arguments). In this paper, I argue that the formalisation of the NAA cannot play the central role in Dawid's programme as intended. This is based on the observation that not all confirmation is non-negligible confirmation. For Dawid's programme to be useful, it must demonstrate the viability not just of non-empirical theory confirmation, but of non-negligible non-empirical theory confirmation. I argue that Dawid et al.‘s appeal to Bayesian confirmation theory to formalise his NAA cannot guarantee non-negligible confirmation. As a result, I conclude that if Dawid's overall project is to succeed, it must do so without the NAA formalised in this way.     

Laboratory and field studies of the female sex pheromone of the olive moth,Prays oleae

Summary Analysis by GC-EAG indicates that abdominal tip extracts of femalePrays oleae contain a tetradecenal. Synthetic (Z)-7-tetradecenal elicits a strong EAG respones from maleP. oleae and field tests it to be comparable in attractancy with the virgin female moth. (Z)-9-Tetradecenal also produces a strong EAG response but it is not an attractant and, when added to (Z)-7-tetradecenal, markedly reduces trap catches.Acknowledgments. The authors are indebted to Mr N. Psylakis, Agricultural Research Centre, Chania, Crete, and to Dr D. Vassilopoulos, Benaki Phytopathological Institute, for providing facilities for this work. They thank the Commonwealth Institute of Entomology, London, for moth species confirmation.     

Scientific realism and empirical confirmation: A puzzle

Scientific realism driven by inference to the best explanation (IBE) takes empirically confirmed objects to exist, independent, pace empiricism, of whether those objects are observable or not. This kind of realism, it has been claimed, does not need probabilistic reasoning to justify the claim that these objects exist. But I show that there are scientific contexts in which a non-probabilistic IBE-driven realism leads to a puzzle. Since IBE can be applied in scientific contexts in which empirical confirmation has not yet been reached, realists will in these contexts be committed to the existence of empirically unconfirmed objects. As a consequence of such commitments, because they lack probabilistic features, the possible empirical confirmation of those objects is epistemically redundant with respect to realism.     

Mechanisms,the interventionist theory,and the ability to use causal relationships

In the area of social science, in particular, although we have developed methods for reliably discovering the existence of causal relationships, we are not very good at using these to design effective social policy. Cartwright argues that in order to improve our ability to use causal relationships, it is essential to develop a theory of causation that makes explicit the connections between the nature of causation, our best methods for discovering causal relationships, and the uses to which these are put. I argue that Woodward's interventionist theory of causation is uniquely suited to meet Cartwright's challenge. More specifically, interventionist mechanisms can provide the bridge from ‘hunting causes’ to ‘using them’, if interventionists (i) tell us more about the nature of these mechanisms, and (ii) endorse the claim that it is these mechanisms—or whatever constitutes them—that make causal claims true. I illustrate how having an understanding of interventionist mechanisms can allow us to put causal knowledge to use via a detailed example from organic chemistry.     

Interweaving categories: Styles,paradigms, and models

Analytical categories of scientific cultures have typically been used both exclusively and universally. For instance, when styles of scientific research are employed in attempts to understand and narrate science, styles alone are usually employed. This article is a thought experiment in interweaving categories. What would happen if rather than employ a single category, we instead investigated several categories simultaneously? What would we learn about the practices and theories, the agents and materials, and the political-technological impact of science if we analyzed and applied styles (à la Hacking and Crombie), paradigms (à la Kuhn), and models (à la van Fraassen and Cartwright) simultaneously? I address these questions in general and for a specific case study: a brief history of systematics.     

Acceptance,values, and probability

This essay makes a case for regarding personal probabilities used in Bayesian analyses of confirmation as objects of acceptance and rejection. That in turn entails that personal probabilities are subject to the argument from inductive risk, which aims to show non-epistemic values can legitimately influence scientific decisions about which hypotheses to accept. In a Bayesian context, the argument from inductive risk suggests that value judgments can influence decisions about which probability models to accept for likelihoods and priors. As a consequence, if the argument from inductive risk is sound, then non-epistemic values can affect not only the level of evidence deemed necessary to accept a hypothesis but also degrees of confirmation themselves.     

The morals of model-making

I address questions about values in model-making in engineering, specifically: Might the role of values be attributable solely to interests involved in specifying and using the model? Selected examples illustrate the surprisingly wide variety of things one must take into account in the model-making itself. The notions of system (as used in engineering thermodynamics), and physically similar systems (as used in the physical sciences) are important and powerful in determining what is relevant to an engineering model. Another example (windfarms) illustrates how an idea to completely re-characterize, or reframe, an engineering problem arose during model-making.I employ a qualitative analogue of the notion of physically similar systems. Historical cases can thus be drawn upon; I illustrate with a comparison between a geoengineering proposal to inject, or spray, sulfate aerosols, and two different historical cases involving the spraying of DDT (fire ant eradication; malaria eradication). The current geoengineering proposal is seen to be like the disastrous and counterproductive case, and unlike the successful case, of the spraying of DDT. I conclude by explaining my view that model-making in science is analogous to moral perception in action, drawing on a view in moral theory that has come to be called moral particularism.     

Hilbert's axiomatic method and Carnap's general axiomatics

This paper compares the axiomatic method of David Hilbert and his school with Rudolf Carnap's general axiomatics that was developed in the late 1920s, and that influenced his understanding of logic of science throughout the 1930s, when his logical pluralism developed. The distinct perspectives become visible most clearly in how Richard Baldus, along the lines of Hilbert, and Carnap and Friedrich Bachmann analyzed the axiom system of Hilbert's Foundations of Geometry—the paradigmatic example for the axiomatization of science. Whereas Hilbert's axiomatic method started from a local analysis of individual axiom systems in which the foundations of mathematics as a whole entered only when establishing the system's consistency, Carnap and his Vienna Circle colleague Hans Hahn instead advocated a global analysis of axiom systems in general. A primary goal was to evade, or formalize ex post, mathematicians' ‘material’ talk about axiom systems for such talk was held to be error-prone and susceptible to metaphysics.     

Feyerabend on politics,education, and scientific culture

The purpose of this paper is to offer a sympathetic reconstruction of the political thought of Paul Feyerabend. Using a critical discussion of the idea of the ‘free society’ it is suggested that his political thought is best understood in terms of three thematic concerns—liberation, hegemony, and the authority of science—and that the political significance of those claims become clear when they are considered in the context of his educational views. It emerges that Feyerabend is best understood as calling for the grounding of cognitive and cultural authorities—like the sciences—in informed deliberation, rather than the uncritical embrace of prevailing convictions. It therefore emerges that a free society is best understood as one of epistemically responsible citizenship rather than epistemically anarchistic relativism of the ‘anything goes’ sort—a striking anticipation of current debates about philosophy of science in society.     

Some surprising facts about (the problem of) surprising facts: (from the Dusseldorf Conference,February 2011)

A common intuition about evidence is that if data x have been used to construct a hypothesis H, then x should not be used again in support of H. It is no surprise that x fits H, if H was deliberately constructed to accord with x. The question of when and why we should avoid such “double-counting” continues to be debated in philosophy and statistics. It arises as a prohibition against data mining, hunting for significance, tuning on the signal, and ad hoc hypotheses, and as a preference for predesignated hypotheses and “surprising” predictions. I have argued that it is the severity or probativeness of the test—or lack of it—that should determine whether a double-use of data is admissible. I examine a number of surprising ambiguities and unexpected facts that continue to bedevil this debate.     

(Mis)Understanding scientific disagreement: Success versus pursuit-worthiness in theory choice

Scientists often diverge widely when choosing between research programs. This can seem to be rooted in disagreements about which of several theories, competing to address shared questions or phenomena, is currently the most epistemically or explanatorily valuable—i.e. most successful. But many such cases are actually more directly rooted in differing judgments of pursuit-worthiness, concerning which theory will be best down the line, or which addresses the most significant data or questions. Using case studies from 16^th-century astronomy and 20^th-century geology and biology, I argue that divergent theory choice is thus often driven by considerations of scientific process, even where direct epistemic or explanatory evaluation of its final products appears more relevant. Broadly following Kuhn's analysis of theoretical virtues, I suggest that widely shared criteria for pursuit-worthiness function as imprecise, mutually-conflicting values. However, even Kuhn and others sensitive to pragmatic dimensions of theory ‘acceptance’, including the virtue of fruitfulness, still commonly understate the role of pursuit-worthiness—especially by exaggerating the impact of more present-oriented virtues, or failing to stress how ‘competing’ theories excel at addressing different questions or data. This framework clarifies the nature of the choice and competition involved in theory choice, and the role of alternative theoretical virtues.     

Inter-theory relations in quantum gravity: Correspondence,reduction, and emergence

Relationships between current theories, and relationships between current theories and the sought theory of quantum gravity (QG), play an essential role in motivating the need for QG, aiding the search for QG, and defining what would count as QG. Correspondence is the broad class of inter-theory relationships intended to demonstrate the necessary compatibility of two theories whose domains of validity overlap, in the overlap regions. The variety of roles that correspondence plays in the search for QG are illustrated, using examples from specific QG approaches. Reduction is argued to be a special case of correspondence, and to form part of the definition of QG. Finally, the appropriate account of emergence in the context of QG is presented, and compared to conceptions of emergence in the broader philosophy literature. It is argued that, while emergence is likely to hold between QG and general relativity, emergence is not part of the definition of QG, and nor can it serve usefully in the development and justification of the new theory.     

Is there just one possible world? Contingency vs the bootstrap

As an example of what might be considered a candidate for an interesting and significant development in the methodology of recent science, I examine some of the epistemological and ontological commitments of the bootstrap conjecture of high energy theoretical physics. This conjecture holds that a well defined but infinite set of self-consistency conditions determines uniquely the entities or paticles which can exist. That is, once we are given any partial information about the actually existing world, nothing else about that world is contingent or arbitrarily adjustable. This almost Leibnizian idea is implemented in S-matrix theory through a unitarity equation, which is a statement of conservation of probability. The S-matrix program is contrasted with quantum field theory which does have arbitrarily assignable quantities. In spite of the highly constrained structure of S-matrix theory, that theory makes far fewer ontological and epistemological assumptions than does quantum field theory.     

<Emphasis Type="Italic">O</Emphasis>-GlcNAc transferase associates with the MCM2–7 complex and its silencing destabilizes MCM–MCM interactions

O-GlcNAcylation of proteins is governed by O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA). The homeostasis of O-GlcNAc cycling is regulated during cell cycle progression and is essential for proper cellular division. We previously reported the O-GlcNAcylation of the minichromosome maintenance proteins MCM2, MCM3, MCM6 and MCM7. These proteins belong to the MCM2–7 complex which is crucial for the initiation of DNA replication through its DNA helicase activity. Here we show that the six subunits of MCM2–7 are O-GlcNAcylated and that O-GlcNAcylation of MCM proteins mainly occurs in the chromatin-bound fraction of synchronized human cells. Moreover, we identify stable interaction between OGT and several MCM subunits. We also show that down-regulation of OGT decreases the chromatin binding of MCM2, MCM6 and MCM7 without affecting their steady-state level. Finally, OGT silencing or OGA inhibition destabilizes MCM2/6 and MCM4/7 interactions in the chromatin-enriched fraction. In conclusion, OGT is a new partner of the MCM2–7 complex and O-GlcNAcylation homeostasis might regulate MCM2–7 complex by regulating the chromatin loading of MCM6 and MCM7 and stabilizing MCM/MCM interactions.     

Interaction of volkensin with HeLa cells: binding,uptake, intracellular localization,degradation and exocytosis

Among two-chain ribosome-inactivating proteins (RIPs), volkensin is the most toxic to cells and animals, and is retrogradely axonally transported in the rat central nervous system, being an effective suicide transport agent. Here we studied the binding, endocytosis, intracellular routeing, degradation and exocytosis of this RIP. The interaction of volkensin with HeLa cells was compared to that of nigrin b, as an example of a type 2 RIP with low toxicity, and of ricin, as a reference toxin. Nigrin b and volkensin bound to cells with comparable affinity (approx. 10^-10 M) and had a similar number of binding sites (2 × 105/cell), two-log lower than that reported for ricin. The cellular uptake of volkensin was lower than that reported for nigrin b and ricin. Confocal microscopy showed the rapid localization of volkensin in the Golgi stacks with a perinuclear localization similar to that of ricin, while nigrin b was distributed between cytoplasmic dots and the Golgi compartment. Consistently, brefeldin A, which disrupts the Golgi apparatus, protected cells from the inhibition of protein synthesis by volkensin or ricin, whereas it was ineffective in the case of nigrin b. Of the cell-released RIPs, 57% of volkensin and only 5% of ricin were active, whilst exocytosed nigrin b was totally inactive. Despite the low binding to, and uptake by, cells, the high cytotoxicity of volkensin may depend on (i) routeing to the Golgi apparatus, (ii) the low level of degradation, (iii) rapid recycling and (iv) the high percentage of active toxin remaining after exocytosis.Received 21 April 2004; received after revision 26 May 2004; accepted 9 June 2004     

An anthropic myth: Fred Hoyle’s carbon-12 resonance level

The case of Fred Hoyle’s prediction of a resonance state in carbon-12, unknown in 1953 when it was predicted, is often mentioned as an example of anthropic prediction. However, an investigation of the historical circumstances of the prediction and its subsequent experimental confirmation shows that Hoyle and his contemporaries did not associate the level in the carbon nucleus with life. Only in the 1980s, after the emergence of the anthropic principle, did it become common to see Hoyle’s prediction as anthropically significant. At about the same time mythical accounts of the prediction and its history began to abound. Not only has the anthropic myth no basis in historical fact, it is also doubtful if the excited levels in carbon-12 and other atomic nuclei can be used as an argument for the predictive power of the anthropic principle.