The evolution of BioBike: Community adaptation of a biocomputing platform

Programming languages are, at the same time, instruments and communicative artifacts that evolve rapidly through use. In this paper I describe an online computing platform called BioBike. BioBike is a trading zone where biologists and programmers collaborate in the development of an extended vocabulary and functionality for computational genomics. In the course of this work they develop interactional expertise with one another’s domains. The extended BioBike vocabulary operates on two planes: as a working programming language, and as a pidgin in the conversation between the biologists and engineers. The flexibility that permits this community to dynamically extend BioBike’s working vocabulary—to form new pidgins—makes BioBike unique among computational tools, which usually are not themselves adapted through the collaborations that they facilitate. Thus BioBike is itself a crucial feature—which it is tempting to refer to as a participant—in the developing interaction.     

‘Physics and fashion’: John Tyndall and his audiences in mid-Victorian Britain

This paper explores how the physicist John Tyndall transformed himself from humble surveyor and schoolmaster into an internationally applauded icon of science. Beginning with his appointment as Professor of Natural Philosophy at the Royal Institution in 1853, I show how Tyndall’s worries about his social class and Irish origins, his painstaking attention to his lecturing performance and skilled use of the material and architectural resources of the Royal Institution were vital to his eventual success as a popular expositor and ambassador for science. Secondly I explore the implications of Tyndall’s ‘popularity’ with respect to debates over the meaning and value of scientific ‘popularisation’. In support of recent work challenging diffusionist models of science communication, I show how Tyndall’s interactions with his audiences illustrate the symbiotic relationship between producer and consumer of ‘popular’ science. By examining the views of Tyndall’s critics—notably the ‘North British’ group of physicists—and his defenders and rivals in the domain of popular scientific lecturing, I show that disputes over Tyndall’s authority reflected anxieties about what constituted popular science and the transient boundaries between instruction and entertainment. The term ‘popularisation’ enjoyed many different uses in these debates, not least of all as a rheorical device with which to either exalt or destroy a scientist’s credibility.     

Interactional expertise and embodiment

In this four part exchange, Evan Selinger starts by stating that Collins’s empirical evidence in respect of linguistic socialization and its bearing on artificial intelligence and expertise is valuable; it advances philosophical and sociological understanding of the relationship between knowledge and language. Nevertheless, he argues that Collins mischaracterizes the data under review and thereby misrepresents how knowledge is acquired and understates the extent to which expert knowers are embodied. Selinger reconstructs the case for the importance of the body in the initial acquisition of language and challenges Collins to show how a disembodied entity could become fluent in any language at all.Collins responds by accepting that his approach does not demonstrate quite as much about the irrelevance of the body as he thought it did but that even though he accepts all of Selinger’s claims, ‘the body’ as needed by the philosophical approach set out by Selinger is still a vestigial thing. Collins’s main point, however, is that the philosophical view of the body—the world is divided into embodied agents and unembodied entities—distracts attention from the more interesting empirically researchable question of how the ability to become socialized diminishes, if it does, as the body become more and more minimal. The right research question is not about whether a person can extrapolate from minimal sensory input but how much extrapolation is possible under different circumstances and how it is done.Dreyfus, having seen the whole of the exchange so far, agrees that both have a point but argues that Collins’s approach still misses the well established importance of bodily engagement for full understanding.Collins responds to this by trying to set out more clearly the position associated with the idea of interactional expertise.     

The literature and the science of ‘two cultures’ historiography

This paper discusses the historiography of the ‘two cultures’ controversy. C. P. Snow’s lament about the ‘two cultures’, literary and scientific, has inspired a wide range of comment—much of which begins by citing Snow and his thesis, before going on to discuss very different things. This paper focuses upon one strand of this commentary, the historical analysis of the controversy itself. A ‘historical’ analysis is defined here as one that resists the impulse to enter the argument on behalf of Snow or Leavis, to conceive of their argument in the terms that Snow defined, or to invoke their argument as a precursor to some contemporary issue. Instead, a historical interpretation registers distance between that day and this, takes the controversy itself as its object of study, and explores the tensions and associations that came to be packed into those now familiar terms. As the fiftieth anniversary of Snow’s Rede Lecture nears, this approach—rather than the repetition of clichés about the bridging of cultures—offers both analytical perspective on the controversy and interpretive possibilities for its examination.     

From Cutting Nature at Its Joints to Measuring It: New Kinds and New Kinds of People in Biology

In the received version of the development of science, natural kinds are established in the preliminary stages (natural history) and made more precise by measurement (exact science). By examining the move from nineteenth- to twentieth-century biology, this paper unpacks the notion of species as ‘natural kinds’ and grounds for discourse, questioning received notions about both kinds and species. Life sciences in the nineteenth century established several ‘monster-barring’ techniques to block disputes about the precise definition of species. Counterintuitively, precision and definition brought dispute and disrupted exchange. Thus, any attempt to add precision was doomed to failure. By intervening and measuring, the new experimental biology dislocated the established links between natural kinds and kinds of people and institutions. New kinds were built in new places. They were made to measure from the very start. This paper ends by claiming that there was no long-standing ‘species problem’ in the history of biology. That problem is a later construction of the ‘modern synthesis’, well after the disruption of ‘kinds’ and kinds of people. Only then would definitions and precision matter. A new, non-linguistic, take on the incommensurability thesis is hinted at.     

Revisiting Galison’s ‘Aufbau/Bauhaus’ in light of Neurath’s philosophical projects

In his article entitled ‘Aufbau/Bauhaus’ and related work, Peter Galison explores the connections between the Vienna Circle and the Dessau Bauhaus. Historically, these groups were related, with members of each group familiar with the ideas of the other. Galison argues that their projects are related as well, through shared political views and methodological approach. The two main figures that connect the Vienna Circle to the Bauhaus—and the figures upon which Galison focuses—are Rudolf Carnap and Otto Neurath. Yet, in our view, the connections that Galison develops do not properly capture the common themes between the Bauhaus and Neurath’s philosophical projects. In this paper, we will examine a few of the historical connections between the Dessau Bauhaus and the Vienna Circle, as well as the philosophical connections that Galison draws between these two groups. By examining in greater depth Neurath’s philosophical commitments, we aim to demonstrate that some of these philosophical connections fail to resonate with Neurath’s projects. And, finally, we develop different connections between Neurath’s projects and the Bauhaus. In our view, these new connections between Neurath and the Dessau Bauhaus are both substantive and philosophically interesting.     

Looking for structure in all the wrong places: Ramsey sentences, multiple realisability, and structure

‘Epistemic structural realism’ (ESR) insists that all that we know of the world is its structure, and that the ‘nature’ of the underlying elements remains hidden. With structure represented via Ramsey sentences, the question arises as to how ‘hidden natures’ might also be represented. If the Ramsey sentence describes a class of realisers for the relevant theory, one way of answering this question is through the notion of multiple realisability. We explore this answer in the context of the work of Carnap, Hintikka and Lewis. Both Carnap and Hintikka offer clear structuralist perspectives which, crucially, accommodate the openness inherent in theory change. Unfortunately there is little purchase for a viable form of realism in either case. Lewis’s approach, on the other hand, offers more scope for realism but, as we shall see, concerns arise as to whether a relevant form of structuralism can be maintained. In particular his thesis of Ramseyan humility undermines certain conceptions of scientific laws that the structural realist might naturally cleave to. Our overall conclusion is that the representational device of Ramsey sentence plus multiple realisability can accommodate either the structuralist or realist aspects of ESR but has difficulties capturing both.     

Scientific realism bit by bit: part I. Kitcher on reference

In this paper, I consider Kitcher’s (1993) account of reference for the expressions of past science. Kitcher’s case study is of Joseph Priestley and his expression ‘dephlogisticated air’. There is a strong intuitive case that ‘dephlogisticated air’ referred to oxygen, but it was underpinned by very mistaken phlogiston theory, so concluding either that dephlogisticated air referred straightforwardly or that it failed to refer both have unpalatable consequences. Kitcher argues that the reference of such terms is best considered relative to each token—some tokens refer, and others do not. His account thus relies crucially on how this distinction between tokens can be made good—a puzzle I call the discrimination problem. I argue that the discrimination problem cannot be solved. On any reading of Kitcher’s defence of the distinction, the grounds provided are either insufficient or illegitimate. On the first reading, Kitcher violates the principle of humanity by making Priestley’s referential success a matter of the mental contents of modern speakers. The second reading sidesteps the problem of beliefs by appealing to mind-independent facts, but I argue that these are insufficient to achieve reference because of the indeterminacy introduced by the qua problem. On the third and final reading, Priestley’s success is given by what he would say in counterfactual circumstances. I argue that even if there are facts about what Priestley would say, and there is reason for doubt, there is no motivation to think that such facts determine how Priestley referred in the actual world.     

Atomism, Poincaré and Planck

Planck's change in attitude to the question of whether atomic hypotheses were scientifically accessible, is discussed. It is argued contra Holton, that Planck's change in attitude to this question did not signal a methodological shift towards realism. The point of doing this is not just to investigate a significant episode in the history of quantum theory, but also to use the episode as a case study in support of a broader historical thesis. This thesis is that there was a widespread late-nineteenth century methodological tradition which motivated the change in status of certain ontological claims — e.g., that atoms exist — from ‘inaccessible to science’ to ‘scientifically acceptable’ even though those claims were not strictly ‘observable’. This methodological tradition is a hybrid of positivist and realist views. Thus, contrary to one popular view, the fin de siécle triumph of atomism is not to be seen as a triumph for a realist view of science Poincare's views are also used as an illustration.     

Thomas Reid and the problem of induction: from common experience to common sense

By the middle of the eighteenth century the new science had challenged the intellectual primacy of common experience in favor of recondite, expert and even counter-intuitive knowledge increasingly mediated by specialized instruments. Meanwhile modern philosophy had also problematized the perceptions of common experience — in the case of David Hume this included our perception of causal relations in nature, a fundamental precondition of scientific endeavor.In this article I argue that, in responding to the ‘problem of induction’ as advanced by Hume, Reid reformulated Aristotelian foundationalism in distinctly modern terms. An educator and mathematician self-consciously working within the framework of the new science, Reid articulated a philosophical foundation for natural knowledge anchored in the human constitution and in processes of adjudication in an emerging modern public sphere of enlightened discourse. Reid thereby transformed one of the bases of Aristotelian science — common experience — into a philosophically and socially justified notion of ‘common sense’. Reid's intellectual concerns had as much to do with the philosophy of science as they did with moral philosophy or epistemology proper, and were bound up with wider social and scientific changes taking place in the early modern period.     

Can the constructive empiricist be a nominalist? Quasi-truth, commitment and consistency

In this paper, I explore Rosen’s (1994) ‘transcendental’ objection to constructive empiricism—the argument that in order to be a constructive empiricist, one must be ontologically committed to just the sort of abstract, mathematical objects constructive empiricism seems committed to denying. In particular, I assess Bueno’s (1999) ‘partial structures’ response to Rosen, and argue that such a strategy cannot succeed, on the grounds that it cannot provide an adequate metalogic for our scientific discourse. I conclude by arguing that this result provides some interesting consequences in general for anti-realist programmes in the philosophy of science.     

Predictivism and the periodic table

This is a comment on the paper by Barnes (2005) and the responses from Scerri (2005) and Worrall (2005), debating the thesis (‘predictivism’) that a fact successfully predicted by a theory is stronger evidence than a similar fact known before the prediction was made. Since Barnes and Scerri both use evidence presented in my paper on Mendeleev’s periodic law (Brush, 1996) to support their views, I reiterate my own position on predictivism. I do not argue for or against predictivism in the normative sense that philosophers of science employ, rather I describe how scientists themselves use facts and predictions to support their theories. I find wide variations, and no support for the assumption that scientists use a single ‘Scientific Method’ in deciding whether to accept a proposed new theory.     

Collecting airs and ideas: Priestley’s style of experimental reasoning

It has often been claimed that Priestley was a skilful experimenter who lacked the capacities to analyze his own experiments and bring them to a theoretical closure. In attempts to revise this view some scholars have alluded to Priestley’s ‘synoptic’ powers while others stressed the contextual role of British Enlightenment in understanding his chemical research. A careful analysis of his pneumatic reports, privileging the dynamics of his experimental practice, uncovers significant yet neglected aspects of Priestley’s science. By focusing on his early experimental conduct and writing on nitrous air, I demonstrate how his methodological and rhetorical devices, far from being consequences of compulsive writing or theoretical naïveté, were deeply entwined with his chemical research. I employ the notion of ‘style of experimental reasoning’ (SER)—derived from A. C. Crombie and I. Hacking—to shed light on the intersection at which Priestley’s unique method, literary style, and epistemology converged to generate scientific knowledge. Establishing Priestley’s SER advances a finer understanding of the interactive character of his pneumatic experimentalism, peculiar dimensions of which have evaded both traditional as well as revisionist scholarship, thus infusing the longstanding historiographic debate over his scientific merits.     

On Minkowskian branching structures

In Belnap's [Branching space-time. Synthese, 92, 385–434. ‘Postprint’ archived at http://philsci-archive.pitt.edu/archive/00001003] theory of branching space-times (BST) Our World's possible histories are thought of as space-times, yet the theory has models in which histories do not resemble relativistic space-times or any other physical space-times. The aim of this paper is to define a certain class of BST models, called ‘Minkowskian Branching Structures’ (MBSs), in which histories are isomorphic to Minkowski space-time. By focusing on these models rather than on general BST models, we hope that one may be able to improve on earlier BST analyses of physical phenomena. Also, introducing MBSs sets the stage for recent discussions about whether or not branching is physically feasible.     

Instruments and rules: R. B. Woodward and the tools of twentieth-century organic chemistry

The paper illustrates how organic chemists dramatically altered their practices in the middle part of the twentieth century through the adoption of analytical instrumentation — such as ultraviolet and infrared absorption spectroscopy and nuclear magnetic resonance spectroscopy — through which the difficult process of structure determination for small molecules became routine. Changes in practice were manifested in two ways: in the use of these instruments in the development of ‘rule-based’ theories; and in an increased focus on synthesis, at the expense of chemical analysis. These rule-based theories took the form of generalizations relating structure to chemical and physical properties, as measured by instrumentation. This ‘Instrumental Revolution’ in organic chemistry was two-fold: encompassing an embrace of new tools that provided unprecedented access to structures, and a new way of thinking about molecules and their reactivity in terms of shape and structure. These practices suggest the possibility of a change in the ontological status of chemical structures, brought about by the regular use of instruments. The career of Robert Burns Woodward (1917–1979) provides the central historical examples for the paper. Woodward was an organic chemist at Harvard from 1937 until the time of his death. In 1965, he won the Nobel Prize in Chemistry.     

Worlds in the Everett interpretation

This is a discussion of how we can understand the world-view given to us by the Everett interpretation of quantum mechanics, and in particular the rôle played by the concept of ‘world’. The view presented is that we are entitled to use ‘many-worlds’ terminology even if the theory does not specify the worlds in the formalism; this is defended by means of an extensive analogy with the concept of an ‘instant’ or moment of time in relativity, with the lack of a preferred foliation of spacetime being compared with the lack of a preferred basis in quantum theory. Implications for identity of worlds over time, and for relativistic quantum mechanics, are discussed.     

Rehabilitating theory: refusal of the ‘bottom-up’ construction of scientific phenomena

In this paper I inquire into Bogen and Woodward’s (1988) data/phenomena distinction, which in a similar way to Cartwright’s construal of the model of superconductivity (1995)—although in a different domain—argues for a ‘bottom-up’ construction of phenomena from data without the involvement of theory. I criticise Bogen and Woodward’s account by analysing their melting point of lead example in depth, which is usually cited in the literature to illustrate the data/phenomenon distinction. Yet, the main focus of this paper lies on Matthias Kaiser’s (1995) case study of the plate tectonic revolution, the most extensive case study that has been put forth to support the bottom-up construction of phenomena. On the basis of new historical evidence, which has been overlooked not only by Kaiser but also by the entire historical literature on the plate tectonic revolution, I demonstrate that phenomena are not constructed from the bottom-up but rather, admittedly counter-intuitively, from the top-down.     

Dogma and dreams: experimental lessons for epilepsy mechanism chasers

Epilepsy mechanism chasers face one major difficulty. Since we don’t know how the normal brain works, we can’t start to understand how the diseased brain fails. Most of today’s hypotheses are based on what we think about ‘normal’ brain function, which may lead to misconceptions, as will be developed here. Furthermore, since there are many different types of epilepsies, some mechanisms may only be relevant to some epilepsies. Here, I shall focus on temporal lobe epilepsy (TLE) the most common form of partial epilepsy in adults. TLE is often drug resistant, as are 30–40% of all forms of epilepsies. The failure of drug-treatments most likely reflects our lack of knowledge of the underlying mechanisms.Received 10 January 2005; received after revision 3 March 2005; accepted 23 March 2005     

History of Science through Koyré's Lenses

Alexandre Koyré was one of the most prominent historians of science of the twentieth century. The standard interpretation of Koyré is that he falls squarely within the internalist camp of historians of science—that he focuses on the history of the ideas themselves, eschewing cultural and sociological interpretations regarding the influence of ideologies and institutions on the development of science. When we read what Koyré has to say about his historical studies (and most of what others have said about them), we find him embracing and championing this Platonic view of his work. Ultimately I think this interpretation of Koyré's history of science is lopsided and in need of correction. I claim, rather, that a careful reading of Koyré's work suggests that a tension exists between internal and external methodological considerations. The external considerations stem from Koyré's commitment to the unity of human thought and the influence he admits that the ‘transscientifiques’ (philosophy, metaphysics, religion) have on the development of science. I suggest in conclusion then, that if we are to put a philosophical label on his work, rather than ‘Platonist’, as has been the custom, ‘Hegelian’ makes a better fit.     

Local Fluctuations and Local Observers in Equilibrium Statistical Mechanics

The distribution function associated with a classical gas at equilibrium is considered. We prove that apart from a factorisable multiplier, the distribution function is fully determined by the correlations among local momenta fluctuations. Using this result we discuss the conditions which enable idealised local observers, who are immersed in the gas and form a part of it, to determine the distribution ‘from within’. This analysis sheds light on two views on thermodynamic equilibrium, the ‘ergodic’ and the ‘thermodynamic limit’ schools, and the relations between them. It also provides an outline for a new definition of equilibrium that is weaker than full ergodicity. Finally, we briefly discuss the possibility that the distribution can be determined by external observers.