An analysis is presented of published methods that have been used by experimenters to justify the reliability of the theory of invasion of microorganisms into cultured cells. The results show that, to demonstrate this invasion, many experimenters used two or more methods that were based on independent technical and theoretical principles, and by doing so improved the reliability of the theory. Subsequently I compare this strategy of 'multiple derivability' with other strategies, discussed in the literature in relation to the mesosome, (...) a bacterial organelle that had been detected with the electron microsope, but which appeared later to be an artifact. I propose that different strategies have been applied in this problem, and multiple derivability may have been the decisive one. Finally I discuss the idea that multiple derivability may help to anchor theories in a larger network of theories. (shrink)

The thesis of theory-ladenness of observations, in its various guises, is widely considered as either ill-conceived or harmless to the rationality of science. The latter view rests partly on the work of the proponents of New Experimentalism who have argued, among other things, that experimental practices are efficient in guarding against any epistemological threat posed by theory-ladenness. In this paper I show that one can generate a thesis of theory-ladenness for experimental practices from an influential New Experimentalist account. The notion (...) I introduce for this purpose is the concept of ‘theory-driven data reliability judgments’, according to which theories which are sought to be tested with a particular set of data guide reliability judgments about those very same data. I provide various prominent historical examples to show that TDRs are used by scientists to resolve data conflicts. I argue that the rationality of the practices which employ TDRs can be saved if the independent support of the theories driving TDRs is construed in a particular way. (shrink)

In 1905 two different microbes were proposed to fill the vacant role of etiologic agent for syphilis, one, the Cytorrhyctes luis, by John Siegel, the other, Spirochaeta pallida, by Fritz Schaudinn. After gathering and reviewing the evidence the majority of medical scientists decided in favor of Schaudinn’s candidate. In a previous issue Jean Lindenmann challenged Ludwik Fleck’s suggestion that under suitable social conditions Siegel’s candidate could just as well have won acceptance by the scientific community . To refute this counterfactual (...) thesis, Lindenmann presented an asymmetric account of the dispute over the etiology of syphilis. He adopted the view of the proponents that Schaudinn’s spirochete had already been there in syphilitic lesions for centuries, only awaiting the discovery of an appropriate staining technique to be revealed. Here a more symmetric analysis of the episode will be attempted, paying serious attention to the arguments put forward by the spirochete’s opponents, who expatiated on the many possibilities of inadvertently creating artifacts through microscopic preparation and staining. The symmetric account that is presented in this rejoinder thus aims to trace the simultaneous construction of facts and artifacts. It will not, however, resurrect Fleck’s counterfactual thesis. (shrink)

In recent years there has been a revival of the debate about the relation between history and philosophy of science. This article seeks to contribute to the discussion by approaching the issue from a new angle. To rethink the relation between the two domains of study, I apply an important insight about scientific practice to the practice of integrating the history and philosophy of science: the insight that the scientific paper does not give a faithful account of the actual research (...) pursued in the laboratory or in the field. Arguably, the scholarly article about science is also not a transparent window to the activity of producing such an article. But if it is not, we need to redirect our attention. If we want to understand the nature and merits of integrating the history and philosophy of science, we need to examine both the actual activity of integrating and the scholarly paper produced by it. To consider what one can learn from such an inquiry, I reflect on my own activity of studying scientific justification through the combination of historical and philosophical analysis. Probing a concrete historical episode, micro-anatomical research on the retina in the 19th century, I pursue two related questions, the first-order question, 'What exactly is scientific justification in the given case?' and the meta-question, 'How do I go about analysing justificatory practices?' I then characterise the nature of my analysis and consider what can be learned from the study of the practice of integrating the history and philosophy of science. (shrink)

Robustness is a common platitude: hypotheses are better supported with evidence generated by multiple techniques that rely on different background assumptions. Robustness has been put to numerous epistemic tasks, including the demarcation of artifacts from real entities, countering the “experimenter’s regress,” and resolving evidential discordance. Despite the frequency of appeals to robustness, the notion itself has received scant critique. Arguments based on robustness can give incorrect conclusions. More worrying is that although robustness may be valuable in ideal evidential circumstances (i.e., (...) when evidence is concordant), often when a variety of evidence is available from multiple techniques, the evidence is discordant. †To contact the author, please write to: Jacob Stegenga, Department of Philosophy, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093; e‐mail: [email protected]. (shrink)

For the last ten years, within molecular life sciences, the reproducibility crisis discourse has been embodied as a crisis of trust in scientific images. Beyond the contentious perception of “questionable research practices” associated with a digital turn in the production of images, this paper highlights the transformations of gel electrophoresis as a family of experimental techniques. Our aim is to analyze the evolving epistemic status of generated images and its connection with a crisis of trust in images within that field.From (...) the 1980s to the 2000s, we identify two key innovations (precast gels and gel docs) leading to a “two‐tiered” gel electrophoresis with different standardization procedures, different epistemic statuses of the produced images and different ways of generating (dis)trust in images. The first tier, exemplified by differential gel electrophoresis (DIGE), is characterized by specialized devices processing images as quantitative data. The second tier, exemplified by polyacrylamide gel electrophoresis (PAGE), is described as a routine technique making use of image as qualitative “virtual witnessing.” The difference between these two tiers is particularly apparent in the ways images are processed, even though both tiers involve image digitization. Our account thus highlights different views on reproducibility within the two tiers. Comparability of images is insisted upon in the first tier while traceability is expected in the second tier. It is striking that these differences occur not only within the same scientific field, but even within the same family of experimental techniques. In the second tier, digitization entails distrust, whereas it implies a collective sentiment of trust in the first tier. (shrink)

In a 1993 paper, I argued that empirical treatments of the epistemologyused by scientists in experimental work are too abstract in practice tocounter relativist efforts to explain the outcome of scientificcontroversies by reference to sociological forces. This was because, atthe rarefied level at which the methodology of scientists is treated byphilosophers, multiple mutually inconsistent instantiations of theprinciples described by philosophers are employed by contestingscientists. These multiple construals change within a scientificcommunity over short time frames, and these different versions ofscientific methodology (...) can determine the outcome of a controversy. Iillustrated with a comparatively detailed analysis of the methodologyused by biologists debating the existence of an entity called thebacterial mesosome between the mid-1950s and the mid-1970s. This 1993piece has drawn several critiques in the philosophical literature. Inthis present piece I respond to these critiques and argue that they failto address the core argument of the original paper, and I reflectfurther on the methodologies of philosophers of science pursuingempirical or `naturalistic' epistemology. (shrink)

Throughout his career David Hull has sought to bring the philosophy of science into closer contact with science and especially with biological science (Hull 1969, 1997b). This effort has taken many forms. Sometimes it has meant ‘either explaining basic biology to philosophers or explaining basic philosophy to biologists’ (Hull 1996, p. 77). The first of these tasks, simple as it sounds, has been responsible for revolutionary changes. It is well known that traditional philosophy of science, modeled as it was on (...) theoretical physics, proved inadequate when philosophers turned their attention to biological science. Biological examples have driven major revisions of accounts of reduction (Hull 1974; Schaffner 1993, Ch. 9), laws of nature (Beatty et al. 1997), theories (Lloyd 1988) and natural kinds (Wilson 1999, Part III). Nor is explaining basic philosophy to biologists a task to be looked down upon. It is useful, not because philosophy has all the answers, but because scientists must think about how to do science, that is doing philosophy of science and scientists frequently reinvent philosophical views with known flaws. Early in his career Hull found biological systematists in the grip of a crude operationalism about scientific concepts and said so in the pages of Systematic Zoology (Hull 1968). For the next thirty years, as biologists debated the nature of species and the correct principles of classification, Hull added a philosophical note at the same congresses and in the same journals (Hull 1970, 1976, 1980, 1997a, 1999). (shrink)

While the term “reactivity” has come to be associated with specific phenomena in the social sciences, having to do with subjects’ awareness of being studied, this paper takes a broader stance on this concept. I argue that reactivity is a ubiquitous feature of the psychological subject matter and that this fact is a precondition of experimental research, while also posing potential problems for the experimenter. The latter are connected to the worry about distorted data and experimental artifacts. But what are (...) experimental artifacts and what is the most productive way of dealing with them? In this paper, I approach these questions by exploring the ways in which experimenters in psychology simultaneously exploit and suppress the reactivity of their subject matter in order to produce experimental data that speak to the question or subject matter at hand. Highlighting the artificiality of experimental data, I raise the question of what distinguishes a genuine experimental result from an experimental artifact. My analysis construes experimental results as the outcomes of inferences from the data that take material background assumptions as auxiliary premises. Artifacts occur when one or more of these background assumptions are false, such that the data do not reliably serve the purposes they were generated for. I conclude by laying out the ways in which my analysis of data quality is relevant to, and informed by, recent debates about the replicability of experimental results. (shrink)

A core, constitutive norm of science is to remove or remedy the artefacts in one’s data. Here, we consider examples of artefacts from many fields of science (for example, astronomy, economics, electrophysiology, psychology, and systems neuroscience) and discuss their contribution to a more general evidential selection problem at the heart of the epistemology of evidence. Synthesizing and building on previously disparate discussions in many areas of the philosophy of science, we provide a novel, causal–pragmatic account that fits the examples and (...) clarifies the practices by which artefacts are discovered and remedied. (shrink)

Multiple determination is the epistemic strategy of establishing the same result by means of multiple, independent procedures. It is an important strategy praised by both philosophers of science and practicing scientists. Despite the heavy appeal to multiple determination, little analysis has been provided regarding the specific grounds upon which its epistemic virtues rest. This article distinguishes between the various dimensions of multiple determination and shows how they can be used to evaluate the epistemic force of the strategy in particular cases. (...) Distinguishing between the various dimensions helps to resolve the disagreements regarding the relevance and epistemic import of multiple determination for scientific research. It also suggests a fruitful mode of interaction between the philosophy of science and (historical) accounts of scientific practice. (shrink)

Robustness arguments hold that hypotheses are more likely to be true when they are confirmed by diverse kinds of evidence. Robustness arguments require the confirming evidence to be independent. We identify two kinds of independence appealed to in robustness arguments: ontic independence —when the multiple lines of evidence depend on different materials, assumptions, or theories—and probabilistic independence. Many assume that OI is sufficient for a robustness argument to be warranted. However, we argue that, as typically construed, OI is not a (...) sufficient independence condition for warranting robustness arguments. We show that OI evidence can collectively confirm a hypothesis to a lower degree than individual lines of evidence, contrary to the standard assumption undergirding usual robustness arguments. We employ Bayesian networks to represent the ideal empirical scenario for a robustness argument and a variety of ways in which empirical scenarios can fall short of this ideal. (shrink)

This paper deals with calibration in scientific practices which investigate relatively well-understood natural phenomena by means of already standardized instrumental devices. Calibration is a crucial topic, since it conditions the reliability of instrumental procedures in science. Yet although important, calibration is a relatively neglected topic. We think more attention should be devoted to calibration. The paper attempts to take a step in this direction. The aims are two-fold: (1) to characterize calibration in a relatively simple kind of scientific practices; (2) (...) to provide conceptual and taxonomic tools of broader scope that help to get a better understanding of calibration in more complex cases and other kinds of scientific practices. For this purpose, we first provide indications for why a conceptual framework is needed. Second, a bibliographic survey of works dealing with calibration is attempted. Third, we introduce different tools to enable a better understanding of calibration. Fourth, we turn to the elaboration of what we call a “simple exemplar” of calibration, illustrated through the case of the calibration of an equal-arm balance. Fifth, the tools previously introduced, and the framework of the simple exemplar, are applied to a more complex case of calibration: calibration procedures in X-ray experiments. This serves to show the work accomplished by the simple exemplar and to emphasize features of more complex cases of calibration. Eventually, we revisit and specify the nature, status, scope and value of the proposed framework. (shrink)

In 1966 the population biologist Richard Levins gave a forceful and in?uential defence of a method called “robustness analysis” (RA). RA is a way of assessing the result of a model by showing that different but related models give the same result. As Levins put it, “our truth is the intersection of independent lies” (1966, 423). Steven Orzack and Elliott Sober (1993) responded with an equally forceful critique of this method, concluding that the idea of robustness “lacks proper de?nition and (...) that its bearing on the question of whether a proposition is true is highly problematic” (533). Replies to Orzack and Sober, from Levins (1993) and Weisberg (2006b), have rejected the idea that RA, on its own, can con?rm the results of models. I argue that these replies have not properly addressed Orzack and Sober’s real criticisms, which focus not on the role of empirical data in RA but on the problem of ensuring that the models used in RA are independent. By drawing on accounts of RA in experimental science, I argue that there is in fact a fallible but viable form of RA that can both con?rm the results of models and incorporate empirical data. However, for reasons other than those of Orzack and Sober, I conclude that RA may be of limited use in model-based science, as the example of ?shery biology can show. (shrink)

In experimental settings, scientists often “make” new things, in which case the aim is to intervene in order to produce experimental objects and processes—characterized as ‘effects’. In this discussion, I illuminate an important performative function in measurement and experimentation in general: intervention-based experimental production. I argue that even though the goal of IEP is the production of new effects, it can be informative for causal details in scientific representations. Specifically, IEP can be informative about causal relations in: regularities under study; (...) ‘intervention systems’, which are measurement/experimental systems; and new technological systems. (shrink)

This article examines a metaphilosophical issue, namely existing disagreements in philosophy of science about the significance of using multiple means of determination in scientific practice. We argue that this disagreement can, in part, be resolved by separating different questions that can be asked about the use of multiple means of determination, including the following: what can be concluded from the convergence of data or the convergence of claims about phenomena? Are the conclusions drawn from the convergence of data and of (...) statements about phenomena of special importance to the debate about realism and antirealism? Do inferences based on multiple means of determination have stronger epistemic force than inferences that are secured in other ways? Is the epistemic goal of deploying multiple means of determination well entrenched within the scientific community? Most of these questions can be discussed both in a formal and in an empirical perspective. If the differences in perspective are taken into account, some disagreements can be easily resolved. In part, however, the disagreements reflect historiographical challenges that are very difficult, if not impossible to meet. (shrink)

The present paper claims that M. S. Tswett’s chromatographic adsorption analysis, which today is a ubiquitous and instrumentally sophisticated chemical technique, was either ignored or outright rejected by chemists and botanists in the first three decades of the twentieth century because it did not make sense in terms of accepted chemical theory or practice. Evidence for this claim is culled from consideration of the botanical and chemical context of Tswett’s technique as well as an analysis of the protracted debate over (...) Tswett’s chromatographic analysis of chlorophyll between him and Leon Marchlewski, a noted chlorophyll chemist of the period. In this way, the paper expands and amends what it calls the ‘textbook story’ of the early history of chromatography, examples of which may be found in historical notes in many textbooks of chemical instrumental analysis and numerous short articles in chemistry journals. The paper also provides an accessible introduction to the early history of chromatography for historians of science likely to know little or nothing about it. (shrink)

This paper examines moral issues concerning a firm''s use of genetic information about a prospective employee''s predisposition to contract occupational and other illnesses. It critically reviews leading social construction literature on genetic abnormality and genetic screening, and it examines the relevance of arguments from justice and meritocratic principles. It concludes that there is a strong moral presumption against genetic screening in employment.

Culp (1994) provides a defense for a form of experimental reasoning entitled 'robustness'. Her strategy is to examine a recent episode in experimental microbiology--the case of the mistaken discovery of a bacterial organelle called a 'mesosome'--with an eye to showing how experimenters effectively used robust experimental reasoning (or could have used robust reasoning) to refute the existence of the mesosome. My plan is to criticize Culp's assessment of the mesosome episode and to cast doubt on the epistemic significance of robustness. (...) In turn, I present a different account of the experimental reasoning microbiologists used in arriving at the conclusion that mesosomes are artifacts. I call this form of reasoning 'reliable process reasoning', and close the paper with a brief discussion of how experimental microbiologists justify the claim that an experimental process is reliable. (shrink)

I respond to H. M. Collins's claim (1985, 1990, 1993) that experimental inquiry cannot be objective because the only criterium experimentalists have for determining whether a technique is "working" is the production of "correct" (i.e., the expected) data. Collins claims that the "experimenters' regress," the name he gives to this data-technique circle, cannot be broken using the resources of experiment alone. I argue that the data-technique circle, can be broken even though any interpretation of the raw data produced by techniques (...) is theory-dependent. However, it is possible to break this circle by eliminating dependence on even those theoretical presuppositions that are shared by an entire scientific community through the use of multiple independently theory-dependent techniques to produce robust bodies of data. Moreover, I argue, that it is the production of robust bodies of data that convinces experimentalists of the objectivity of their data interpretations. (shrink)

: Most work done in philosophy of experiment has focused on experiments taken from the domain of physics. The present essay tests whether Allan Franklin's (1984, 1986, 1989, 1990) philosophy of experiment developed in the context of high energy physics can be extended to include examples from evolutionary biology, such as H. B. D. Kettlewell's (1955, 1956, 1958) famous studies of industrial melanism in the peppered moth, Biston betularia. The analysis demonstrates that many of the techniques used by evolutionary biologists (...) exemplify the strategies Franklin lists, and identifies an additional strategy that can likewise be justified by appeal to Bayes's Theorem. (shrink)

The concordance of results that are “robust” across multiple scientific modalities is widely considered to play a critical role in the epistemology of science. But what should we make of those cases where such multimodal evidence is discordant? Jacob Stegenga has recently argued that robustness is “worse than useless” in these cases, suggesting that “different kinds of evidence cannot be combined in a coherent way.” In this article I respond to this critique and illustrate the critical methodological role that robustness (...) plays as an aim of scientific inquiry. (shrink)

There is currently a gap in our understanding of how figures produced by mechanical imaging techniques play evidential roles: several studies based on close examination of scientific practice show that imaging techniques do not yield data whose significance can simply be read off the image. If image-making technology is not a simple matter of nature re-presenting itself to us in a legible way, just how do the images produced provide support for scientific claims? In this article I will first show (...) that there is a distinct question about the semiotics of mechanically produced images that has not yet been answered. I show that my account of visual representations can do so, and I argue that the role of convention involved in my account is compatible with the view that visual representations produced through mechanized imaging techniques can play genuine evidential roles in scientific reasoning. (shrink)

Contemporary visual epistemic practices in the biological sciences raise new questions of how to transform an iconic data measurements into images, and how the process of an imaging technique may change the material it is ‘depicting’. This case-oriented study investigates microscopic imagery, which is used by system and synthetic biologists alike. The core argument is developed around the analysis of two recent methods, developed between 2003 and 2006: localization microscopy and photo-induced cell death. Far from functioning merely as illustrations of (...) work done by other means, images can be determined as tools for discovery in their own right and as objects of investigation. Both methods deploy different constellations of intended and unintended interactions between visual appearance and underlying biological materiality. To characterize these new ways of interaction, the article introduces the notions of ‘operational images’ and ‘operational agency’. Despite all their novelty, operational images are still subject to conventions of seeing and depicting: Phenomena emerging with the new method of localization microscopy have to be designed according to image traditions of older, conventional fluorescence microscopy to function properly as devices for communication between physicists and biologists. The article emerged from a laboratory study based on interviews conducted with researchers from the Kirchhoff-Institute for Physics and German Cancer Research Center at Bioquant, Heidelberg, in 2011. (shrink)

This paper examines the vital role played by electron microscopy toward the modern definition of viruses, as formulated in the late 1950s. Before the 1930s viruses could neither be visualized by available technologies nor grown in artificial media. As such they were usually identified by their ability to cause diseases in their hosts and defined in such negative terms as “ultramicroscopic” or invisible infectious agents that could not be cultivated outside living cells. The invention of the electron microscope, with magnification (...) and resolution powers several orders of magnitude better than that of optical instruments, opened up possibilities for biological applications. The hitherto invisible viruses lent themselves especially well to investigation with this new instrument. We first offer a historical consideration of the development of the instrument and, more significantly, advances in techniques for preparing and observing specimens that turned the electron microscope into a routine biological tool. We then describe the ways in which the electron microscopic images, or micrographs, functioned as forms of new knowledge about viruses and resulted in a paradigm shift in the very definition of these entities. Micrographs were not mere illustrations since they did the work for the electron microscopists. Drawing extensively on primary publications, we adduce the role of the new instrument in understanding the so-called eclipse phase in virus multiplication and the unexpected spinoffs of data from electron microscopy in naming and classifying viruses. Thus, we show that electron microscopy functioned not only to provide evidence, but also arguments in facilitating a reordering of the world that it brought into the visual realm. (shrink)

Scientists aim to remediate artifacts in their experimental datasets. However, the remediation of one artifact can result in another. Why might this happen, and what does this consequence tell us about how we should account for artifacts and their control? In this paper, I explore a case in functional neuroimaging where remediation appears to have caused this problem. I argue that remediation amounts to a change to an experimental arrangement. These changes need not be surgical, and the arrangement need not (...) satisfy the criterion of causal modularity. Thus, remediation can affect more than just the factor responsible for the artifact. However, if researchers can determine the consequences of their remediation, they can make adjustments that control for the present artifact as well as for previously controlled ones. Current philosophical accounts of artifacts and the factors responsible for them cannot adequately address this issue, as they do not account for what is needed for artifact remediation (and specifically correction). I support my argument by paralleling it with ongoing concerns regarding the transparency of complex computational systems, as near future remediation across the experimental life sciences will likely make greater use of AI tools to correct for artifacts. (shrink)