The ArgumentWhat kind of objects are computer programs used for simulation purposes in scientific settings? The current investigation treats a special case. It focuses on “event generators,” the program packages that particle physicists construct and use to simulate mechanisms of particle production. The paper is an attempt to bring the multiplex and unfolding character of such knowledge objects to the fore: Multiple meanings and functions are embodied in the object and can be drawn out selectively according to the requirements of (...) a work setting. The object's conceptual complexity governs its application in some contexts, while the object is considered a mere “black box,” transparent and ready-to-hand, in others. These two poles span a full spectrum of object aspects, functions, and conceptions. Event generators are ideas turned into software, testing grounds for models, just a tool to study the performance of a detector, etc. The object's multiplex nature is submitted to negotiation among different actors. (shrink)

Experimental modeling in biology involves the use of living organisms (not necessarily so-called "model organisms") in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call "in vivo representations" where one kind of causal process is used to stand in for a physically (...) different kind of process. I discuss the advantages of this approach in the context of evolutionary biology. (shrink)

A major strategy in the creation of sustainable economies is the establishment of alternative market institutions, such as fair trade and local market systems. However, the dynamics of these alternative markets are poorly understood. What are the rules of behavior by which these markets function? How do these markets maintain their separate identity as “alternative”: apart from the conventional (“free”) market system? Building on Lyson’s notion of civic agriculture, we argue that alternative markets maintain themselves through civic engagement. However, we (...) argue that the civically-engaged practices of alternative markets are poorly understood. We seek, therefore, to begin a conversation about the everyday forms of civic engagement in alternative practice and to do this we introduce a few useful conceptual tools. Building upon ideas in science studies about the collaboration of scientists (Hess, Alternative pathways in science and industry, 2007) we argue that civic markets have their own “market fields” and “modes of governance” (Bulkeley et al., Environment and Planning A 39:2733–2753, 2007), their own fields of social interaction in which rules of behavior become stabilized and determine how the market works. The creation of a social field also requires the demarcation of boundaries, referred to in the science studies literature as “boundary work” (Gieryn, Cultural boundaries of science: Credibility on the line, 1999). We apply the idea of boundary work to understand how alternative market actors maintain boundaries between alternative and conventional markets. Finally, studies of collaboration in science have often centered on the object created through these interactions, an object that is partially material and partially a product of knowledge, what (Rheinberger, Toward a history of epistemic things: Synthesizing proteins in the test tube, 1997) calls an “epistemic object.” We use this idea to understand that the creation of alternative objects of exchange, such as organic food, are epistemic objects in that they combine both particular materialities and particular ways of knowing. Using these concepts, we will carry out a close analysis of the mode of governance in the national organic market, looking specifically a recent governance crisis in organic agriculture known as the Harvey lawsuit. (shrink)

In the context of 1960s research on biological membranes, scientists stumbled upon a curiously coloured material substance, which became called the “purple membrane.” Interactions with the material as well as chemical analyses led to the conclusion that the microbial membrane contained a photoactive molecule similar to rhodopsin, the light receptor of animals’ retinae. Until 1975, the find led to the formation of novel objects in science, and subsequently to the development of a field in the molecular life sciences that comprised (...) biophysics, bioenergetics as well as membrane and structural biology. Furthermore, the purple membrane and bacteriorhodopsin, as the photoactive membrane transport protein was baptized, inspired attempts at hybrid bio-optical engineering throughout the 1980s. A central motif of the research field was the identification of a functional biological structure, such as a membrane, with a reactive material substance that could be easily prepared and manipulated. Building on this premise, early purple membrane research will be taken as a case in point to understand the appearance and transformation of objects in science through work with material substances. Here, the role played by a perceptible material and its spontaneous change of colour, or reactivity, casts a different light on objects and experimental practices in the late twentieth century molecular life sciences. With respect to the impact of chemical working and thinking, the purple membrane and rhodopsins represent an influential domain straddling the life and chemical sciences as well as bio- and material technologies, which has received only little historical and philosophical attention. Re-drawing the boundary between the living and the non-enlivened, these researches explain and model organismic activity through the reactivity of macromolecular structures, and thus palpable material substances. (shrink)

I present a case study of scientific discovery, where building two functional and behavioral approximations of neurons, one physical and the other computational, led to conceptual and implementation breakthroughs in a neural engineering laboratory. Such building of external systems that mimic target phenomena, and the use of these external systems to generate novel concepts and control structures, is a standard strategy in the new engineering sciences. I develop a model of the cognitive mechanism that connects such built external systems with (...) internal models, and I examine how new discoveries, and consensus on discoveries, could arise from this external‐internal coupling and the building process. The model is based on the emerging framework of common coding, which proposes a shared representation in the brain between the execution, perception, and imagination of movement. (shrink)

While scientific terms lack the stability of physical objects, they are generally far more stable than the various meanings associated with them. As a consequence, they tend to carry older conceptions alongside those more recently acquired, thereby exerting an effective drag against conceptual change. I illustrate this claim with an analysis of the shifting meanings of the term genome, originally used to refer to a collectivity of genes, but more recently to an organism’s complement of DNA. While genes were originally (...) regarded as effectively autonomous formal agents, and DNA as collections of genes, contemporary research suggests that an organism’s DNA constitutes a far more complex system designed to adapt and respond to the environment in which it finds itself. (shrink)

In 1957, Francis Crick outlined a startling vision of life in which the great diversity of forms and shapes of macromolecules was encoded in the one-dimensional sequence of nucleic acids. This paper situates Crick's new vision in the debates of the 1950s about protein synthesis and gene action. After exploring the reception of Crick's ideas, it shows how they differed radically from a different model of protein synthesis which enjoyed wide currency in that decade. In this alternative model, advocated by (...) Linus Pauling and other luminaries, three-dimensional templates directed the folding of proteins. Even though it was always considered somewhat speculative, this theory was supported by a number of empirical results originating in different experimental systems. It was eventually replaced by a model in which the forms and shapes of macromolecules resulted solely from their amino acid sequence, dramatically simplifying the problem of protein synthesis which Crick was attempting to solve in 1957. (shrink)

The article reevaluates the reception of Mendelism in France, and more generally considers the complex relationship between Mendelism and plant breeding in the first half on the 20th century. It shows on the one side that agricultural research and higher education institutions have played a key role in the development and institutionalization of genetics in France, whereas university biologists remained reluctant to accept this approach on heredity. But on the other side, plant breeders, and agricultural researchers, despite an interest in (...) Mendelism, never came to see it as the breeders' panacea, and regarded it instead as of only limited value for plant breeding. I account for this judgment in showing that the plant breeders and Mendelism designed two contrasting kinds of experimental systems and inhabited distinct experimental cultures. While Mendelian geneticists designed experimental systems that allowed the production of definite ratios of different forms that varied in relation to a few characters, plant breeders' experimental systems produced a wide range of variation, featuring combinations between hundreds of traits. Rather than breaking this multiple variation down into simple elements, breeders designed and monitored a genetic lottery. The gene was a unit in a Mendelian experimental culture, an "epistemic thing" as Rheinberger put it, that could be grasped by means of statistical regularities, but it remained of secondary importance for French plant breeders, for whom the strain or the variety -- not the gene -- was the fundamental unit of analysis and manipulation. (shrink)

The history of biochemistry and molecular biology is replete with examples of erroneous theories that persisted for considerable lengths of time before they were rejected. This paper examines patterns of dissolution of three such erroneous hypotheses: The idea that nucleic acids are tetrads of the four nucleobases (‘the tetranucleotide hypothesis’); the notion that proteins are collinear with their encoding genes in all branches of life; and the hypothesis that proteins are synthesized by reverse action of proteolytic enzymes. Analysis of these (...) cases indicates that amassed contradictory empirical findings did not prompt critical experimental testing of the prevailing theories nor did they elicit alternative hypotheses. Rather, the incorrect models collapsed when experiments that were not purposely designed to test their validity exposed new facts. (shrink)

Making sense of modeling: beyond representation Content Type Journal Article Category Original paper in Philosophy of Science Pages 335-352 DOI 10.1007/s13194-011-0032-8 Authors Isabelle Peschard, Philosophy Department, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA Journal European Journal for Philosophy of Science Online ISSN 1879-4920 Print ISSN 1879-4912 Journal Volume Volume 1 Journal Issue Volume 1, Number 3.

Discovery proceeds in stages of construction, evaluation, and revision. Each of these stages is constrained by what is known or conjectured about what is being discovered. A new characterization of mechanism aids in specifying what is to be discovered when a mechanism is sought. Guidance in discovering mechanisms may be provided by the reasoning strategies of schema instantiation, modular subassembly, and forward/backward chaining. Examples are found in mechanisms in molecular biology, biochemistry, immunology, and evolutionary biology.

Watson and Crick’s discovery of the structure of DNA led to developments that transformed many biological sciences. But what were the relevant developments and how did they transform biology? Much of the philosophical discussion concerning this question can be organized around two opposing views: theoretical reductionism and layer-cake antireductionism. Theoretical reductionist and their anti-reductionist foes hold two assumptions in common. First, both hold that biological knowledge is structured like a layer cake, with some biological sciences, such as molecular biology cast (...) at lower levels of organization, and others, such as classical genetics, cast at higher levels. Second, both assume that scientific knowledge is structured by theory and that the productivity of scientific research depends on whether the underlying theory identifies the fundamentals upon which the phenomena to be explained and investigated depend. In the first part of this paper, I challenge these assumptions. In the second part, I show how recasting the basic theory of classical genetics made it possible to retool the methodologies of genetics. It was the investigative power of these retooled methodologies, and not the explanatory power of a gene-based theory, that transformed biology. (shrink)

The aim of this paper is to discuss a key question in the history and philosophy of medicine, namely how scholars should treat the practices and experimental hypotheses of modern life science laboratories. The paper seeks to introduce some prominent historiographical methods and theoretical approaches associated with biomedical research. Although medical scientists need no convincing that experimentation has a significant function in their laboratory work, historians, philosophers, and sociologists long neglected its importance when examining changes in medical theories or progress (...) in scientific knowledge. The reason appears to have been the academic influence of the then dominant tradition in the history of ideas, but was also due to a misconception of what could usefully be termed the view on “historical ontology.” During the last two decades, there have been many books and research articles that have turned towards the subject, so that the study of experimental practice has become a major trend in the contemporary history and philosophy of medicine. A closer look at the issue of laboratory research shows that concepts in medicine and the life sciences cannot be understood as historically constant, free-standing ideas, but have to be regarded as dependent on local research settings. They often carry particular “social memories” with them and thus acquire important ethical implications. (shrink)

: In 1856, Michael Faraday (1791–1867) conducted nearly a year's worth of research on the optical properties of gold, in the course of which he discovered the first metallic colloids. Following our own discovery of hundreds of the specimens prepared by Faraday for this research, the present paper describes the cognitive role of these "epistemic artifacts" in the dynamics of Faraday's research practices. Analysis of the specimens, Faraday's Diary records, and replications of selected procedures (partly to replace missing kinds of (...) specimens and partly to understand the "tacit knowledge" implicated in Faraday's research) are outlined, and a reconstruction of the events surrounding the initial discovery of metallic colloids is presented. (shrink)

: The increasing attention on experiment in the last two decades has led to important insights into its material, cultural and social dimensions. However, the role of experiment as a tool for generating knowledge has been comparatively poorly studied. What questions are asked in experimental research? How are they treated and eventually resolved? And how do questions, epistemic situations, and experimental activity cohere and shape each other? In my paper, I treat these problems on the basis of detailed studies of (...) research practice. After presenting several cases from the history of electricity—Dufay, Ampère, and Faraday—I discuss a specific type of experiment—the "exploratory experiment"—and analyze how it works in concept formation. I argue that a fuller understanding of experiment can only be achieved by intertwining historical and philosophical perspectives in such a way that the very separation of the two become questioable. (shrink)

The dominant neuroscientific theory of spatial memory is, like many theories in neuroscience, a multilevel description of a mechanism. The theory links the activities of molecules, cells, brain regions, and whole organisms into an integrated sketch of an explanation for the ability of organisms to navigate novel environments. Here I develop a taxonomy of interlevel experimental strategies for integrating the levels in such multilevel mechanisms. These experimental strategies include activation strategies, interference strategies, and additive strategies. These strategies are mutually reinforcing, (...) providing a kind of interlevel and intratheoretic robustness that has not previously been recognized. (shrink)

In earlier work I have claimed that emotion and some emotions are not `natural kinds'. Here I clarify what I mean by `natural kind', suggest a new and more accurate term, and discuss the objection that emotion and emotions are not descriptive categories at all, but fundamentally normative categories.

According to Kuhn's speciation analogy, scientific specialisation is fundamentally analogous to biological speciation. In this paper, we extend Kuhn's original language-centred formulation of the speciation analogy, to account for episodes of scientific specialisation centred around methodological differences. Building upon recent views in evolutionary biology about the process of speciation by genetic divergence, we will show how these methodology-centred episodes of scientific specialisation can be understood as cases of specialisation driven by value divergence. We will apply our model of specialisation by (...) value divergence to an episode of methodology-centred scientific specialisation: the emergence of molecular biology. (shrink)

Masui Kiyoshi (1887–1981), a prominent Japanese geneticist, is best known for inventing the sex-sorting method of chicks and his contributions to experimental genetics in Japan. Masui drew inspiration from Goldschmidt’s sex determination theory and used chickens, transplantation techniques, and his own “chick sexing” methods in his scientific work. This paper examines the intersection of genetics and industrial breeding by tracing the evolution of Masui’s experimental systems. During the early 20th century, poultry farming emerged as a significant industry in Japan, resulting (...) in the development of standardized organisms and techniques for chicken farming. Masui, a professor at Tokyo Imperial University, collaborated with the Imperial Zootechnical Experimental Station to use these organisms as models for sex determination theory while exploring their further industrial possibilities. First, the paper show how Masui viewed chickens as epistemological objects and transformed his anatomical discoveries into standardized industrial practices. Next, it describes how Masui’s collaboration with German geneticist Richard Goldschmidt led to new academic questions about sex determination mechanisms and how he integrated his knowledge of chicken physiology into his research on “experimental gynandromorphs” to elaborate the theories. Lastly, the paper discusses the biotechnological ideals that Masui aimed to achieve and how they were co-constructed with his mass-production method of intersex chickens from the early 1930s. The trajectory of Masui’s experimental systems highlights the dynamic relationship between agroindustry and genetics in the early twentieth century and demonstrates the ‘biology of history’ in which the biological processes of organisms intertwine with their epistemological history. (shrink)

This article argues that historical epistemology offers the history of philosophy and science more than a mere tool to write the history of concepts. It does this, first of all, by rereading historical epistemology through Michel Foucault's “techniques of the self.” Second, it turns to the work of Léon Brunschvicg and Gaston Bachelard. In their work we see a proposal for what the subjectivity of scientists and philosophers should be. The article thus argues that their work is driven by a (...) normative psychology: a set of prescriptions for which mental constitution a scholarly self has to have. In the Conclusion, it returns to existing analyses of “open‐mindedness” as a virtue and explores in what way these cases challenge these analyses, as well as to what extent Foucault's “techniques of the self” can be applied to other cases in the history of French philosophy. (shrink)

Si bien en la filosofía de las ciencias ya se han explorado algunos ejemplos provenientes de la bioquímica como casos de estudio, la filosofía de la bioquímica es una subdisciplina naciente. En este artículo estudiaremos dos problemas filosóficos de relevancia contemporánea en esta ciencia. Por un lado, examinaremos las bases epistemológicas del problema del plegamiento de proteínas. En particular lo relacionado con la predicción de la estructura tridimensional de las proteínas a partir de su secuencia, asunto que ha dado mucho (...) que hablar debido a los nuevos avances utilizando deep learning. Por otro lado, exploraremos el problema in-vitro/in-vivo y, más generalmente, el problema de la extrapolación en las ciencias biológicas. Finalmente, a partir de las consecuencias de ambos temas consideraremos algunas reflexiones filosóficas generales acerca del reduccionismo, el pluralismo y el lugar de la bioquímica en las ciencias biológicas. Palabras clave: Bioquímica, Plegamiento de proteínas, In-vitro/in-vivo, Pluralismo, Reduccionismo. (shrink)

Developing tools is a crucial aspect of experimental practice, yet most discussions of scientific change traditionally emphasize theoretical over technological change. To elaborate on the role of tools in scientific change, I offer an account that shows how scientists use tools in exploratory experiments to form novel concepts. I apply this account to two cases in neuroscience and show how tool development and concept formation are often intertwined in episodes of tool-driven change. I support this view by proposing common normative (...) principles that specify when exploratory concept formation and tool development succeed to initiate scientific change. (shrink)

Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...) is to consider the role of the activity of reification within the research process. Reification consists in the identification of more or less stable features of the flux, and treating these as constituting stable things. As we illustrate with reference to biological and biomedical research on COVID-19, reification is a necessary component of any process of inquiry and comes in at least two forms: means reification, when researchers create objects meant to capture features of the world, or phenomena, in order to be able to study them; and target reification, when researchers infer an understanding of phenomena from an investigation of the epistemic objects created to study them. We note that both objects and phenomena are dynamic processes and argue that have no reason to assume that changes in objects and phenomena track one another. We conclude that failure to acknowledge these forms of reification and their epistemic role in scientific inquiry can have dire consequences for how the resulting knowledge is interpreted and used. (shrink)

Within science fiction the topic of ‘first contact’ is a popular theme. How will an encounter with aliens unfold? Will we succeed in communicating with them? Although such questions are present in the background of many science fiction novels, they are not always explicitly dealt with and even if so, often in a poor way. In this article, I will introduce a typology of five dominant types of solutions to the problem of first contact in science fiction works. The first (...) four solutions are the more dominant, but also the least interesting ones. There is a fifth category that addresses the question of first contact in a more interesting way, exemplified by the work of Stanisław Lem. This fifth option defines itself as a critique of the four previous categories, or of their shared assumption of what Lem (1967) has called ‘the myth of cognitive universality’. Lem is sceptical of the common optimism that first contact will always be successful. In books such as Solaris (1961), His Master’s Voice (1967) and Fiasco (1986), humanity makes first contact with an alien phenomenon, but fails to comprehend the phenomenon. Fundamentally, it will be argued that Lem’s work shows that in such an encounter we will typically not only lack the right answers to our questions, but that we also often lack the correct questions: we simply do not have the right categories or instruments to even recognize, let alone meaningfully interrogate, the alien phenomenon. The article ends with an exploration of the implications of Lem’s pessimism and whether it is the most plausible option for first contact. Moreover, the article will draw some lessons for philosophy of science, by exploring the parallel with the confrontation of novel or deviant phenomena in science. Lem’s work is helpful here because it succeeds in articulating what has not always been appreciated in the philosophy of science, namely that the right questions by which to interrogate scientific phenomena are not given, but that their articulation always requires work. (shrink)

In this talk I present the main results from Anta (2021), namely, that the theoretical division between Boltzmannian and Gibbsian statistical mechanics should be understood as a separation in the epistemic capabilities of this physical discipline. In particular, while from the Boltzmannian framework one can generate powerful explanations of thermal processes by appealing to their microdynamics, from the Gibbsian framework one can predict observable values in a computationally effective way. Finally, I argue that this statistical mechanical schism contradicts the Hempelian (...) (1958) thesis that the predictive power of a scientific theory is directly proportional to its explanatory potential, and vice versa. (shrink)

This groundbreaking, open access volume analyses and compares data practices across several fields through the analysis of specific cases of data journeys. It brings together leading scholars in the philosophy, history and social studies of science to achieve two goals: tracking the travel of data across different spaces, times and domains of research practice; and documenting how such journeys affect the use of data as evidence and the knowledge being produced. The volume captures the opportunities, challenges and concerns involved in (...) making data move from the sites in which they are originally produced to sites where they can be integrated with other data, analysed and re-used for a variety of purposes. The in-depth study of data journeys provides the necessary ground to examine disciplinary, geographical and historical differences and similarities in data management, processing and interpretation, thus identifying the key conditions of possibility for the widespread data sharing associated with Big and Open Data. The chapters are ordered in sections that broadly correspond to different stages of the journeys of data, from their generation to the legitimisation of their use for specific purposes. Additionally, the preface to the volume provides a variety of alternative “roadmaps” aimed to serve the different interests and entry points of readers; and the introduction provides a substantive overview of what data journeys can teach about the methods and epistemology of research. (shrink)

When radiocarbon dating techniques were applied to archaeological material in the 1950s they were hailed as a revolution. At last archaeologists could construct absolute chronologies anchored in temporal data backed by immutable laws of physics. This would make it possible to mobilize archaeological data across regions and time-periods on a global scale, rendering obsolete the local and relative chronologies on which archaeologists had long relied. As profound as the impact of 14C dating has been, it has had a long and (...) tortuous history now described as proceeding through three revolutions, each of which addresses distinct challenges of capturing, processing and packaging radiogenic data for use in resolving chronological puzzles with which archaeologists has long wrestled. In practice, mobilizing radiogenic data for archaeological use is a hard-won achievement; it involves multiple transformations that, at each step of the way, depend upon a diverse array of technical expertise and background knowledge. I focus on strategies of triangulation and traceability that establish the integrity of these data and their relevance as anchors for evidential reasoning in archaeology. (shrink)

Synthetic biology aims to synthesize novel biological systems or redesign existing ones. The field has raised numerous philosophical questions, but most especially what is novel to this field. In this article I argue for a novel take, since the dominant ways to understand synthetic biology’s specificity each face problems. Inspired by the examination of the work of a number of chemists, I argue that synthetic biology differentiates itself by a new regime of articulation, i.e. a new way of articulating the (...) questions and phenomena it wants to address. Instead of describing actual existing biological systems, the field aims to describe biological possibilities. In the second part I corroborate this hypothesis through a comparison between early research in the field of the origins of life and contemporary synthetic biologists, who are not so much interested in the historical origin of life on Earth, but rather in a universal biology of the possible origins of any life whatsoever. (shrink)

This contribution explores the aesthetic dimensions of culinary practice. Starting point is an investigation of the menu “The Elementary” by the Swiss avantgarde and Michelin-starred chef Stefan Wiesner. The methodological interweaving of phenomenology, speech act, pictorial, and design analysis points to an innovative cooking mindset which takes on shape in the menu “Elementary”: Wiesner renders nature experienceable with regard to taste in an essential manner. It is based on a concept of radical simplicity, which he calls “monotype”. “Monotype” mimicries neither (...) existent nature nor conventional cooking styles. Rather, Wiesner sets out from very few elements which he then unfolds inwards taste-wise. The sequence of courses creates a spatio-temporal reference field that is inspired by nature but does not replicate it, instead it takes us through a culinary transformation of its elements. “Elementary”, so my argument, develops a new definition of the relationship between nature and food through a singular cooking practice out of which derives a desideratum for a culinary aesthetics. (shrink)

The “Human Brain Project” (HBP) is a large-scale European neuroscience and information communication technology (ICT) project that has been a matter of heated controversy since its inception. With its aim to simulate the entire human brain with the help of supercomputing technologies, the HBP plans to fundamentally change neuroscientific research practice, medical diagnosis, and eventually the use of computers itself. Its controversial nature and its potential impacts render the HBP a subject of crucial importance for critical studies of science and (...) society. In this paper, we provide a critical exploratory analysis of the potential mid- to long-term impacts the HBP and its ICT infrastructure could be expected to have, provided its agenda will indeed be implemented and executed to a substantive degree. We analyse how the HBP aspires to change current neuroscientific practice, what impact its novel infrastructures could have on research culture, medical practice and the use of ICT, and how, given a certain degree of successful execution of the project’s aims, potential clinical and methodological applications could even transform society beyond scientific practice. Furthermore, we sketch the possibility that research such as that projected by the HBP may eventually transform our everyday world, even beyond the scope of the HBP’s explicit agenda, and beyond the isolated ‘application’ of some novel technological device. Finally, we point towards trajectories for further philosophical, historical and sociological research on the HBP that our exploratory analysis might help to inspire. Our analysis will yield important insights regardless of the actual success of the HBP. What we drive at, for the most part, is the broader dynamics of scientific and technological development of which the HBP agenda is merely one particularly striking exemplification. (shrink)

in a nervous system of a given species. This chapter provides a critical perspective on the role of connectomes in neuroscientific practice and asks how the connectomic approach fits into a larger context in which network thinking permeates technology, infrastructure, social life, and the economy. In the first part of this chapter, we argue that, seen from the perspective of ongoing research, the notion of connectomes as “complete descriptions” is misguided. Our argument combines Rachel Ankeny’s analysis of neuroanatomical wiring diagrams (...) as “descriptive models” with Hans-Joerg Rheinberger’s notion of “epistemic objects,” i.e., targets of research that are still partially unknown. Combining these aspects we conclude that connectomes are constitutively epistemic objects: there just is no way to turn them into permanent and complete technical standards because the possibilities to map connection properties under different modeling assumptions are potentially inexhaustible. In the second part of the chapter, we use this understanding of connectomes as constitutively epistemic objects in order to critically assess the historical and political dimensions of current neuroscientific research. We argue that connectomics shows how the notion of the “brain as a network” has become the dominant metaphor of contemporary brain research. We further point out that this metaphor shares (potentially problematic) affinities to the form of contemporary “network societies.” We close by pointing out how the relation between connectomes and networks in society could be used in a more fruitful manner. (shrink)

This article examines how minimal genome research mobilizes philosophical concepts such as minimality and essentiality. Following a historical approach the article aims to uncover what function this terminology plays and which problems are raised by them. Specifically, four historical moments are examined, linked to the work of Harold J. Morowitz, Mitsuhiro Itaya, Eugene Koonin and Arcady Mushegian, and J. Craig Venter. What this survey shows is a historical shift away from historical questions about life or descriptive questions about specific organisms (...) towards questions that explore biological possibilities: what are possible forms of minimal genomes, regardless of whether they exist in nature? Moreover, it highlights a fundamental ambiguity at work in minimal genome research between a universality claim and a standardization claim: does a minimal genome refer to the minimal gene set for any organism whatsoever? Or does it refer rather to a gene set that will provide stable, robust and predictable behaviour, suited for biotechnological applications? Two diagnoses are proposed for this ambiguity: a philosophical diagnosis of how minimal genome research either misunderstands the ontology of biological entities or philosophically misarticulates scientific practice. Secondly, a historical diagnosis that suggests that this ambiguity is part of a broader shift towards technoscience. (shrink)

This paper discusses the claim that science is “messy.” Part I argues first, that a good portion of today’s discussions about messy science is just a portrayal of familiar features of science in new terms. In the paper, I refer to this as “messy science talk.” Second, Part I draws out rhetorical functions of messy science talk, namely the denigration of science in the popular media and the celebration of the maverick. Part II identifies one way in which it is (...) enlightening to think about mess in current science, namely in reference to the problems that scientists need to address. It also shows that we do not need an entirely new conceptual inventory to analyze these problems. “Mess” and “wicked problems” were a theme in operations research and theories of social planning in the 1970s. These older analyses can illuminate important characteristics of today’s scientific problems. Wicked problems cut across different disciplines, engage different stakeholders (including non-scientists), are fluid, and cannot even be clearly formulated. They are urgent and need to be addressed before sufficient evidence is in. (shrink)

In this dissertation, I present a novel account of the components that have a peculiar epistemic role in our scientific inquiries, since they contribute to establishing a form of coordination. The issue of coordination is a classic epistemic problem concerning how we justify our use of abstract conceptual tools to represent concrete phenomena. For instance, how could we get to represent universal gravitation as a mathematical formula or temperature by means of a numerical scale? This problem is particularly pressing when (...) justification for using these abstract tools comes, in part or entirely, from knowledge which is not independent from them, thus leading to threats of circularity. Achieving coordination between some abstract conceptual tools and the concrete phenomena that they are supposed to represent is usually a complex process, which involves several epistemic components. Some of these components eventually provide stable conditions for applying those abstract representations to concrete phenomena. It is in this sense of providing certain conditions of applicability that different philosophical traditions, as well as some contemporary reappraisals, view these components as constitutive or a priori. In this work, I present a new gradualist, contextualist, and relational approach to understand these constitutive components of scientific inquiry. It is gradualist inasmuch as the degree to which some component is constitutive depends on three quantifiable features: quasi-axiomaticity, generative potential, and empirical shielding. Since the quantification of these three features impinges on the history and practice of using these components in a scientific context, my approach is a contextualist one. Finally, my approach is relational in a double sense: first, it identifies ordinal relationships among epistemic components with respect to their constitutive character; second, these relationships are relative to a scientific framework of inquiry. After introducing my account and a classic example of constitutively a priori principles, i.e., Friedman’s (2001) analysis of Newtonian mechanics, I turn to my own case studies to demonstrate the advantages of my approach. Firstly, I discuss Okasha’s (2018) view of endogenization as a pervasive theoretical strategy in evolutionary biology and suggest that the constitutive character of the core Darwinian principles progressively increases with endogenization. Secondly, I apply a conceptual distinction between two varieties or scopes of coordination – general coordination and coordination in measurement – to Ohm’s work on electrical conductivity. This distinction allows me to pinpoint to what extent components along different dimensions (e.g., instrumentation, measurement, theorising, etc.) were constitutive of the forms of coordination which Ohm relied on. Thirdly, I discuss the epistemic function of the Hardy-Weinberg principle in the history and practice of population genetics. I assess this principle in terms of my account and identify approximation and stability as two components that are highly constitutive, in that they contribute to justifying its use in population genetics. Finally, applying my account to these case studies enables me to identify at least three qualitatively different types of constitutive components: domain-specific theoretical principles, material components, and domain-independent assumptions underlying reasoning abilities. In the light of my results, I draw some general conclusions on epistemic justification and scientific knowledge. (shrink)

In the most inclusive sense, psychological mechanisms offer a type of causal explanation of mental states and behavior, often with reference to underlying processes, systems, activities, or entities. By postulating and investigating such mechanisms, researchers have sought explanations of a wide range of psychological phenomena. However, the concept has been deployed in dramatically different ways, with very different meanings, depending upon the particular school or tradition of psychology (and specific research program therein). In fact, usage has been so diverse as (...) to defy easy categorization or definition. But a historical perspective, even if rather selective, can trace the broad outlines of the significance of psychological mechanisms for the study of the mind. Perhaps most notable is the role they have played in the psychoanalytic tradition; research efforts within behaviorism and cognitive science have also made liberal use of versions of the concept in their explanatory frameworks (for discussion of evolutionary psychology, see the entry “evolved psychological mechanisms”). Cutting across all of these traditions are several key themes relating to psychological mechanisms, including questions concerning the scope of the relevant causal claims, debates about causal determinism and regularity, and the unresolved relation between mind and body. (shrink)

A number of examples of studies from the field ‘The Philosophy of Mathematical Practice’ (PMP) are given. To characterise this new field, three different strands are identified: an agent-based, a historical, and an epistemological PMP. These differ in how they understand ‘practice’ and which assumptions lie at the core of their investigations. In the last part a general framework, capturing some overall structure of the field, is proposed.

Although there is increasing recognition that theory and practice in science are often inseparably intertwined, discussions of scientific controversies often continue to focus on theory, and not practice or methodologies. As a contribution to constructing a framework towards understanding controversies linked to scientific practices, we introduce the notion of borrowed epistemic credibility, to describe the situation in which scientists exploit fallacious similarities between accepted tenets in other fields to garner support for a given position in their own field. Our proposal (...) is based on the analysis of a recent controversy in phylogeography, a biological subdiscipline concerned with the study of the historical causes of variation in genetic diversity within species in concrete biogeographical locations. Through a review of the arguments that support the two conflicting phylogeographic schools, we show that ‘theory’ plays essentially no role as a foundation of the controversy, whereas both sides borrow epistemic credibility from sources such as formal logic, similarity of results to those in other scientific areas, the authority of prominent scientists, or the presumed superiority of quantitative vs. verbal reasoning. Our case study underscores the indivisibility of theory and practice and provide a means to re-examine important philosophical issues such as the meaning of inference, rationality, justification, and objectivity in scientific practice. (shrink)

Molecular biologists exploit information conveyed by mechanistic models for experimental purposes. In this article, I make sense of this aspect of biological practice by developing Keller’s idea of the distinction between ‘models of’ and ‘models for’. ‘Models of (phenomena)’ should be understood as models representing phenomena and are valuable if they explain phenomena. ‘Models for (manipulating phenomena)’ are new types of material manipulations and are important not because of their explanatory force, but because of the interventionist strategies they afford. This (...) is a distinction between aspects of the same model. In molecular biology, models may be treated either as ‘models of’ or as ‘models for’. By analysing the discovery and characterization of restriction–modification systems and their exploitation for DNA cloning and mapping, I identify the differences between treating a model as a ‘model of’ or as a ‘model for’. These lie in the cognitive disposition of the modeller towards the model: a modeller will look at a model as a ‘model of’ if interested in its explanatory force, or as a ‘model for’ if interested in the material manipulations it can possibly afford. (shrink)

REVIEW (1): "Jeff Kochan’s book offers both an original reading of Martin Heidegger’s early writings on science and a powerful defense of the sociology of scientific knowledge (SSK) research program. Science as Social Existence weaves together a compelling argument for the thesis that SSK and Heidegger’s existential phenomenology should be thought of as mutually supporting research programs." (Julian Kiverstein, in Isis) ---- REVIEW (2): "I cannot in the space of this review do justice to the richness and range of Kochan's (...) discussion [...]. There is a great deal in this foundational portion of Kochan's discussion that I find tremendously interesting and engaging [...]." (David R. Cerbone, in Studies in History and Philosophy of Science) ---- REVIEW (3): "Science as Social Existence will be of interest not only to Heidegger scholars but to anyone engaged in science and technology studies. [...] This is an informative and original book. Kochan should be praised for his clear, pleasant-to-read prose." (Michael Butler, in CHOICE). (shrink)

Computer simulations and experiments share many important features. One way of explaining the similarities is to say that computer simulations just are experiments. This claim is quite popular in the literature. The aim of this paper is to argue against the claim and to develop an alternative explanation of why computer simulations resemble experiments. To this purpose, experiment is characterized in terms of an intervention on a system and of the observation of the reaction. Thus, if computer simulations are experiments, (...) either the computer hardware or the target system must be intervened on and observed. I argue against the first option using the non-observation argument, among others. The second option is excluded by e.g. the over-control argument, which stresses epistemological differences between experiments and simulations. To account for the similarities between experiments and computer simulations, I propose to say that computer simulations can model possible experiments and do in fact often do so. (shrink)

Developing models of biological mechanisms, such as those involved in respiration in cells, often requires collaborative effort drawing upon techniques developed and information generated in different disciplines. Biochemists in the early decades of the 20th century uncovered all but the most elusive chemical operations involved in cellular respiration, but were unable to align the reaction pathways with particular structures in the cell. During the period 1940-1965 cell biology was emerging as a new discipline and made distinctive contributions to understanding the (...) role of the mitochondrion and its component parts in cellular respiration. In particular, by developing techniques for localizing enzymes or enzyme systems in specific cellular components, cell biologists provided crucial information about the organized structures in which the biochemical reactions occurred. Although the idea that biochemical operations are intimately related to and depend on cell structures was at odds with the then-dominant emphasis on systems of soluble enzymes in biochemistry, a reconceptualization of energetic processes in the 1960s and 1970s made it clear why cell structure was critical to the biochemical account. This paper examines how numerous excursions between biochemistry and cell biology contributed a new understanding of the mechanism of cellular respiration. (shrink)

In recent years, the emergence of a new trend in contemporary philosophy has been observed in the increasing usage of empirical research methods to conduct philosophical inquiries. Although philosophers primarily use secondary data from other disciplines or apply quantitative methods (experiments, surveys, etc.), the rise of qualitative methods (e.g., in-depth interviews, participant observations and qualitative text analysis) can also be observed. In this paper, I focus on how qualitative research methods can be applied within philosophy of science, namely within the (...) philosophical debate on modeling. Specifically, I review my empirical investigations into the issues of model de-idealization, model justification and performativity. (shrink)

Science studies has often been against the normative dimension of epistemology, which made a naturalistic study of science impossible. But this is not to say that a new type of normativity cannot be detected at work inscience studies. This is especially true in the second wave of studies dealing with the body, which has aimed at criticizing the physicalization of the body without falling into the various traps of a phenomenology simply added to a physical substrate. This article explores the (...) work of Isabelle Stengers and Vinciane Despret in that respect, and shows how it can be used to rethink the articulation between the various levels that make up a body. (shrink)

Csikszentmihalyi (1999: 314) argues that 'creativity is a process that can be observed only at the intersection where individuals, domains, and fields intersect'. This article discusses the relationship between creativity and interdisciplinarity in science. It is specifically concerned with interdisciplinary collaboration, interrogating the processes that contribute to the collaborative creation of original ideas and the practices that enable creative integration of diverse domains. It draws on results from a novel real-world experiment in which small interdisciplinary groups of graduate students were (...) tasked with producing an innovative scientific research problem and an integrative research proposal. Results show that while bisociative thinking assists in the creation of original research problems, both disciplinary skills and an interdisciplinary disposition are core to the integration of creative research proposals. Extrapolating from the results of this experiment, the article discusses the feasibility of preparing students for such work and the implications for universities and other intellectual centers. (shrink)

This paper uses Pierre Bourdieu’s field theory to develop tools for analyzing interdisciplinary scientific fields. Interdisciplinary fields are scientific spaces where no single form of scientific capital has a monopoly and therefore multiple forms of scientific capital constitute the structures and stakes of scientific competition. Scientists compete to accumulate and define forms of scientific capital and also to set the rates of exchange between them. The paper illustrates this framework by applying it to the interdisciplinary field of behavior genetics. Most (...) behavior geneticists envision their participation in the field as a means to compete for scientific capital in other fields. However, the scientific capital of behavior genetics has different values for scientists attempting to deploy it in different neighboring fields. These values depend on situations in each field and the ways behavior genetics mediates relationships among them. The pattern of relationships of exchange helps explain the social hierarchy and several features of knowledge production within behavior genetics. (shrink)

In this essay Clarence Joldersma explores radical constructivism through the work of its most well-known advocate, Ernst von Glasersfeld, who combines a sophisticated philosophical discussion of knowledge and truth with educational practices. Joldersma uses Joseph Rouse's work in philosophy of science to criticize the antirealism inherent in radical constructivism, emphasizing that Rouse's Heideggerian critique differs from the standard realist defense of modernist epistemology. Next, Joldersma develops an alternative conception of truth, in terms of disclosure, based on Lambert Zuidervaart's work in (...) aesthetics. Joldersma concludes by arguing that this notion of truth avoids the pitfalls of both realism and antirealism, giving educational theorists a way forward to accept some of the major insights of constructivism with respect to learning and teaching without having to relinquish a robust notion of truth. (shrink)