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)

This essay presents a unified account of safety, sensitivity, and severe testing. S’s belief is safe iff, roughly, S could not easily have falsely believed p, and S’s belief is sensitive iff were p false S would not believe p. These two conditions are typically viewed as rivals but, we argue, they instead play symbiotic roles. Safety and sensitivity are both valuable epistemic conditions, and the relevant alternatives framework provides the scaffolding for their mutually supportive roles. The relevant alternatives condition (...) holds that a belief is warranted only if the evidence rules out relevant error possibilities. The safety condition helps categorise relevant from irrelevant possibilities. The sensitivity condition captures ‘ruling out’. Safety, sensitivity, and the relevant alternatives condition are typically presented as conditions on warranted belief or knowledge. But these properties, once generalised, help characterise other epistemic phenomena, including warranted inference, legal verdicts, scientific claims, reaching conclusions, addressing questions, warranted assertion, and the epistemic force of corroborating evidence. We introduce and explain Mayo’s severe testing account of statistical inference. A hypothesis is severely tested to the extent it passes tests that probably would have found errors, were they present. We argue Mayo’s account is fruitfully understood using the resulting relevant alternatives framework. Recasting Mayo’s condition using the conceptual framework of contemporary epistemology helps forge fruitful connections between two research areas—philosophy of statistics and the analysis of knowledge—not currently in sufficient dialogue. The resulting union benefits both research areas. (shrink)

Jonathan Y. Tsou examines and defends positions on central issues in philosophy of psychiatry. The positions defended assume a naturalistic and realist perspective and are framed against skeptical perspectives on biological psychiatry. Issues addressed include the reality of mental disorders; mechanistic and disease explanations of abnormal behavior; definitions of mental disorder; natural and artificial kinds in psychiatry; biological essentialism and the projectability of psychiatric categories; looping effects and the stability of mental disorders; psychiatric classification; and the validity of the DSM's (...) diagnostic categories. The main argument defended by Tsou is that genuine mental disorders are biological kinds with harmful effects. This argument opposes the dogma that mental disorders are necessarily diseases that result from biological dysfunction. Tsou contends that the broader ideal of biological kinds offers a more promising and empirically ascertainable naturalistic standard for assessing the reality of mental disorders and the validity of psychiatric categories. (shrink)

The 2011 Nobel Prize in Physics was awarded to researchers from the Supernova Cosmology Project and the High-z Supernova Search Team for the discovery of the accelerating expansion of the universe. In this paper, I provide a historical analysis of the supernova cosmology evidence put forward by these teams for the accelerating universe, in terms of an iterative model of scientific progress developed by Hasok Chang in the context of his study of the development of measurement standards. I argue, using (...) the key concept of epistemic iteration, that the iterative model adequately accounts for evidence production in experimental science as well. In order to apply Chang’s model to the experimental evidence for the accelerating universe, I introduce the concept of endorsement as a particular mode of progress, and argue that supernova scientists produced an endorsed measurement system to claim evidence for their discovery. Furthermore, I show that the credibility of the evidence was not based on a particular measurement, rather, what proved to be decisive was the “robust consistency” of many individual results. (shrink)

Although scientific realism is the default position in the life sciences, philosophical accounts of realism are geared towards physics and run into trouble when applied to fields such as biology or neuroscience. In this paper, I formulate a new robustness-based version of entity realism, and show that it provides a plausible account of realism for the life sciences that is also continuous with scientific practice. It is based on the idea that if there are several independent ways of measuring, detecting (...) or deriving something, then we are justified in believing that it is real. I also consider several possible objections to robustness-based entity realism, discuss its relationship to ontic structural realism, and show how it has the potential to provide a novel response to the pessimistic induction argument. (shrink)

Philosophical investigation in synthetic biology has focused on the knowledge-seeking questions pursued, the kind of engineering techniques used, and on the ethical impact of the products produced. However, little work has been done to investigate the processes by which these epistemological, metaphysical, and ethical forms of inquiry arise in the course of synthetic biology research. An attempt at this work relying on a particular area of synthetic biology will be the aim of this chapter. I focus on the reengineering of (...) metabolic pathways through the manipulation and construction of small DNA-based devices and systems synthetic biology. Rather than focusing on the engineered products or ethical principles that result, I will investigate the processes by which these arise. As such, the attention will be directed to the activities of practitioners, their manipulation of tools, and the use they make of techniques to construct new metabolic devices. Using a science-in-practice approach, I investigate problems at the intersection of science, philosophy of science, and sociology of science. I consider how practitioners within this area of synthetic biology reconfigure biological understanding and ethical categories through active modelling and manipulation of known functional parts, biological pathways for use in the design of microbial machines to solve problems in medicine, technology, and the environment. We might describe this kind of problem-solving as relying on what Helen Longino referred to as “social cognition” or the type of scientific work done within what Hasok Chang calls “systems of practice”. My aim in this chapter will be to investigate the relationship that holds between systems of practice within metabolic engineering research and social cognition. I will attempt to show how knowledge and normative valuation are generated from this particular network of practitioners. In doing so, I suggest that the social nature of scientific inquiry is ineliminable to both knowledge acquisition and ethical evaluations. (shrink)

Experimental design is one aspect of a scientific method. A well-designed, properly conducted experiment aims to control variables in order to isolate and manipulate causal effects and thereby maximize internal validity, support causal inferences, and guarantee reliable results. Traditionally employed in the natural sciences, experimental design has become an important part of research in the social and behavioral sciences. Experimental methods are also endorsed as the most reliable guides to policy effectiveness. Through a discussion of some of the central concepts (...) associated with experimental design, including controlled variation and randomization, this chapter will provide a summary of key ethical issues that tend to arise in experimental contexts. In addition, by exploring assumptions about the nature of causation and by analyzing features of causal relationships, systems, and inferences in social contexts, this chapter will summarize the ways in which experimental design can undermine the integrity of not only social and behavioral research but policies implemented on the basis of such research. (shrink)

The life sciences are said to be in the midst of a replication crisis because a majority of published results are irreproducible, and scientists rarely replicate existing data. Here I argue that point 2 of this assessment is flawed because there is a hitherto unidentified form of replication in the experimental life sciences, which I call ‘microreplications’. Using a case study from biochemistry, I illustrate how MRs depend on a key element of experimentation, namely, experimental controls. I end by reflecting (...) on what MRs mean for the broader debate about the replication crisis. (shrink)

There are at least twelve major virtues of good theories: evidential accuracy, causal adequacy, explanatory depth, internal consistency, internal coherence, universal coherence, beauty, simplicity, unification, durability, fruitfulness, and applicability. These virtues are best classified into four classes: evidential, coherential, aesthetic, and diachronic. Each virtue class contains at least three virtues that sequentially follow a repeating pattern of progressive disclosure and expansion. Systematizing the theoretical virtues in this manner clarifies each virtue and suggests how they might have a coordinated and cumulative (...) role in theory formation and evaluation across the disciplines—with allowance for discipline specific modification. An informal and flexible logic of theory choice is in the making here. Evidential accuracy, according to my systematization, is not a largely isolated trait of good theories, as some have made it out to be. Rather, it bears multifaceted relationships, constituting significant epistemic entanglements, with other theoretical virtues. (shrink)

Archaeological data are shadowy in a number of senses. Not only are they notoriously fragmentary but the conceptual and technical scaffolding on which archaeologists rely to constitute these data as evidence can be as constraining as it is enabling. A recurrent theme in internal archaeological debate is that reliance on sedimented layers of interpretative scaffolding carries the risk that “preunderstandings” configure what archaeologists recognize and record as primary data, and how they interpret it as evidence. The selective and destructive nature (...) of data capture in archeology further suggests that there may be little scope for putting “legacy” data to work in new ways. And yet archaeologists have been strikingly successful in mining old datasets for new insights. I situate these concerns in the broader context of debate about the epistemic standing of the historical sciences, and then consider three strategies by which archaeologists address the challenges posed by legacy data. The first two – secondary retrieval and recontextualization – are a matter of reconfiguring the scaffolding that underpins evidential reasoning. The third turns on redeploying old data in the context of computational models that support the experimental simulation of the cultural systems and contexts under study. (shrink)

In psychiatry, pharmacological research has played a crucial role in the formulation, revision, and refinement of neurobiological theories of psychopathology. Besides being utilized as potential treatments for various mental disorders, pharmacological drugs play an important epistemic role as experimental instruments that help scientists uncover the neurobiological underpinnings of mental disorders (Tsou, 2012). Interventions with psychiatric patients using pharmacological drugs provide researchers with information about the neurobiological causes of mental disorders that cannot be obtained in other ways. This important source of (...) evidence for the biological causes of mental disorder is often overlooked in philosophical analyses of psychiatry, especially in skeptical analyses that debase the biological aspects of psychopathology (e.g., Szasz, 1960; Scheff, 1963; Laing, 1967). In discussing pharmacological interventions as a form of evidence for the physical basis of mental disorders, this paper aims to clarify the nature, reliability, and limitations of this evidence. In addition, it illustrates the central role that pharmacological findings in applied clinical contexts play in the acquisition of neurobiological knowledge in research contexts. (shrink)

The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...) libraries of standardized parts with known functions. In this paper, we investigate how the practice of synthetic biology reconfigures biological understanding of the key concepts of modularity and evolvability. We illustrate how this practice approach takes engineering knowledge and uses it to try to understand biological organization by showing how the construction of functional parts and processes can be used in synthetic experimental evolution. We introduce a new approach within synthetic biology that uses the premise of a parts-based ontology together with that of organismal self-organization to optimize orthogonal metabolic pathways in E. coli. We then use this and other examples to help characterize semisynthetic categories of modularity, parthood, and evolvability within the discipline. (shrink)

Robustness is often presented as a guideline for distinguishing the true or real from mere appearances or artifacts. Most of recent discussions of robustness have focused on the kind of derivational robustness analysis introduced by Levins, while the related but distinct idea of robustness as multiple accessibility, defended by Wimsatt, has received less attention. In this paper, I argue that the latter kind of robustness, when properly understood, can provide justification for ontological commitments. The idea is that we are justified (...) in believing that things studied by science are real insofar as we have robust evidence for them. I develop and analyze this idea in detail, and based on concrete examples show that it plays an important role in science. Finally, I demonstrate how robustness can be used to clarify the debate on scientific realism and to formulate new arguments. (shrink)

“Proof of concept” is a phrase frequently used in descriptions of research sought in program announcements, in experimental studies, and in the marketing of new technologies. It is often coupled with either a short definition or none at all, its meaning assumed to be fully understood. This is problematic. As a phrase with potential implications for research and technology, its assumed meaning requires some analysis to avoid it becoming a descriptive category that refers to all things scientifically exciting. I provide (...) a short analysis of proof of concept research and offer an example of it within synthetic biology. I suggest that not only are there activities that circumscribe new epistemological categories but there are also associated normative ethical categories or principles linked to the research. I examine these and provide an outline for an alternative ethical account to describe these activities that I refer to as “extended agency ethics”. This view is used to explain how the type of research described as proof of concept also provides an attendant proof of principle that is the result of decision-making that extends across practitioners, their tools, techniques, and the problem solving activities of other research groups. (shrink)

In recent decades many sociologists and philosophers of science, especially the so-called ‘new experimentalists’, have stressed the need for detailed studies of real, ongoing experimental practices, and have claimed that a new image of science results from such an approach. Among the new objects of interest that have emerged from laboratory studies, an important one is the tacit dimension of scientific practices. Harry Collins, in particular, has insisted that irreducibly tacit presuppositions and skills are inevitably involved in experimental practices, and (...) that these tacit resources play an essential role in the stabilization of successful scientific achievements. What I will call the ‘opacity of experimental practices’ has been analyzed in different ways, but on the whole, it has been claimed to have harmful epistemological consequences with respect to crucial issues such as the nature of experimental facts, scientific realism, scientific rationality, and the contingency of what acquires the status of an established scientific result in practitioners’ eyes. Such claims remain highly controversial. The aim of this paper is to discuss the epistemological implications of the involvement of tacit resources in experimental practices and to provide helpful conceptual tools with respect to the issue of tacit resources in science. Specifically, the paper provides an analytical clarification of the relation between the opacity of experimental practices and the principle of experimenters substitutability, the latter being a principle commonly viewed as a necessary feature of any good science. Serious doubts are finally raised about the validity of the experimenters substitutability principle, and the impact of these doubts with respect to the contingency of scientific facts and results is considered. (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)

Reports from integrative researchers who have followed calls for sociotechnical integration emphasize that the potential of interdisciplinary collaboration to inflect the social shaping of technoscience is often constrained by their liminal position. Integrative researchers tend to be positioned as either adversarial outsiders or co-opted insiders. In an attempt to navigate these dynamics, we show that attending to affective disturbances can open up possibilities for productive engagements across disciplinary divides. Drawing on the work of Helen Verran, we analyze “disconcertment” in three (...) sociotechnical integration research studies. We develop a heuristic that weaves together disconcertment, affective labor, and responsivity to analyze the role of the body in interdisciplinary collaborations. We draw out how bodies do affective labor when generating responsivity between collaborators in moments of disconcertment. Responsive bodies can function as sensors, sources, and processors of disconcerting experiences of difference. We further show how attending to disconcertment can stimulate methodological choices to recognize, amplify, or minimize the difference between collaborators. Although these choices are context-dependent, each one examined generates responsivity that supports collaborators to readjust the technical in terms of the social. This analysis contributes to science and technology studies scholarship on the role of affect in successes and failures of interdisciplinary collaboration. (shrink)

In this paper we examine the epistemic value of highly idealized agent-based models of social aspects of scientific inquiry. On the one hand, we argue that taking the results of such simulations as informative of actual scientific inquiry is unwarranted, at least for the class of models proposed in recent literature. Moreover, we argue that a weaker approach, which takes these models as providing only “how-possibly” explanations, does not help to improve their epistemic value. On the other hand, we suggest (...) that if ABMs of science underwent two types of robustness analysis, they could indeed have a clear epistemic function, namely by providing evidence for philosophical and historical hypotheses. In this sense, ABMs can obtain evidential and explanatory properties and thus be a useful tool for integrated history and philosophy of science. We illustrate our point with an example of a model—building on the work by Kevin Zollman—which we apply to a concrete historical case study. (shrink)

The French physicist Jean Baptiste Perrin is widely credited with providing the conclusive argument for atomism. The most well-known part of Perrin’s argument is his description of thirteen different procedures for determining Avogadro’s number (N)–the number of atoms, ions, and molecules contained in a gram-atom, gram-ion, and gram-mole of a substance, respectively. Because of its success in ending the atomism debates Perrin’s argument has been the focus of much philosophical interest. The various philosophers, however, have reached different conclusions, not only (...) about the argument’s general rationale but also the role that the multiple determination of N played in it. This paper emphasizes the historical development of Perrin’s experimental work in order to understand the role that the multiple determination of molecular magnitudes played in his argument for molecular reality. It claims that Perrin used the multiple determination strategy to put forward an exceptionally strong no-coincidence argument to argue for both the correctness of the values for the molecular magnitudes determined and the validity of the auxiliary assumptions upon which the different determinations were based. The historicist approach also allows the identification of the elements responsible for the epistemic strength of Perrin’s no-coincidence argument. (shrink)

The goal of this dissertation is to contribute to the epistemology of science by addressing a set of related questions arising from current discussions in the philosophy and science of climate change: (1) Given the imperfection of computer models, how do they provide information about large and complex target systems? (2) What is the relationship between consilient reasoning and robust evidential support in the production of scientific knowledge? (3) Does taking the mean of a set of model outputs provide epistemic (...) advantages over using the output of a single ‘best model’? Synthesizing research in philosophy and science, the thesis analyzes connections among consilient inductions, robustness analysis, and the aggregation of various sources of evidence, including computer simulations, by investigating case studies of climate change that exemplify the strength of consilient reasoning and the security of robust evidential support. It also explains the rationale and epistemic conditions for improving estimates by averaging multiple estimates, comparing a simple case of averaging estimates to practices in multi-model ensemble studies. I argue: (A) the concepts of consilience and robustness account for the strength and security of inferences that rely on imperfect computer modelling methods, (B) consilient reasoning is conducive to attaining robust evidential support, and (C) an analogy can explain why averaging the outputs of multiple models can improve estimates of a target system, given that conditions of model independence, skill and unequal weighting are taken into account. (shrink)

Discussions over whether these natural kinds exist, what is the nature of their existence, and whether natural kinds are themselves natural kinds aim to not only characterize the kinds of things that exist in the world, but also what can knowledge of these categories provide. Although philosophically critical, much of the past discussions of natural kinds have often answered these questions in a way that is unresponsive to, or has actively avoided, discussions of the empirical use of natural kinds and (...) what I dub “activities of natural kinding” and “natural kinding practices”. The natural kinds of a particular discipline are those entities, events, mechanisms, processes, relationships, and concepts that delimit investigation within it—but we might reasonably ask: How are these natural kinds discovered?, How are they made?, Are they revisable?, and Where do they come from? A turn to natural kinding practices reveals a new set of questions open for investigation: How do natural kinds explain through practice?, What are natural kinding practices and classifications and why should we care?, What is the nature of natural kinds viewed as a set of activities?, and How do practice approaches to natural kinds shape and reconfigure scientific disciplines? Natural kinds have traditionally been discussed in terms of how they classify the contents of the world. The metaphysical project has been one which identifies essences, laws, sameness relations, fundamental properties, and clusters of family resemblances and how these map out the ontological space of the world. But actually how this is done has been less important in the discussion than the resultant categories that are produced. I aim to rectify these omissions and suggest a new metaphysical project investigating kinds in practice. (shrink)