Philosophers have recently focused on critical, epistemological challenges that arise from the opacity of deep neural networks. One might conclude from this literature that doing good science with opaque models is exceptionally challenging, if not impossible. Yet, this is hard to square with the recent boom in optimism for AI in science alongside a flood of recent scientific breakthroughs driven by AI methods. In this paper, I argue that the disconnect between philosophical pessimism and scientific optimism is driven by a (...) failure to examine how AI is actually used in science. I show that, in order to understand the epistemic justification for AI-powered breakthroughs, philosophers must examine the role played by deep learning as part of a wider process of discovery. The philosophical distinction between the 'context of discovery' and the 'context of justification' is helpful in this regard. I demonstrate the importance of attending to this distinction with two cases drawn from the scientific literature, and show that epistemic opacity need not diminish AI's capacity to lead scientists to significant and justifiable breakthroughs. (shrink)

Abstract: Research on the nature and varieties of the format of cognitive representations in philosophy and cognitive science have been partly shaped by analogies to external, public representations. In this paper, we argue that relying on such analogies contributes to framing the question of cognitive formats in problematic, potentially counterproductive ways. We show that cognitive and public representations differ in many of their central features, making analogies to public representations ill-suited to improving our understanding of cognitive formats. We illustrate these (...) points by examining two case studies in which analogies to public representations may have had a negative impact on research: the 80’s-90’s debate about compositionality and cognitive architecture between symbolicists and connectionists; and contemporary discussions about the nature of visual demonstratives. Finally, we outline an alternative, computational account of formats that does not share the shortcomings of appeal to public representations. (shrink)

Novel computational representations, such as simulation models of complex systems and video games for scientific discovery, are dramatically changing the way discoveries emerge in science and engineering. The cognitive roles played by such computational representations in discovery are not well understood. We present a theoretical analysis of the cognitive roles such representations play, based on an ethnographic study of the building of computational models in a systems biology laboratory. Specifically, we focus on a case of model-building by an (...) engineer that led to a remarkable discovery in basic bioscience. Accounting for such discoveries requires a distributed cognition analysis, as DC focuses on the roles played by external representations in cognitive processes. However, DC analyses by and large have not examined scientific discovery, and they mostly focus on memory offloading, particularly how the use of existing external representations changes the nature of cognitive tasks. In contrast, we study discovery processes and argue that discoveries emerge from the processes of building the computational representation. The building process integrates manipulations in imagination and in the representation, creating a coupled cognitive system of model and modeler, where the model is incorporated into the modeler's imagination. This account extends DC significantly, and we present some of the theoretical and application implications of this extended account. (shrink)

In 1983, Dr. J. Robin Warren and Dr. Barry Marshall reported finding a new kind of bacteria in the stomachs of people with gastritis. Warren and Marshall were soon led to the hypothesis that peptic ulcers are generally caused, not by excess acidity or stress, but by a bacterial infection. Initially, this hypothesis was viewed as preposterous, and it is still somewhat controversial. In 1994, however, a U. S. National Institutes of Health Consensus Development Panel concluded that infection appears to (...) play an important contributory role in the pathogenesis of peptic ulcers, and recommended that antibiotics be used in their treatment. Peptic ulcers are common, affecting up to 10% of the population, and evidence has mounted that many ulcers can be cured by eradicating the bacteria responsible for them. (shrink)

Critiques of case studies as an epistemic genre usually focus on the domain of justification and hinge on comparisons with statistics and laboratory experiments. In this domain, case studies can be defended by the notion of “infirming”: they use many different bits of evidence, each of which may independently “infirm” the account. Yet their efficacy may be more powerful in the domain of discovery, in which these same different bits of evi- dence must be fully integrated to create an (...) explanatory account with internal validity. (shrink)

When philosophers discuss the possibility of machines making scientific discoveries, they typically focus on discoveries in physics, biology, chemistry and mathematics. Observing the rapid increase of computer-use in science, however, it becomes natural to ask whether there are any scientific domains out of reach for machine discovery. For example, could machines also make discoveries in qualitative social science? Is there something about humans that makes us uniquely suited to studying humans? Is there something about machines that would bar them (...) from such activity? A close look at the methodology of interpretive social science reveals several abilities necessary to make a social scientific discovery, and one capacity necessary to possess any of them is imagination. For machines to make discoveries in social science, therefore, they must possess imagination algorithms. (shrink)

The purpose of my paper is to challenge the binary classification of authenticity, which is currently employed in the bioethical debate on enhancement technologies. According to the standard dichotomy, there is a stark opposition between the self-discovery model, which depicts the self as a substantial and original inwardness, and the self-creation model, which assumes that the self is an open project, that has to be constituted by one’s free actions. My claim is that the so-called self-creation model actually conflates (...) two distinct versions of authenticity: one that is decisionist and one that is experimentalist. Hence, my proposal is to distinguish between three different models of authenticity: (i) self-discovery, which is an expressivist model of authenticity; (ii) existential commitment, which is a decisionist model; and (iii) reinvention of the self, which is an experimentalist model. Such a three-fold distinction will vast a more nuanced and clear light upon the enhancement debate. (shrink)

This study examines the tension between the academic evaluation system and the development of unconventional research agendas. While scholars have studied the evaluation of research that crosses disciplinary boundaries from the perspective of peer reviewers, they have paid comparatively little attention to the experiences of the performers of unconventional science. This study asks how researchers develop unconventional research agendas to address a long-standing health problem and, in the process, make sense of the actions of a site visit committee organized to (...) advise a foundation funding the project. This study develops a process narrative on the development of a specific transdisciplinary team proposing to study premature birth. The findings show that when the performers and the evaluators of unconventional science developed competing understandings of the research agenda, transdisciplinary discovery became limited as a particular research topic became taboo. Yet, the study also reveals how the performers of unconventional science challenged the power of the site visit committee by making it seem as though they followed the committee’s decisions. These findings raise questions about the role of private foundations as funders of academic research and the suitability of traditional evaluation procedures for assessing transdisciplinary discovery. (shrink)

Meier shows how the structure of Greek communal life gave individuals a civic role and discusses a crucial reform that institutionalized the idea of equality ...

Knowledge of residual perturbations in the orbit of Uranus in the early 1840s did not lead to the refutation of Newton's law of gravitation but instead to the discovery of Neptune in 1846. Karl Popper asserts that this case is atypical of science and that the law of gravitation was at least prima facie falsified by these perturbations. I argue that these assertions are the product of a false, a priori methodological position I call, 'Weak Popperian Falsificationism'. Further, on (...) the evidence the law was not prima facie false and was not generally considered so by astronomers at the time. Many of Popper's commentators presuppose WPF and their views on this case and its implications for scientific rationality and method suffer from this same defect. (shrink)

Jan G. Michel argues that we need a philosophy of scientific discovery. Before turning to the question of what such a philosophy might look like, he addresses two questions: Don’t we have a philosophy of scientific discovery yet? And do we need one at all? To answer the first question, he takes a closer look at history and finds that we have not had a systematic philosophy of scientific discovery worthy of the name for over 150 years. (...) To answer the second question, Michel puts forward three arguments that show the importance of a philosophy of scientific discovery. Briefly, he arrives at the following answers: No, we don’t yet have a philosophy of scientific discovery, and yes, we definitely need one. To remedy this shortcoming, Michel analyzes the concept of discovery, leading him to the insight that scientific discoveries have an underlying structure with certain structural features. Some of these features may be important but not indispensable to scientific discovery processes; these include eureka moments, serendipities, joint discoveries, special science funding, and others. In addition, Michel identifies three indispensable structural features which he examines in detail and which he places in a picture with a certain dynamics according to which the process of making scientific discoveries can be seen as a path, leading us from finding and acceptance to knowledge. (shrink)

This book offers the first full exploration of the religious, ethical, and social dimensions of Michael Polanyi's philosophy, and its implications for the crisis of modern culture.

There has recently been a growth in research that examines how corporations respond to allegations of unethical actions. Although scholars have gained much insight about the range of responses available to and used by organizations, there has been almost no study of why firms choose one response over another. In this article, the authors present a framework of likely organizational response choices to allegations of wrongdoing; we propose that response choices are based on the degree of reputational risk from stakeholder (...) withdrawal of support and on perceived threats to the firm’s primary or secondary identity. (shrink)

Historically there have been two main freewill problems, the problem of freedom versus predestination, which is mainly theological, and the problem of freedom versus determinism, which has exercised the minds of many of the great modern philosophers. The latter problem is seldom stated in full detail, for its elements are taken as so obvious that they do not need to be stated. The problem is seen as an attempt to reconcile the belief in human freedom, which is essential if men (...) are to be able to act morally, with determinism, the belief that every event is fully determined in all its details by the sum of its precedent causes. But even the meticulous Moore does not trouble to explore at length what is meant by determinism. He devotes one very short paragraph to the matter, and sums it up immediately afterwards as the view that ‘everything … has a cause’. (shrink)

Hans Reichenbach introduced two seemingly separate sets of distinctions in his epistemology at different times. One is between the axioms of coordination and the axioms of connections. The other distinction is between the context of discovery and the context of justification. The status and nature of each of these distinctions have been subject-matter of an ongoing debate among philosophers of science. Thus, there is a significant amount of works considering both distinctions separately. However, the relevance of Reichenbach's two distinctions (...) to each other does not seem to have enjoyed the same amount of interest so far. This is what I would like to consider in this paper. In other words, I am concerned with the question: what kind of relationship is there between his two distinctions, if there is any? (shrink)

Is there such a thing as a ‘Logic of Discovery’? Do we even have a consistent idea of such a thing? The approved answer to this seems to be “No.” Thus Popper argues “The initial stage, the act of conceiving or inventing a theory, seems to me neither to call for logical analysis nor to be susceptible of it.” Again, “… there is no such thing as a logical method of having new ideas, or a logical reconstruction of this (...) process.” Reichenbach writes that philosophy of science “… cannot be concerned with [reasons for suggesting hypotheses], but only with [reasons for accepting hypotheses].” Braithwaite elaborates: “The solution of these historical problems involves the individual psychology of thinking and the sociology of thought. None of these questions are our business here.”. (shrink)

This title is part of UC Press's Voices Revived program, which commemorates University of California Press's mission to seek out and cultivate the brightest minds and give them voice, reach, and impact. Drawing on a backlist dating to 1893, Voices Revived makes high-quality, peer-reviewed scholarship accessible once again using print-on-demand technology. This title was originally published in 1985.

Causal discovery becomes especially challenging when the possibility of latent confounding and/or selection bias is not assumed away. For this task, ancestral graph models are particularly useful in that they can represent the presence of latent confounding and selection effect, without explicitly invoking unobserved variables. Based on the machinery of ancestral graphs, there is a provably sound causal discovery algorithm, known as the FCI algorithm, that allows the possibility of latent confounders and selection bias. However, the orientation rules (...) used in the algorithm are not complete. In this paper, we provide additional orientation rules, augmented by which the FCI algorithm is shown to be complete, in the sense that it can, under standard assumptions, discover all aspects of the causal structure that are uniquely determined by facts of probabilistic dependence and independence. The result is useful for developing any causal discovery and reasoning system based on ancestral graph models. (shrink)

Proteolysis-targeting chimeric molecules represent an emerging technique that is receiving much attention for therapeutic intervention. The mechanism is based on the inhibition of protein function by hijacking a ubiquitin E3 ligase for protein degradation. The hetero-bifunctional PROTACs contain a ligand for recruiting an E3 ligase, a linker, and another ligand to bind with the protein targeted for degradation. Thus, PROTACs have profound potential to eliminate “undruggable” protein targets, such as transcription factors and non-enzymatic proteins, which are not limited to physiological (...) substrates of the ubiquitin-proteasome system. These findings indicate great prospects for PROTACs in the development of therapeutics. However, there are several limitations related to poor stability, biodistribution, and penetrability in vivo. This review provides an overview of the main PROTAC-based approaches that have been developed and discusses the promising opportunities and considerations for the application of this technology in therapies and drug discovery. The hetero-bifunctional PROTAC molecules contain a ligand for recruiting an E3 ligase linked with a ligand to bind with the protein targeted for degradation. Thus, PROTACs have profound potential to eliminate “undruggable” disease-causing proteins, which are not limited to physiological substrates of the ubiquitin-protease system, suggesting great prospects for therapeutic development. (shrink)

ABSTRACTThe distinction between ‘context of discovery’ and ‘context of justification’ in philosophy of science appears simple at first but contains interesting complexities. Paul Hoyningen-Huene has catalogued some of these complexities and suggested that the core usefulness of the ‘context distinction’ is in distinguishing between descriptive and normative perspectives. Here, I expand on Hoyningen-Huene’s project by tracing the label ‘context of discovery and context of justification’ to its origin. I argue that, contrary to initial appearances, Hans Reichenbach’s initial context (...) distinction from 1938 does not easily map onto Hoyningen-Huene’s distinction between descriptive and normative perspectives on science. However, this is not a reason to reject Hoyningen-Huene’s simplified context distinction, nor do I recommend returning to Reichenbach’s initial proposal. It is, however, further reason to believe that the context distinction does not have a single, easily understood meaning. Along the way, I revisit Reichenbach’s version of ‘rational reconstruction’ and highlight its usefulness as a tool for philosophy in general. (shrink)

The sum of all objects of a science, the objects’ features and their mutual relations compose the reality described by that sense. The reality described by mathematics consists of objects such as sets, functions, algebraic structures, etc. Generally speaking, the use of terms reality and existence, in relation to describing various objects’ characteristics, usually implies an employment of physical and perceptible attributes. This is not the case in mathematics. Its reality and the existence of its objects, leaving aside its application, (...) are completely virtual and yet clearly organized. This organization can be recognized in the creation of axioms or in the arrival at new theorems and definitions. It results either from a formalization of an intuitive idea or from a combinatorics that has not been guided by intuition. In all four possible cases—therefore, also in the two in which there is no intuitive “lead”, we can plausibly talk about a discovery of mathematical facts and thus support the Platonist view. (shrink)

What if someone asked you to keep a four-kilometer-long ruler absolutely still so that you could measure deformations of length of ~1x10^-18m using light? On September 14, 2015, physicists and engineers at the Laser Interferometer Gravitational-Wave Observatory (LIGO) accomplished this absurd feat when they first detected gravitational wave signals—the result of the most violent events in our universe, such as the collision of two black holes—using two immense L-shaped instruments with arms four-kilometers in length and placed in what seemed to (...) be the middle of nowhere. -/- The focus of this dissertation centers on how scientists must have an intricate understanding of the environment surrounding LIGO’s instruments to understand the vast and active universe through the detection of gravitational waves. I explore how LIGO physicists and engineers constructed stillness to distinguish the surrounding natural and built environment from gravitational wave signals. I explore how the pre-LIGO and LIGO laboratory spaces became an expanded laboratory extending as an overlay into the surrounding environment and beyond. I show that the metes and bounds of the expanded laboratory are defined by what the interferometers are sensitive to. I further explore how physicists, engineers, and data scientists theorized an experiment that required such an extreme sensitivity (i.e., imagining stillness), developed methods to investigate, understand, and abate noise, disturbances, and aberrations (i.e., engineering stillness), found sites with minimal noise profiles, both physical and social, that would accommodate the size and function of the instruments despite land uses in conflict with the experiment (i.e., finding stillness), and understood the overlapping human and non-human uses of the land that jeopardized the ability to make these highly precise detections and mediate solutions that would allow for concurrent use of the land (i.e., negotiating stillness). -/- Through this history, I conclude that the level of sensitivity the physicists and engineers can attain in the LIGO interferometers is predicated on constructed stillness. This determines the instruments’ ability to measure the minute deformations in length caused by gravitational waves such that the physicists, engineers, and data scientists can rule out the geography of noise and make the claim that the heterogeneity of their locations at Hanford and Livingston does not negate their assertion of twin detections of gravitational wave signals across their two sites. (shrink)

With his distinction between the "context of discovery" and the "context of justification", Hans Reichenbach gave the traditional difference between genesis and validity a modern standard formulation. Reichenbach's distinction is one of the well-known ways in which the expression "context" is used in the theory of science. My argument is that Reichenbach's concept is unsuitable and leads to contradictions in the semantic fields of genesis and validity. I would like to demonstrate this by examining the different meanings of Reichenbach's (...) context distinction. My investigation also shows how the difference between genesis and validity precedes Reichenbach's context distinction and indicates approaches for meaningful applications of the concept of context to the phenomena designated by Reichenbach. I will begin by reconstructing the way in which Reichenbach introduces the distinction between discovery and justification as a difference of contexts (I). Drawing on the numerous meanings of the term "context", I will then emphasize some chief characteristics and review, through exemplification, the usage of this term. First of all, I turn to the context of discovery as the nonrational part of all scientific knowledge and show that this meaning cannot be defined consistently (la). For the context of justification, one can distinguish two main cases: the context of justification is either contrasted with the context of discovery, or it forms a unit there with. In the first case, the use of the context term becomes paradoxical, insofar as justification separated from scientific practice does not represent a field of reference which could be specifically contrasted with another field of reference (I b). In the second case, the unifying definitions contradict the contextual meaning of discovery and justification (1 c). In the last section, I point to a useful application of the concept of context which can be found in Reichenbach's argumentation and which refers to the practical conditions of justification(2). (shrink)

In this paper I discuss Mark Steiner’s view of the contribution of mathematics to physics and take up some of the questions it raises. In particular, I take up the question of discovery and explore two aspects of this question – a metaphysical aspect and a related epistemic aspect. The metaphysical aspect concerns the formal structure of the physical world. Does the physical world have mathematical or formal features or constituents, and what is the nature of these constituents? The (...) related epistemic question concerns humans’ cognitive ability to reach the formal structure of the physical world. Among other things, I explore the interaction of mathematical and non-mathematical cognition in physical discovery. (shrink)

A number of authors, including me, have argued that the output of our most complex climate models, that is, of global climate models and Earth system models, should be assessed possibilistically. Worries about the viability of doing so have also been expressed. I examine the assessment of the output of relatively simple climate models in the context of discovery and point out that this assessment is of epistemic possibilities. At the same time, I show that the concept of epistemic (...) possibility used in the relevant studies does not fit available analyses of this concept. Moreover, I provide an alternative analysis that does fit the studies and broad climate modelling practices as well as meshes with my existing view that climate model assessment should typically be of real possibilities. On my analysis, to assert that a proposition is epistemically possible is to assert that it is not known to be false and is consistent with at least approximate knowledge of the basic way things are. I, finally, consider some of the implications of my discussion for available possibilistic views of climate model assessment and for worries about such views. I conclude that my view helps to address worries about such assessment and permits using the full range of climate models in it. (shrink)

Philosophical analyses of scientific methodology have long understood intuition to be incompatible with a rule based reasoning that is often considered necessary for a rational scientific method. This paper seeks to challenge this contention by highlighting the indispensable role that intuition plays in the application of methodologies for scientific discovery. In particular, it seeks to outline a positive role for intuition and personal judgment in scientific discovery by exploring a comparison between the use of heuristic reasoning in scientific (...) practice and engineering design. While these discussions share many features, it will also be shown that the successful use of heuristics in engineering design is often considered to depend on a crucial factor that is markedly absent from accounts of the use of heuristics in scientific discovery; experienced judgment. In the final sections of this paper, I will compare attitudes to the role of computer analysis in scientific and engineering practices, with the aim of showing how the limitations of scientific discovery machines reveal the need for including intuition in philosophical accounts of heuristic reasoning in scientific discovery. (shrink)

BackgroundIdentifying biomarkers for autism can improve outcomes for those affected by autism. Engaging the diverse stakeholders in the research process using community-based participatory research can accelerate biomarker discovery into clinical applications. However, there are limited examples of stakeholder involvement in autism research, possibly due to conceptual and practical concerns. We evaluate the applicability of CBPR principles to biomarker discovery in autism and critically review empirical studies adopting these principles.MethodsUsing a scoping review methodology, we identified and evaluated seven studies (...) using CBPR principles in biomarker discovery.Results and conclusionsThe limited number of studies in biomarker discovery adopting CBPR principles coupled with their methodological limitations suggests that such applications are feasible but challenging. These studies illustrate three CBPR themes: community assessment, setting global priorities, and collaboration in research design. We propose that further research using participatory principles would be useful in accelerating the pace of discovery and the development of clinically meaningful biomarkers. For this goal to be successful we advocate for increased attention to previously identified conceptual and methodological challenges to participatory approaches in health research, including improving scientific rigor and developing long-term partnerships among stakeholders. (shrink)

In his influential paper, 'Why Was the Logic of Discovery Abandoned?', Laudan contends that there has been no philosophical rationale for a logic of discovery since the emergence of consequentialism in the 19th century. It is the purpose of this paper to show that consequentialism does not involve the rejection of all types of logic of discovery. Laudan goes too far in his interpretation of the historical shift from generativism to consequentialism, and his claim that the context (...) of pursuit belongs to neither discovery nor justification is based on narrow interpretations of the contexts of discovery and justification. As a result, Laudan draws unwarranted conclusions concerning both the early and contemporary defenders of a logic of discovery. A methodological logic of discovery - which involves self-corrective methods of hypothesis generation that promote the long-term goals of science and which require consequential support for justification - is a type of logic of discovery that survives the shift to consequentialism. (shrink)