Experimentation in Science

I praise Franklin's full descriptions of important and exemplary experiments, and wish that he had said more about why they are exemplary.

Experiments are actions, performed in order to gain information. Like other acts, there are virtues of performing them well. I discuss one virtue of experimentation, that of knowing how to trade its information-gaining potential against other goods.

This is a work in the epistemology of functional neuroimaging (fNI) and it applies the error-statistical (ES) philosophy to inferential problems in fNI to formulate and address these problems. This gives us a clear, accurate, and more complete understanding of what we can learn from fNI and how we can learn it. I review the works in the epistemology of fNI which I group into two categories; the first category consists of discussions of the theoretical significance of fNI findings and (...) the second category discusses methodological difficulties of fNI. Both types of works have shortcomings; the first category has been too theory-centered in its approach and the second category has implicitly or explicitly adopted the assumption that methodological difficulties of fNI cannot be satisfactorily addressed. In this dissertation, I address these shortcomings and show how and what kind of experimental knowledge fNI can reliably produce which would be theoretically significant. I take fMRI as a representative fNI procedure and discuss the history of its development. Two independent trajectories of research in physics and physiology eventually converge to give rise to fMRI. Thus, fMRI findings are laden in the theories of physics and physiology and I propose how this creates a kind of useful theory-ladenness which allows for the representation of and intervention in the constructs of cognitive neuroscience. Duhemian challenges and problems of underdetermination are often raised to argue that fNI is of little, if any, epistemic value for psychology. I show how the ES notions of severe tests and error probabilities can be applied in epistemological analyses of fMRI. The result is that hemodynamic hypotheses can be severely tested in fMRI experiments and I demonstrate how these hypotheses are theoretically significant and fuel the growth of experimental knowledge in cognitive neuroscience. Throughout this dissertation, I put the emphasis on the experimental knowledge we obtain from fNI and argue that this is the fruitful approach that enables us to see how fNI can contribute to psychology. In doing so, I offer an error-statistical epistemology of fNI, which hopefully will be a significant contribution to the philosophy of psychology. (shrink)

This paper examines the experiment in macroeconometrics, the different forms it has taken and the rules that have been proposed for its proper conduct. Here an ?experiment? means putting a question to a model and getting an answer. Different types of experiment are distinguished and the justification that can be provided for a particular choice of experiment is discussed. Three types of macroeconometric modelling are considered: the Cowles (system of equations) approach, the vector autoregressive model approach and the computational experiment. (...) JEL Classifications: B41, C5, E37. (shrink)

Abstract During the Copernican revolution the supporters of the Ptolemaic theory argued that the tower experiment refuted the Copernican hypothesis of the (diurnal) motion of the earth, but was in agreement with the Ptolemaic theory. In his defence of the Copernican theory Galileo argued that the experiment was in agreement both with Copernican and Ptolemaic theory. The reason for these different views of the same experiment was not that the two theories were incommensurable, as Paul Feyerabend argues, but that Galileo (...) introduced a new theory of motion which he used as an auxiliary hypothesis in his discussion of the tower experiment, while those defending the Ptolemaic theory used the old Aristotelian theory of motion. Already before the Copernican revolution the Aristotelian theory of motion was criticized by philosophers in Paris, who suggested the impetus theory of motion. The later versions of this theory had the consequence that the tower experiment no longer refuted the hypothesis of the (diurnal) motion of the earth. Thus the impetus theory removed an old and important objection to the heliocentric theory. Galileo's inertial dynamics had the same function in the discussion of the tower experiment. (shrink)

In this paper I investigate the prospects of integrated history and philosophy of science, by examining how philosophical issues concerning experimental practice and scientific realism can enrich the historical investigation of the careers of "hidden entities", entities that are not accessible to unmediated observation. Conversely, I suggest that the history of those entities has important lessons to teach to the philosophy of science. My overall aim is to illustrate the possibility of a fruitful two-way traffic between history and philosophy of (...) science. (shrink)

This paper provides an account of the experimental conditions required for establishing whether correlating or causally relevant factors are constitutive components of a mechanism connecting input (start) and output (finish) conditions. I argue that two-variable experiments, where both the initial conditions and a component postulated by the mechanism are simultaneously manipulated on an independent basis, are usually required in order to differentiate between correlating or causally relevant factors and constitutively relevant ones. Based on a typical research project molecular biology, a (...) flowchart model detailing typical stages in the formulation and testing of hypotheses about mechanistic components is also developed. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl. (shrink)

Im Herbst des Jahres 20– breiten sich Gerüchte aus, dass am Genfer Kernforschungszentrum CERN, den gegenteiligen Versicherungen führender Teilchenphysiker zum Trotz, stabile schwarze Löcher erzeugt wurden. Daraufhin kommt es vielerorts zu Plünderungen. Auch vermelden zahlreiche Firmen und öffentliche Arbeitgeber, dass ein erheblicher Anteil der Belegschaft nicht am Arbeitsplatz erschienen ist. Rund um den Globus fragen sich Menschen ob der Hiobsbotschaften aus Genf: Steht nun der Weltuntergang tatsächlich kurz bevor? In der Sendung „Kontrovers“ im Deutschlandfunk diskutieren ein Teilchenphysiker, eine Juristin, ein (...) Wissenschaftsjournalist und ein Philosoph diese Ereignisse. Wir freuen uns, hier einen Mitschnitt der Sendung vorab veröffentlichen zu können. (shrink)

In contrast to the common notion of experiments as a means for testing theories, Science Studies currently emphasize the explorative character of experiments, thus elevating their systematic epistemological relevance. Consequently the experiment has become another challenge to Reichenbach′s distinction between discovery and justification, which has been valid in the philosophy of science for several decades. Repeatedly the experiment has served as an epistemological paradigm in philosophy. Engaging with recent positions in Science Studies the paper investigates Kant′s understanding of the use, (...) meaning, and function of the experiment, focusing on its specifications with the catch words touchstone and the art of attempt. The historical and systematic approach shows to what extent the experiment is situated between freedom and coercion. (shrink)

By analysing the historical case of the proportionality between inertia and gravitation, it is possible to reconstruct one of the most relevant moments in the history of physics, that is to say, the one linked with Eötvös' experiments. At the same time, this reconstruction offers the opportunity to carry out philosophical considerations about the relationship between theory and experiment and about the concept of incommensurability.

Hypocretin regulates brain reward function and cocaine consumption in rats. The hypocretinergic (Hcrt) system is implicated in energy homeostasis, feeding and sleep regulation. Hypocretinergic cell bodies are located in the lateral hypothalamus (LH) and project throughout the brain. The aim of the present studies was to investigate the role of the Hcrt system in regulating brain reward function and the reinforcing properties of cocaine in rats. Intracranial self-stimulation (ICSS) thresholds provide an accurate measure of brain reward function in rats. Here (...) we show that a single injection of Hcrt-1 (5 µg icv) induced persistent, long-lasting elevations in ICSS thresholds in drug-naïve rats. Indeed, Hrct-1 elevated ICSS thresholds for 36 h, with peak elevations between 6 and 12 hours after injection. Hrct-1-induced threshold elevations were attenuated by an antibody known to neutralize the binding of hcrt-1 to its receptors. Taken together, these observations suggest that Hrct-1 negatively regulates brain reward function in rats. Because Hrct-1 negatively regulates brain reward function, we hypothesized that it may attenuate the increased brain reward function usually observed after cocaine consumption, and thereby alter cocaine self-administration behavior. A daily injection of Hrct-1 (1 µg icv), for 4 consecutive days, slightly increased cocaine self-administration (0.25 mg/infusion) in rats. Overall, these data demonstrate that Hrct-1 negatively regulates brain reward function, and as such may indirectly alter cocaine self-administration. Given the well-established role of hypocretin neurons in regulating feeding behavior and sleep, we hypothesize that hypocretinergic regulation of brain reward function may provide a mechanism by which appropriate and competing behaviors (e.g. sleep or feeding) may be engaged to maintain energy homeostasis. (shrink)

In the first part of this paper, I will sketch the main features of traditional models of evidence, indicating idealizations in such models that I regard as doing more harm than good. I will then proceed to elaborate on an alternative model of evidence that is functionalist, complex, dynamic, and contextual, which I will call DYNAMIC EVIDENTIAL FUNCTIONALISM. I will demonstrate its application to an illuminating example of scientific inquiry, and defend it from some likely objections. In the second part, (...) I will use that alternative to solve a variety of classic and contemporary problems in the literature on scientific evidence having to do with the empirical basis of science and the use of evidence in public policy. (shrink)

This article sketches the main features of traditional philosophical models of evidence, indicating idealizations in such models that it regards as doing more harm than good. It then proceeds to elaborate on an alternative model of evidence that is functionalist, complex, dynamic, and contextual, a view the author calls dynamic evidential functionalism (DEF). This alternative builds on insights from philosophy of scientific practice, Kuhnian philosophy of science, pragmatist epistemology, philosophy of experimentation, and functionalist philosophy of mind. Along the way, the (...) article raises concerns about the total evidence condition, requirements of certainty or incorrigibility on evidence, and accounts that restrict the type of things that can serve as evidence (to, for example, sense data, facts about particulars). DEF can also help us see the special value of novel predictions and experiments as evidence, as well as help us think about how to critically evaluate the putative evidence to determine whether it is evidence. (shrink)

In recent years, pragmatism in general and John Dewey in particular have been of increasing interest to philosophers of science. Dewey's work provides an interesting alternative package of views to those which derive from the logical empiricists and their critics, on problems of both traditional and more recent vintage. Dewey's work ought to be of special interest to recent philosophers of science committed to the program of analyzing ``science in practice.'' The core of Dewey's philosophy of science is his theory (...) of inquiry---what he called ``logic.'' There is a major lacuna in the literature on this point, however: no contemporary philosophers of science have engaged with Dewey's logical theory, and scholars of Dewey's logic have rarely made connections with philosophy of science. This paper aims to fill this gap, to correct some significant errors in the interpretation of key ideas in Dewey's logical theory, and to show how Dewey's logic provides resources for a philosophy of science. (shrink)

I resolve several pressing and recalcitrant problems in contemporary philosophy of science using resources from John Dewey's philosophy of science. I begin by looking at Dewey's epistemological and logical writings in their historical context, in order to understand better how Dewey's philosophy disappeared from the limelight, and I provide a reconstruction of his views. Then, I use that reconstruction to address problems of evidence, the social dimensions of science, and pluralism. Generally, mainstream philosophers of science with an interest in Dewey (...) pay little attention to the body of scholarship on Dewey and tend to misinterpret or miss important features of his work, while Dewey scholars generally do not connect his work to the nuanced problems of the contemporary scene (with some notable exceptions). My dissertation helps to fill this important gap and correct common interpretive mistakes by reconstructing and clarifying Dewey's philosophy of science and using it to resolve several contemporary problems. Though his is the road less traveled, Dewey's views provide a good starting place for addressing current concerns. He worked towards a model of science that is both fully naturalistic and fundamentally oriented towards human practice, demands that have been strongly argued for but poorly assimilated by most mainstream philosophers of science. He treats scientific practice, and human thinking generally, as not only embodied but also socially and technologically embedded, and thus can be used to open up a dialogue with much of the social studies of science. He has an anti- foundationalist but structured epistemology, and he offers a way to navigate the narrow paths between an immodest and simplistic realism and the pessimistic extremes of anti-realism and social constructivism, a pursuit of interest to many major philosophers of science at present. Philosophy of science took a different path in the twentieth century, beginning with the "received view'' of logical positivism that left many of the nuances of the original movement by the wayside. No aspect of that starting point has avoided disrepute in recent decades. I show that Dewey avoided the wrong turns of mid- century philosophy of science which are now blocking the way forward. (shrink)

On the relation between experiment and thought experiment in the natural sciences. To understand the reciprocal autonomy and complementarity of thought and real experiment, it is necessary to distinguish between a ‘positive’ (empirical or formal) and a transcendental perspective. Empirically and formally, real and thought experiments are indistinguishable. However, from a reflexive-transcendental viewpoint thought experiment is at the same time irreducible and complementary to real experiment. This is due to the fact that the hypothetical-anticipatory moment is in principle irreducible to (...) physical reality—even though it refers to physical reality and is bound with the empirical use of our understanding. The presence of counterfactuals is the condition of the possibility for thought experiments to become in principle real ones, by means of a series of technical realisations that gradually approximate the idealisations that they contain. (shrink)

The standard methodology for testing theories about syntax and semantics, which has been attacked both by philosophers and by sociolinguists, depends heavily on the personal introspection of the professionals. An improved data-collection methodology is proposed and an extended example of its application to a long-standing data dispute on a question of theoretical interest is given.

This paper addresses concerns raised recently by Datteri (Biol Philos 24:301–324, 2009) and Craver (Philos Sci 77(5):840–851, 2010) about the use of brain-extending prosthetics in experimental neuroscience. Since the operation of the implant induces plastic changes in neural circuits, it is reasonable to worry that operational knowledge of the hybrid system will not be an accurate basis for generalisation when modelling the unextended brain. I argue, however, that Datteri’s no-plasticity constraint unwittingly rules out numerous experimental paradigms in behavioural and systems (...) neuroscience which also elicit neural plasticity. Furthermore, I propose that Datteri and Craver’s arguments concerning the limitations of prosthetic modelling in basic neuroscience, as opposed to neuroengineering, rests on too narrow a view of the ways models in neuroscience should be evaluated, and that a more pluralist approach is needed. I distinguish organisational validity of models from mechanistic validity. I argue that while prosthetic models may be deficient in the latter of these explanatory virtues because of neuroplasticity, they excel in the former since organisational validity tracks the extent to which a model captures coding principles that are invariant with plasticity. Changing the brain, I conclude, is one viable route towards explaining the brain. (shrink)

Conference instructions for [2010] Philosophy of Scientific Experimentation: A Challenge to Philosophy of Science.

Traditionally, experimentation is considered a privileged means of confirmation. However, how experiments are a better confirmatory source than other strategies is unclear, and recent discussions have identified experiments with various modeling strategies on the one hand, and with ‘natural’ experiments on the other hand. We argue that experiments aiming to test theories are best understood as controlled investigations of specimens. ‘Control’ involves repeated, fine-grained causal manipulation of focal properties. This capacity generates rich knowledge of the object investigated. ‘Specimenhood’ involves possessing (...) relevant properties given the investigative target and the hypothesis in question. Specimens are thus representative members of the class which a hypothesis refers to. It is in virtue of both control and specimenhood that experiments provide powerful confirmatory evidence. This explains the distinctive power of experiments: although modelers exert extensive control, they do not exert this control over specimens; although natural experiments are of specimens, control is diminished. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

In a backward masking paradigm Epstein, Hatfield, and Muise (1977) found that presentation of a frontoparallel pattern mask caused the perceived shape of elliptical figures which were rotated in depth to conform to a projective shape function. The current study extended the masking function by examining the effect of a mask which was partially or wholly cotemporal with the target. The study also assessed the functional equivalence of the masking treatment and the conventional treatment for minimizing depth information. Reports of (...) perceived shape and perceived orientation were obtained under three conditions: binocular without mask, binocular with mask, monocular without mask. Under the first condition, perceived shape conformed to objective shape and perceived orientation was proportional to objective orientation. Under the latter two conditions, perceived shape was in very close agreement to projective shape and the two functions did not differ. Orientation was underestimated greatly under both conditions. We concluded that the effect of the mask on perceived shape is mediated by its effect on encoding of orientation information, although an additional effect on the subsequent stage of shape-slant integration cannot be excluded. (shrink)

Twelve subjects provided shape and orientation judgments for a set of projectively equivalent, variously rotated rectangles under three viewing conditions—monoptic, dichoptic, and binocular—with and without the presence of a pattern mask. In the absence of the mask, partial constancy was exhibited under the first two conditions and near perfect constancy under the binocular condition. Orientation was discriminated. Presence of the mask produced projective shape matching and diminished orientation discrimination. It is argued that the site of masking was postchiasmal, and the (...) results are related to previous work with pattern masking of projectively equivalent ellipses. (shrink)

On 30 April, 1897, J. J. Thomson announced the results of his previous four months' experiments on cathode rays. The rays, he suggested, were negatively charged subatomic particles. He called the particles ‘corpuscles’. They have since been re-named ‘electrons’ and Thomson has been hailed as their ‘discoverer’. Contrary to the accounts of most later writers, I show that this discovery was not the outcome of a concern with the nature of cathode rays which had occupied Thomson since 1881 and had (...) shaped the course of his experiments during the period 1881–1897. An examination of his work shows that he paid scant attention to cathode rays until late 1896. (shrink)

This paper argues that whereas philosophical discussions of first-person methods often turn on the veridicality of first-person reports, more attention should be paid to the experimental circumstances under which the reports are generated, and to the purposes of designing such experiments. After pointing to the ‘constructedness’ of first-person reports in the science of perception, I raise questions about the criteria by which to judge whether the reports illuminate something about the nature of perception. I illustrate this point with a historical (...) debate between Gestalt psychologist and atomists, both of whom used first-person methods to investigate perception. (shrink)

The last two decades have seen a rising interest in (a) the notion of a scientific phenomenon as distinct from theories and data, and (b) the intricacies of experimentally producing and stabilizing phenomena. This paper develops an analysis of the stabilization of phenomena that integrates two aspects that have largely been treated separately in the literature: one concerns the skills required for empirical work; the other concerns the strategies by which claims about phenomena are validated. I argue that in order (...) to make sense of the process of stabilization, we need to distinguish between two types of phenomena: phenomena as patterns in the data ( surface regularities ) and phenomena as underlying (or hidden ) regularities. I show that the epistemic relationships that data bear to each of these types of phenomena are different: Data patterns are instantiated by individual data, whereas underlying regularities are indicated by individual data, insofar as they instantiate a data pattern. Drawing on an example from memory research, I argue that neither of these two kinds of phenomenon can be stabilized in isolation. I conclude that what is stabilized when phenomena are stabilized is the fit between surface regularities and hidden regularities. (shrink)

The authors provide an overview of philosophical discussions about the roles of experiment in science. First, they cover two approaches that took shape under the heading of “new experimentalism” in the 1980s and 1990s. One approach was primarily concerned with questions about entity realism, robustness, and epistemological strategies. The other has focused on exploratory experiments and the dynamic processes of experimental research as such, highlighting its iterative nature and drawing out the ways in which such research is grounded in experimental (...) systems, concepts and operational definitions. Second, the authors look at more recent philosophical work on the epistemology of causal inference, in particular highlighting discussions in the philosophy of the behavioral and social sciences, concerning the extrapolation from laboratory contexts to the world. (shrink)