In this paper we will offer a few examples to illustrate the orientation of contemporary research in data analysis and we will investigate the corresponding role of mathematics. We argue that the modus operandi of data analysis is implicitly based on the belief that if we have collected enough and sufficiently diverse data, we will be able to answer most relevant questions concerning the phenomenon itself. This is a methodological paradigm strongly related, but not limited to, biology, and we label (...) it the microarray paradigm. In this new framework, mathematics provides powerful techniques and general ideas which generate new computational tools. But it is missing any explicit isomorphism between a mathematical structure and the phenomenon under consideration. This methodology used in data analysis suggests the possibility of forecasting and analyzing without a structured and general understanding. This is the perspective we propose to call agnostic science, and we argue that, rather than diminishing or flattening the role of mathematics in science, the lack of isomorphisms with phenomena liberates mathematics, paradoxically making more likely the practical use of some of its most sophisticated ideas. (shrink)

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

This article identifies conditions under which robust predictive modeling results have special epistemic significance---related to truth, confidence, and security---and considers whether those conditions hold in the context of present-day climate modeling. The findings are disappointing. When today’s climate models agree that an interesting hypothesis about future climate change is true, it cannot be inferred---via the arguments considered here anyway---that the hypothesis is likely to be true or that scientists’ confidence in the hypothesis should be significantly increased or that a claim (...) to have evidence for the hypothesis is now more secure. (shrink)

Van Fraassen argues that data provide the target-end structures required by structuralist accounts of scientific representation. But models represent phenomena not data. Van Fraassen agrees but argues that there is no pragmatic difference between taking a scientific model to accurately represent a physical system and accurately represent data extracted from it. In this article I reconstruct his argument and show that it turns on the false premise that the pragmatic content of acts of representation include doxastic commitments.

Though the concept of ‘stylized fact’ plays an important role in the economic literature, there is little analysis of the definition and evaluative use of the term. A permissive account of stylized facts is developed which focuses on their mediating role between models and empirical evidence. The mediation relationship restricts stylized facts by requiring concrete empirical targets. On the other hand, there is much legitimate diversity within the permissive account; key dimensions of diversity are argued to be the part of (...) the model targeted (explanans vs. explanandum) and degree of partiality of correspondence. The use of stylized fact in model evaluation points to the downside of stylization: decreased ability to support strong claims about particular targets. In the final analysis, the role of stylized facts in model-based explanation depends on the view taken of the relative importance of generality and empirical adequacy. (shrink)

I propose a framework that explicates and distinguishes the epistemic roles of data and models within empirical inquiry through consideration of their use in scientific practice. After arguing that Suppes’ characterization of data models falls short in this respect, I discuss a case of data processing within exploratory research in plant phenotyping and use it to highlight the difference between practices aimed to make data usable as evidence and practices aimed to use data to represent a specific phenomenon. I then (...) argue that whether a set of objects functions as data or models does not depend on intrinsic differences in their physical properties, level of abstraction or the degree of human intervention involved in generating them, but rather on their distinctive roles towards identifying and characterizing the targets of investigation. The paper thus proposes a characterization of data models that builds on Suppes’ attention to data practices, without however needing to posit a fixed hierarchy of data and models or a highly exclusionary definition of data models as statistical constructs. (shrink)

I propose a framework that explicates and distinguishes the epistemic roles of data and models within empirical inquiry through consideration of their use in scientific practice. After arguing that Suppes’ characterization of data models falls short in this respect, I discuss a case of data processing within exploratory research in plant phenotyping and use it to highlight the difference between practices aimed to make data usable as evidence and practices aimed to use data to represent a specific phenomenon. I then (...) argue that whether a set of objects functions as data or models does not depend on intrinsic differences in their physical properties, level of abstraction or the degree of human intervention involved in generating them, but rather on their distinctive roles towards identifying and characterizing the targets of investigation. The paper thus proposes a characterization of data models that builds on Suppes’ attention to data practices, without however needing to posit a fixed hierarchy of data and models or a highly exclusionary definition of data models as statistical constructs. (shrink)

According to the hierarchy of models account of scientific experimentation developed by Patrick Suppes and elaborated by Deborah Mayo, theoretical considerations about the phenomena of interest are involved in an experiment through theoretical models that in turn relate to experimental data through data models, via the linkage of experimental models. In this paper, I dispute the HoM account in the context of present-day high-energy physics experiments. I argue that even though the HoM account aims to characterize experimentation as a model-based (...) activity, it does not involve a modeling concept for the process of data acquisition, and it thus fails to provide a model-based characterization of the theory-experiment relationship underlying this process. In order to characterize the foregoing relationship, I propose the concept of a model of data acquisition and illustrate it in the case of the ATLAS experiment at CERN’s Large Hadron Collider, where the Higgs boson was discovered in 2012. I show that the process of data acquisition in the ATLAS experiment is performed according to a model of data acquisition that specifies and organizes the experimental procedures necessary to select the data according to a predetermined set of selection criteria. I also point out that this data acquisition model is theory-laden, in the sense that the underlying data selection criteria are determined by considering the testable predictions of the theoretical models that the ATLAS experiment is aimed to test. I take this sense of theory-ladenness to indicate that the relationship between the procedures of the ATLAS experiment and the theoretical models of the phenomena of interest is first established, prior to the formation of data models, through the data acquisition model of the experiment, thus not requiring the intermediary of other types of models as suggested by the HoM account. I therefore conclude that in the context of present-day HEP experiments, the HoM account does not consistently extend to the process of data acquisition so as to include models of data acquisition. (shrink)

Zkoumání je založeno na reflexi sémantického pojetí vědec- kých teorií Ronalda Giera. Gierova východiska a závěry jsou podrobeny kritice, na jejímž základě autor buduje svou vlastní variantu modelově založeného pojetí teorií. Hlavním cílem příspěvku je konceptualizace vztahu mezi principy a modely s důrazem na to, že tento vztah může zakládat dynamiku teorie, respektive posloupnosti teorií. Souhrnně bude v příspěvku prověřována řada tezí: 1) Základními prvky teorie jsou modely, které slouží jako nosiče principů. 2) Modely hrají rozhodující roli při pojmové výstavbě (...) teorie. 3) Modely artikulací principů odhalují poznatky, které ze samotných principů neplynou. 4) Principy mohou být někdy souhrnně definovány až poté, co existuje odpovídající množina modelů. 5) Nová teorie nastoupí ve chvíli, kdy je cluster nových modelů dostatečně komplexní a když si vědecké společenství ujasní, že tento nový cluster je založen na určité množině nových principů. (shrink)

The replication or reproducibility crisis in psychological science has renewed attention to philosophical aspects of its methodology. I provide herein a new, functional account of the role of replication in a scientific discipline: to undercut the underdetermination of scientific hypotheses from data, typically by hypotheses that connect data with phenomena. These include hypotheses that concern sampling error, experimental control, and operationalization. How a scientific hypothesis could be underdetermined in one of these ways depends on a scientific discipline’s epistemic goals, theoretical (...) development, material constraints, institutional context, and their interconnections. I illustrate how these apply to the case of psychological science. I then contrast this “bottom-up” account with “top-down” accounts, which assume that the role of replication in a particular science, such as psychology, must follow from a uniform role that it plays in science generally. Aside from avoiding unaddressed problems with top-down accounts, my bottom-up account also better explains the variability of importance of replication of various types across different scientific disciplines. (shrink)

Inductive reasoning aims at constructing rules and models of general applicability from a restricted set of observations. Induction is a keystone in natural sciences, and it influences diverse application fields such as engineering, medicine and economics. More generally, induction plays a major role in the way humans learn and operate in their everyday life. The level of reliability that a model achieves depends on how informative the observations are relative to the flexibility of the process by which the model is (...) constructed. When the process is articulated so that the model can incorporate descriptive details and subtleties, a large set of informative observations are required to reliably tune the model, whereas models obtained from simple procedures can be tuned with fewer observations. This article introduces the concept of “dominance”, which refers to the situation in which a reduced subset of observations suffices to reconstruct the model. A mathematical framework is presented to quantify the reliability of learning procedures as a function of the size of the subset of dominant observations. Although limited in scope, we believe that our study can contribute to the understanding of some fundamental mechanisms by which knowledge is generated from observations in inductive reasoning. (shrink)

We critically engage two traditional views of scientific data and outline a novel philosophical view that we call the pragmatic-representational view of data. On the PR view, data are representations that are the product of a process of inquiry, and they should be evaluated in terms of their adequacy or fitness for particular purposes. Some important implications of the PR view for data assessment, related to misrepresentation, context-sensitivity, and complementary use, are highlighted. The PR view provides insight into the common (...) but little-discussed practices of iteratively reusing and repurposing data, which result in many datasets’ having a phylogeny—an origin and complex evolutionary history—that is relevant to their evaluation and future use. We relate these insights to the open-data and data-rescue movements, and highlight several future avenues of research that build on the PR view of data. (shrink)

Deep neural networks have become increasingly successful in applications from biology to cosmology to social science. Trained DNNs, moreover, correspond to models that ideally allow the prediction of new phenomena. Building in part on the literature on ‘eXplainable AI’, I here argue that these models are instrumental in a sense that makes them non-explanatory, and that their automated generation is opaque in a unique way. This combination implies the possibility of an unprecedented gap between discovery and explanation: When unsupervised models (...) are successfully used in exploratory contexts, scientists face a whole new challenge in forming the concepts required for understanding underlying mechanisms. (shrink)

Many decades ago Patrick Suppes argued rather convincingly that theoretical hypotheses are not confronted with the direct, raw results of an experiment, rather, they are typically compared with models of data. What exactly is a data model however? And how do the interactions of particles at the subatomic scale give rise to the huge volumes of data that are then moulded into a polished data model? The aim of this paper is to answer these questions by presenting a detailed case (...) study of the construction of data models at the LHCb for testing Lepton Flavour Universality in rare decays of B-mesons. The close examination of the scientific practice at the LHCb leads to the following four main conclusions: raw data in their pure form are practically useless for the comparison of experimental results with theory, and processed data are in some cases epistemically more reliable, real and simulated data are involved in the co-production of the final data model and cannot be easily distinguished, theory-ladenness emerges at three different levels depending on the scope and the purpose for which background theory guides the overall experimental process and the overall process of acquiring and analysing data in high energy physics is too complicated to be fully captured by a generic methodological description of the experimental practice. (shrink)

Przedmowa Problematyka związana z zależnościami przyczynowymi, ich modelowaniem i odkrywa¬niem, po długiej nieobecności w filozofii i metodologii nauk, budzi współcześnie duże zainteresowanie. Wiąże się to przede wszystkim z dynamicznym rozwojem, zwłaszcza od lat 1990., technik obli¬czeniowych. Wypracowane w tym czasie sieci bayesowskie uznaje się za matematyczny język przyczynowości. Pozwalają one na daleko idącą auto¬matyzację wnioskowań, co jest także zachętą do podjęcia prób algorytmiza¬cji odkrywania przyczyn. Na potrzeby badań naukowych, które pozwalają na przeprowadzenie eksperymentu z randomizacją, standardowe metody ustalania zależności przyczynowych (...) opracowano na początku XX wieku. Zupełnie inaczej sprawa przedstawia się w przypadku badań nieeksperymentalnych, gdzie podobne rozwiązania pozostają kwestią przyszłości. Zadaniem tej książki jest podanie warunków, które powinny być spełnione przez te rozwiązania, oraz sformułowanie proceduralnego kryterium zależności przy¬czynowych jako szczegółowej realizacji tych warunków. Pociąga ono waż¬kie konsekwencje dla filozofii i metodologii nauk, które ujawnia – podany w Części II – zarys me-todolo¬gii proceduralnej. W literaturze przedmiotu brakuje w miarę wszechstronnego i systema¬tycznego omówie¬nia najnowszych filozoficznych i metodologicznych dys¬kusji na temat przy¬czynowości, co niech będzie wytłumaczeniem, dlaczego w niektórych punktach obecnej książki szczegółowo referuję trudno dos¬tępne teksty źró¬dłowe. Przymiotnik „proceduralny” używam tu w znaczeniu węższym niż Huw Price (w którego pracach właściwszy byłby termin „kryterialny”) dla podkre¬ślenia – zgodnie z łacińskim źródłosłowem procedo – że dla ustalenia przy¬czyny niezbędne jest podjęcie przez uczonych określonych interakcji z ba¬daną rzeczywistością. Zalążki zamysłu prezentowanego w tej książce przedstawiłem podczas warsztatów filozoficznych „Philosophy and Probability” w roku 2002, zor¬ganizowanych przez Instytut Filozofii Uniwersytetu w Konstancji. Wdzięczny jestem uczestnikom tych warsztatów za uwagi, a przede wszyst¬kim następującym osobom: Luc Bovens, Brandon Fitelson, Alan Hájek, Stephan Hartmann oraz Jon Williamson. Podczas międzynarodowej konferencji „Analytical Pragmatism”, zorgani¬zowanej w Lublinie w roku 2003 przez Wydział Filo¬zofii Katolickiego Uniwersytetu Lubelskiego, odniosłem swoją koncepcję do prac Nancy Cartwright. Szczególnie inspirujący okazał się komentarz Huw Price’a do mojego referatu i przeprowadzona z nim dysku¬sja. Ujęcie koncepcji metodologii proceduralnej na szerszym tle współ-czes¬nego nurtu empirystycznego w filozofii nauki przedstawiłem w roku 2004 podczas konferencji „5th Quadrennial Fellows Conference”, zorgani¬zowanej przez Instytut Filozofii Uniwersytetu Jagiellońskiego oraz Centrum Filozofii Nauki w Pittsburghu. Szczególnie pomocne w dalszych moich pra¬cach były uwagi Jamesa Bogena, Janet Kourany, Jamesa Lennoxa, Johna Nortona, Thomasa Bonka, Jana Woleńskiego i Johna Worralla, za które wyra¬żam swoją wdzięczność. Korpus książki powstał podczas mojego stażu w Centrum Filozofii Nauki w Pittsburghu, który odbyłem jako stypendysta Fundacji na Rzecz Nauki Polskiej w roku akademickim 2004-2005. Uczestniczyłem w tym czasie w życiu naukowym Centrum i w pracach badawczych zespołu z Instytutu Filozofii Uniwersytetu Carnegie-Mellon w Pittsburghu kierowanego przez Clarka Glymoura. Na jego ręce składam podziękowanie za wiele po¬mocnych uwag do moich wy¬stąpień oraz tekstów i za dyskusje przede wszystkim z nim samym i z jego najbliższymi współpracownikami: Peterem Spirtesem oraz Richardem Scheinesem, a także pozostałymi członkami tego zes¬połu, doktorantami i uczestnikami seminarium badawczego „Causality in the Social Sciences”. Za wieloletnie wsparcie, wielopłaszczyznowe inspiracje towarzyszące pi¬saniu tej książki, a także liczne pomocne uwagi do jej wcześniejszych wersji dziękuję przede wszystkim Księdzu Profesorowi Andrzejowi Bronkowi oraz Księdzu Profesorowi Józefowi Herbutowi, współprowadzącemu seminarium doktorskie w Katedrze Metodologii Nauk Katolickiego Uniwersytetu Lubel¬skiego im. Jana Pawła II, jak również pozostałym uczestnikom tego semina¬rium. Dziękuję mojej Żonie, dr Annie Kawalec za wiele wysiłku włożonego w ulepszenie redakcji – językowej i merytorycznej – obecnej książki. Książkę tę można czytać na kilka sposobów. Czytelnikom zainteresowa¬nym przede wszystkim prowadzeniem badań empirycznych polecałbym rozpoczęcie od Rozdziału 2. i kontynuację pozostałych rozdziałów Części I, a następnie Dodatków. Czytelnikom zainteresowanym problemami filozo¬fii i metodologii nauk polecałbym rozpoczęcie lektury książki od Części II i uzupełniającą lekturę Rozdziału 2., a następnie Wprowadzenia i Zakończenia. Czytelnikom mniej zainteresowanym zagadnieniami teoretycznymi pole¬całbym zapoznanie się z fascynującymi dziejami odkrycia przyczyn cholery przez Johna Snowa, które rekonstruuję w Rozdziale 1. W dalszej części nato¬miast polecałbym przejście do Wprowadzenia i Zakończenia, które w mniej specjalistyczny sposób przybliżają proponowane tu rozstrzygnięcia. Tekst książki nie był dotąd publikowany. Wyjątkiem są pewne fragmenty Rozdziału 8. oraz 9., które w zmienionej postaci ukazały się w Rocznikach Filozoficznych (Kawalec 2004). -/- Lublin, luty 2006 r. (shrink)

I show that Eric Winsberg’s principles of model-building given in Science in the Age of Computer Simulation are insufficient to argue for the external validation of simulation data in cases in which simulation results conflict, and that laboratory experiments have an advantage over simulations because conflicting experimental results can be decided between on the basis of reproducibility. I also argue that robustness of predictions serves the same function for simulations as repeatability does for laboratory experiments in either adjudicating between conflicting (...) results or allowing us to say that we do not have sufficient justification to validate the results. Finally, I argue for an interpretation of the argument from robustness that appeals to the convergence of many well-built and diverse models rather than the more common interpretation which appeals to the probability that one of a set of models is likely to be true. (shrink)

This chapter provides an introduction to the study of the philosophical notions of mechanisms and causality in biology and economics. This chapter sets the stage for this volume, Mechanism and Causality in Biology and Economics, in three ways. First, it gives a broad review of the recent changes and current state of the study of mechanisms and causality in the philosophy of science. Second, consistent with a recent trend in the philosophy of science to focus on scientific practices, it in (...) turn implies the importance of studying the scientific methods employed by researchers. Finally, by way of providing an overview of each chapter in the volume, this chapter demonstrates that biology and economics are two fertile fields for the philosophy of science and shows how biological and economic mechanisms and causality can be synthesized. (shrink)

Scientific models are important, if not the sole, units of science. This thesis addresses the following question: in virtue of what do scientific models represent their target systems? In Part i I motivate the question, and lay out some important desiderata that any successful answer must meet. This provides a novel conceptual framework in which to think about the question of scientific representation. I then argue against Callender and Cohen’s attempt to diffuse the question. In Part ii I investigate the (...) ideas that scientific models are ‘similar’, or structurally morphic, to their target systems. I argue that these approaches are misguided, and that at best these relationships concern the accuracy of a pre-existing representational relationship. I also pay particular attention to the sense in which target systems can be appropriately taken to exhibit a ‘structure’, and van Fraassen’s recent argument concerning the pragmatic equivalence between representing phenomena and data. My next target is the idea that models should not be seen as objects in their own right, but rather what look like descriptions of them are actually direct descriptions of target systems, albeit not ones that should be understood literally. I argue that these approaches fail to do justice to the practice of scientific modelling. Finally I turn to the idea that how models represent is grounded, in some sense, in their inferential capacity. I compare this approach to anti-representationalism in the philosophy of language and argue that analogous issues arise in the context of scientific representation. Part iii contains my positive proposal. I provide an account of scientific representation based on Goodman and Elgin’s notion of representation-as. The result is a highly conventional account which is the appropriate level of generality to capture all of its instances, whilst remaining informative about the notion. I illustrate it with reference to the Phillips-Newlyn machine, models of proteins, and the Lotka-Volterra model of predator-prey systems. These examples demonstrate how the account must be understood, and how it sheds light on our understanding of how models are used. I finally demonstrate how the account meets the desiderata laid out at the beginning of the thesis, and outline its implications for further questions from the philosophy of science; not limited to issues surrounding the applicability of mathematics, idealisation, and what it takes for a model to be ‘true’. (shrink)

Neuroimaging technology is the most widely used tool to study human cognition. While originally a promising tool for mapping the content of cognitive theories onto the structures of the brain, recently developed tools for the analysis, handling and sharing of data have changed the theoretical landscape of cognitive neuroscience. Even with these advancements philosophical analyses of evidence in neuroimaging remain skeptical of the promise of neuroimaging technology. These views often treat the analysis techniques used to make sense of data produced (...) in a neuroimaging experiment as one, attributing the inferential limitations of analysis pipelines to the technology as a whole. Situated against the neuroscientists own critical assessment of their methods and the limitations of those methods, this skepticism appears based on a misunderstanding of the role data analysis techniques play in neuroimaging research. My project picks up here, examining how data analysis techniques, such as pattern classification analysis, are used to assess the evidential value of neuroimaging data. The project takes the form of three papers. In the first I identify the use of multiple data analysis techniques as an important aspect of the data interpretation process that is overlooked by critics. In the second I develop an account of inferences in neuroimaging research that is sensitive to this use of data analysis techniques, arguing that interpreting neuroimaging data is a process of isolating and explaining a variety of data patterns. In the third I argue that the development and uptake of new techniques for analyzing data must be accompanied by changes in research practices and standards of evidence if they are to promote knowledge generation. My approach to this work is both traditionally philosophical, insofar as it involves reading and analyzing the work of philosophers and neuroscientists, and embedded insofar as most of the research was conducted while engaged in attending lab meetings and participating in the work of those scientists whose work is the object of my research. (shrink)