Starting with some illustrative examples, I develop a systematic account of a specific type of experimentation--an experimentation which is not, as in the "standard view", driven by specific theories. It is typically practiced in periods in which no theory or--even more fundamentally--no conceptual framework is readily available. I call it exploratory experimentation and I explicate its systematic guidelines. From the historical examples I argue furthermore that exploratory experimentation may have an immense, but hitherto widely neglected, epistemic significance.

Despite an enormous philosophical literature on models in science, surprisingly little has been written about data models and how they are constructed. In this paper, I examine the case of how paleodiversity data models are constructed from the fossil data. In particular, I show how paleontologists are using various model-based techniques to correct the data. Drawing on this research, I argue for the following related theses: first, the ‘purity’ of a data model is not a measure of its epistemic reliability. (...) Instead it is the fidelity of the data that matters. Second, the fidelity of a data model in capturing the signal of interest is a matter of degree. Third, the fidelity of a data model can be improved ‘vicariously’, such as through the use of post hoc model-based correction techniques. And, fourth, data models, like theoretical models, should be assessed as adequate for particular purposes. (shrink)

In 2012, the Geological Time Scale, which sets the temporal framework for studying the timing and tempo of all major geological, biological, and climatic events in Earth’s history, had one-quarter of its boundaries moved in a widespread revision of radiometric dates. The philosophy of metrology helps us understand this episode, and it, in turn, elucidates the notions of calibration, coherence, and consilience. I argue that coherence testing is a distinct activity preceding calibration and consilience, and I highlight the value of (...) discordant evidence and trade-offs scientists face in calibration. The iterative nature of calibration, moreover, raises the problem of legacy data. (shrink)

Philosophers of experiment have acknowledged that experiments are often more than mere hypothesis-tests, once thought to be an experiment's exclusive calling. Drawing on examples from contemporary biology, I make an additional amendment to our understanding of experiment by examining the way that `wide' instrumentation can, for reasons of efficiency, lead scientists away from traditional hypothesis-directed methods of experimentation and towards exploratory methods.

It is commonly held that research efforts in the cognitive and behavioral sciences are mainly directed toward providing explanations and that phenomena figure into scientific practice qua explananda. I contend that these assumptions convey a skewed picture of the research practices in question and of the role played by phenomena. I argue that experimental research often aims at exploring and describing “objects of research” and that phenomena can figure as components of, and as evidence for, such objects. I situate my (...) analysis within the existing literature and illustrate it with examples from memory research. (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)

Bogen and Woodward claim that the function of scientific theories is to account for 'phenomena', which they describe both as investigator-independent constituents of the world and as corresponding to patterns in data sets. I argue that, if phenomena are considered to correspond to patterns in data, it is inadmissible to regard them as investigator-independent entities. Bogen and Woodward's account of phenomena is thus incoherent. I offer an alternative account, according to which phenomena are investigator-relative entities. All the infinitely many patterns (...) that data sets exhibit have equal intrinsic claim to the status of phenomenon: each investigator may stipulate which patterns correspond to phenomena for him or her. My notion of phenomena accords better both with experimental practice and with the historical development of science. (shrink)

There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and "high-throughput" instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order (...) to distinguish these and other activities more effectively, the paper proposes a taxonomy that includes three dimensions along which types of EE vary: (1) the aim of the experimental activity, (2) the role of theory in the activity, and (3) the methods or strategies employed for varying experimental parameters. (shrink)

Many philosophers of biology have embraced a version of pluralism in response to the failure of theory reduction but overlook how concepts, methods, and explanatory resources are in fact coordinated, such as in interdisciplinary research where the aim is to integrate different strands into an articulated whole. This is observable for the origin of evolutionary novelty—a complex problem that requires a synthesis of intellectual resources from different fields to arrive at robust answers to multiple allied questions. It is an apt (...) locus for exploring new dimensions of explanatory integration because it necessitates coordination among historical and experimental disciplines . These coordination issues are widespread for the origin of novel morphologies observed in the Cambrian Explosion. Despite an explicit commitment to an integrated, interdisciplinary explanation, some potential disciplinary contributors are excluded. Notable among these exclusions is the physics of ontogeny. We argue that two different dimensions of integration—data and standards—have been insufficiently distinguished. This distinction accounts for why physics-based explanatory contributions to the origin of novelty have been resisted: they do not integrate certain types of data and differ in how they conceptualize the standard of uniformitarianism in historical, causal explanations. Our analysis of these different dimensions of integration contributes to the development of more adequate and integrated explanatory frameworks. (shrink)

In this paper, I investigate the nature of empirical findings that provide evidence for the characterization of a scientific phenomenon, and the defeasible nature of this evidence. To do so, I explore an exemplary instance of the rejection of a characterization of a scientific phenomenon: memory transfer. I examine the reason why the characterization of memory transfer was rejected, and analyze how this rejection tied to researchers’ failures to resolve experimental issues relating to replication and confounds. I criticize the presentation (...) of the case by Harry Collins and Trevor Pinch, who claim that no sufficient reason was provided to abandon research on memory transfer. I argue that skeptics about memory transfer adopted what I call a defeater strategy, in which researchers exploit the defeasibility of the evidence for a characterization of a phenomenon. (shrink)

This paper is devoted to an examination of the discovery, characterization, and analysis of the functions of microRNAs, which also serves as a vehicle for demonstrating the importance of exploratory experimentation in current (post-genomic) molecular biology. The material on microRNAs is important in its own right: it provides important insight into the extreme complexity of regulatory networks involving components made of DNA, RNA, and protein. These networks play a central role in regulating development of multicellular organisms and illustrate the importance (...) of epigenetic as well as genetic systems in evolution and development. The examination of these matters yields principled arguments for the historicity of the functions of key biological molecules and for the indispensability of exploratory experimentation in contemporary molecular biology as well as some insight into the complex interplay between exploratory experimentation and hypothesis-driven science. This latter result is not only important for philosophy of science, but also of practical importance for the evaluation of grant proposals, although the elaboration of this latter claim must be left for another occasion. (shrink)

New Mechanist philosophical models of "phenomenon reconstitution" understand the process to be driven by explanatory considerations. Here I discuss an episode of phenomenon reconstitution that occurred entirely within an experimental program dedicated to characterizing the phenomenon of kinesin motility. Rather than being driven by explanatory considerations, as standard mechanist views maintain, I argue that the phenomenon of kinesin motility was reconstituted to enhance researchers’ primary experimental tool—the single molecule motility assay.

This essay attempts to provide additional motivation for the data/phenomena framework advocated in Bogen and Woodward, “Saving the Phenomena”.

Explanation is a perennially hot topic in philosophy of science. Yet philosophers have exhibited a curious blind spot to the questions of how explanatory projects develop over time, as well as what processes are involved in generating their developmental trajectories. This paper examines these questions using research into the end-Permian mass extinction as a case study. It takes as its jumping-off point the observation that explanations of historical events tend to grow more complex over time, but it goes beyond this (...) observation by scrutinizing the processes responsible for generating this pattern. Surveying several decades of research into the end-Permian extinction, I suggest that the principal “driver” of explanation in geohistory is non-explanatory work: work that is undertaken to increase our descriptive understanding of a phenomenon, not to test a particular explanatory claim. Non-explanatory work drives explanation by imposing or eliminating demands on explanation, and by furnishing new resources for constructing explanatory models. Explanations grow more complex because the demands on explanation tend to increase with ongoing characterization of the target phenomenon, and characterization tends grows the roster of explanatory resources. However, the fact that non-explanatory work sometimes eliminates demands on explanation means that this trend is not irreversible. I suggest that to achieve a more rounded view of the dynamics of explanation, philosophers should ask how research into complex phenomena is organized, as well as how explanatory progress depends upon the coordination of different kinds of material and epistemic resources. (shrink)

This article is about a start-up problem in scientific practice. Specifically, it is about the problem of justifying paleontological correlation—the practice of using fossils to establish time relations among fossiliferous rocks. Paleontological correlation was the key to assembling a geological timescale during the nineteenth century and remains an important practice in stratigraphic geology to this day. Yet contrary to philosophical expectations, this practice lacked a robust theoretical justification during the first half of the nineteenth century. This article examines what this (...) lack of justification amounted to, as well as how the method of paleontological correlation was justified in practice. (shrink)

Developmental biology is the science of explaining how a variety of interacting processes generate the heterogeneous shapes, size, and structural features of an organism as it develops rom embryo to adult, or more generally throughout its life cycle (Love, 2008b; Minelli, 2011a). Although it is commonplace in philosophy to associate sciences with theories such that the individuation of a science is dependent on a constitutive theory or group of models, it is uncommon to find presentations of developmental biology making reference (...) to a theory or theories of development. For example, in the third edition of Essential Developmental Biology (Slack, 2013), three families of approaches are described (developmental genetics, experimental embryology, and molecular and cell biology), and the appendix contains a catalogue of ‘key molecular components’ (genes, transcription factor, families, inducing factor families, cytoskeleton, cell adhesion molecules, and extracellular matrix components); however, no standard theory or group of models provides a theoretical scaffolding to the book nor is any mentioned. (shrink)

The Burgess Shale, a set of fossil beds containing the exquisitely preserved remains of marine invertebrate organisms from shortly after the Cambrian explosion, was discovered in 1909, and first brought to widespread popular attention by Stephen Jay Gould in his 1989 bestseller Wonderful life: The Burgess Shale and the nature of history. Gould contrasted the initial interpretation of these fossils, in which they were ‘shoehorned’ into modern groups, with the first major reexamination begun in the 1960s, when the creatures were (...) perceived as ‘weird wonders’, possessing unique body plans and unrelated to modern organisms. More recently, a third phase of Burgess Shale studies has arisen, which has not yet been historically examined. This third phase represents a revolutionary new understanding, brought about, I believe, by a change in taxonomic methodology that led to a new perception of the Burgess creatures, and a new way to comprehend their relationships with modern organisms. The adoption of cladistics, and its corollary, the stem group concept, has forged a new understanding of the Burgess Shale … but has it also changed the questions we are allowed to ask about evolution? (shrink)

Recent studies challenge the classical view that the origin of animal life was primarily controlled by atmospheric oxygen levels. For example, some modern sponges, representing early‐branching animals, can live under 200 times less oxygen than currently present in the atmosphere – levels commonly thought to have been maintained prior to their origination. Furthermore, it is increasingly argued that the earliest animals, which likely lived in low oxygen environments, played an active role in constructing the well‐oxygenated conditions typical of the modern (...) oceans. Therefore, while oxygen is still relevant to understanding early animal evolution, the relationships between the two might be less straightforward than previously thought. (shrink)

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.

The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown‐representatives of most animal phyla in the (...) Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record. Critical assessment of both records may permit better resolution of the tempo and mode of early animal evolution. (shrink)