•  8
    Objectivity and Underdetermination in Statistical Model Selection
    with Scott Lidgard
    British Journal for the Philosophy of Science. forthcoming.
    The growing range of methods for statistical model selection is inspiring new debates about how to handle the potential for conflicting results when different methods are applied to the same data. While many factors enter into choosing a model selection method, we focus on the implications of disagreements among scientists about whether, and in what sense, the true probability distribution is included in the candidate set of models. While this question can be addressed empirically, the data ofte…Read more
  •  3
    Bats, objectivity, and viral spillover risk
    with Steve Elliott, Nate Upham, and Nico Franz
    History and Philosophy of the Life Sciences 43 (1): 1-5. 2021.
    What should the best practices be for modeling zoonotic disease risks, e.g. to anticipate the next pandemic, when background assumptions are unsettled or evolving rapidly? This challenge runs deeper than one might expect, all the way into how we model the robustness of contemporary phylogenetic inference and taxonomic classifications. Different and legitimate taxonomic assumptions can destabilize the putative objectivity of zoonotic risk assessments, thus potentially supporting inconsistent and …Read more
  •  3
    Making coherent senses of success in scientific modeling
    European Journal for Philosophy of Science 11 (1): 1-20. 2021.
    Making sense of why something succeeded or failed is central to scientific practice: it provides an interpretation of what happened, i.e. an hypothesized explanation for the results, that informs scientists’ deliberations over their next steps. In philosophy, the realism debate has dominated the project of making sense of scientists’ success and failure claims, restricting its focus to whether truth or reliability best explain science’s most secure successes. Our aim, in contrast, will be to exp…Read more
  •  13
    The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation a…Read more
  •  14
    The Objectivity of Organizational Functions
    with Samuel Cusimano
    Acta Biotheoretica 68 (2): 253-269. 2020.
    We critique the organizational account of biological functions by showing how its basis in the closure of constraints fails to be objective. While the account treats constraints as objective features of physical systems, the number and relationship of potential constraints are subject to potentially arbitrary redescription by investigators. For example, we show that self-maintaining systems such as candle flames can realize closure on a more thorough analysis of the case, contradicting the claim…Read more
  •  126
    Integrative pluralism for biological function
    with Samuel Cusimano
    Biology and Philosophy 34 (6): 1-21. 2019.
    We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain th…Read more
  •  35
    Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus …Read more
  •  175
    Moving Past the Systematics Wars
    with Scott Lidgard
    Journal of the History of Biology 51 (1): 31-67. 2018.
    It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shif…Read more
  •  303
    Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data
    with Nico M. Franz
    Biological Theory 12 (2): 99-111. 2017.
    Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-of…Read more
  •  147
    Individuating population lineages: a new genealogical criterion
    Biology and Philosophy 32 (5): 683-703. 2017.
    Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution…Read more
  •  80
    The Practical Value of Biological Information for Research
    Philosophy of Science 81 (2). 2014.
    Many philosophers are skeptical about the scientific value of the concept of biological information. However, several have recently proposed a more positive view of ascribing information as an exercise in scientific modeling. I argue for an alternative role: guiding empirical data collection for the sake of theorizing about the evolution of semantics. I clarify and expand on Bergstrom and Rosvall’s suggestion of taking a “diagnostic” approach that defines biological information operationally as …Read more
  •  38
    Agent-based computer simulation and ethics Content Type Journal Article Category Book Review Pages 1-5 DOI 10.1007/s11016-012-9660-7 Authors Beckett Sterner, Conceptual and Historical Studies of Science, The University of Chicago, Social Sciences Building 205, 1126 E 59th St, Chicago, IL 60637, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796
  •  623
    Well-Structured Biology: Numerical Taxonomy's Epistemic Vision for Systematics
    In Andrew Hamilton (ed.), The Evolution of Phylogenetic Systematics, University of California Press. pp. 213-244. 2014.
    What does it look like when a group of scientists set out to re-envision an entire field of biology in symbolic and formal terms? I analyze the founding and articulation of Numerical Taxonomy between 1950 and 1970, the period when it set out a radical new approach to classification and founded a tradition of mathematics in systematic biology. I argue that introducing mathematics in a comprehensive way also requires re-organizing the daily work of scientists in the field. Numerical taxonomists so…Read more
  •  167
    Pathways to pluralism about biological individuality
    Biology and Philosophy 30 (5): 609-628. 2015.
    What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properti…Read more
  •  175
    Object spaces: An organizing strategy for biological theorizing
    Biological Theory 4 (3): 280-286. 2009.
    A classic analytic approach to biological phenomena seeks to refine definitions until classes are sufficiently homogenous to support prediction and explanation, but this approach founders on cases where a single process produces objects with similar forms but heterogeneous behaviors. I introduce object spaces as a tool to tackle this challenging diversity of biological objects in terms of causal processes with well-defined formal properties. Object spaces have three primary components: (1) a com…Read more
  •  118
    The normative structure of mathematization in systematic biology
    with Scott Lidgard
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 46 (1): 44-54. 2014.
    We argue that the mathematization of science should be understood as a normative activity of advocating for a particular methodology with its own criteria for evaluating good research. As a case study, we examine the mathematization of taxonomic classification in systematic biology. We show how mathematization is a normative activity by contrasting its distinctive features in numerical taxonomy in the 1960s with an earlier reform advocated by Ernst Mayr starting in the 1940s. Both Mayr and the n…Read more
  •  498
    The Epistemology of Causal Selection: Insights from Systems Biology
    In C. Kenneth Waters (ed.), Causal Reasoning in Biology, University of Minnesota Press. forthcoming.
    Among the many causes of an event, how do we distinguish the important ones? Are there ways to distinguish among causes on principled grounds that integrate both practical aims and objective knowledge? Psychologist Tania Lombrozo has suggested that causal explanations “identify factors that are ‘exportable’ in the sense that they are likely to subserve future prediction and intervention” (Lombrozo 2010, 327). Hence portable causes are more important precisely because they provide objective infor…Read more