Beckett Sterner

Beckett Sterner
Arizona State University | ASU · School of Life Sciences

PhD

About

42
Publications
10,842
Reads
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245
Citations
Introduction
I earned by PhD in the Conceptual and Historical Studies of Science at the University of Chicago. After studying computational biology in college, I was inspired to study the philosophical underpinnings of mathematical and computational methods in biology. My philosophical research addresses the question, "When and why is math useful for biology?"
Additional affiliations
June 2016 - present
Arizona State University
Position
  • Professor (Assistant)
September 2014 - present
University of Michigan
Position
  • Postdoctoral Researcher, Society of Fellows
August 2012 - August 2014
Field Museum of Natural History
Position
  • NSF Postdoctoral Researcher

Publications

Publications (42)
Article
Full-text available
Taxonomy is at the center of modern biodiversity science, since it defines the dual name and meaning of species that jointly allows biologists to study and classify organisms while linking observations from multiple sources. With the accelerating digitization of biodiversity data has come the increased need for readily available taxonomic products,...
Article
Full-text available
Taxonomy is at the center of modern biodiversity science. No species can be systematically studied until it is defined, and no observation can be linked to related data without a taxonomic label. However, taxonomy is also a science in constant flux—even well-studied groups like Mammalia have fluctuated by >25% in recognized species in the last deca...
Article
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The idea that ambiguity can be productive in data science remains controversial. Efforts to make scientific publications and data intelligible to computers generally assume that accommodating multiple meanings for words, known as polysemy, undermines reasoning and communication. This assumption has nonetheless been contested by historians, philosop...
Article
Biodiversity scientists often describe their field as aiming to save life and humanity, but the field has yet to reckon with the history and contemporary practices of colonialism and systematic racism inherited from natural history. The online data portals scientists use to store and share biodiversity data are a growing class of organizations whos...
Article
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Making the most of biodiversity data requires linking observations of biological species from multiple sources both efficiently and accurately (Bisby 2000, Franz et al. 2016). Aggregating occurrence records using taxonomic names and synonyms is computationally efficient but known to experience significant limitations on accuracy when the assumption...
Article
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Connecting basic data about bats and other potential hosts of SARS-CoV-2 with their ecological context is crucial to the understanding of the emergence and spread of the virus. However, when lockdowns in many countries started in March, 2020, the world's bat experts were locked out of their research laboratories, which in turn impeded access to lar...
Article
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The current crisis in global natural resource management makes it imperative that we better leverage the vast data sources associated with taxonomic entities (such as recognized species of plants and animals), which are known collectively as biodiversity data. However, these data pose considerable challenges for artificial intelligence: while growi...
Article
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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 fa...
Article
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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...
Preprint
Full-text available
Connecting basic data about bats and other potential mammal hosts of SARS-CoV-2 with their ecological context is now critical for understanding the emergence and spread of COVID-19. However, when global lockdown started in March 2020, the world’s bat experts were locked out of their research laboratories, which, in turn, locked up large volumes of...
Article
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Translating information between the domains of systematics and conservation requires novel information management designs. Such designs should improve interactions across the trading zone between the domains, herein understood as the model according to which knowledge and uncertainty are productively translated in both directions (cf. Collins et al...
Article
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“What is crucial for your ability to communicate with me… pivots on the recipient’s capacity to interpret—to make good inferential sense of the meanings that the declarer is able to send” (Rescher 2000, p148). Conventional approaches to reconciling taxonomic information in biodiversity databases have been based on string matching for unique taxonom...
Article
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We present a visual and interactive taxonomic Artificial Intelligence (AI) tool, the Automated Taxonomic Concept Reasoner (ATCR), whose graphical web interface is under development and will also become available via an Application Programming Interface (API). The tool employs automated reasoning (Beeson 2014) to align multiple taxonomies visually,...
Article
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Symbiota (Gries et al. 2014) is an open-source software platform designed to function as a biodiversity Content Management System (CMS) for specimen-based datasets. Primarily in North America though also increasingly on other continents, the Symbiota software platform has risen to prominence in the past ten years as one of the more heavily accessed...
Article
Life scientists generate big data by pooling many smaller datasets and by ensuring that those datasets combine to form a trustworthy body of information with a net increase in use value. Most proceed by constructing a maximally comprehensive dataset based on universal standards for representing the data’s empirical content and fit for different use...
Article
Full-text available
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. O...
Article
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The Akaike Information Criterion (AIC) and related information criteria are powerful and increasingly popular tools for comparing multiple, non-nested models without the specification of a null model. However, existing procedures for information-theoretic model selection do not provide explicit and uniform control over error rates for the choice be...
Article
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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 s...
Article
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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 exa...
Article
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We provide an overview and update on initiatives and approaches to add taxonomic data intelligence to distributed biodiversity knowledge networks. "Taxonomic intelligence" for biodiversity data is defined here as the ability to identify and renconcile source-contextualized taxonomic name-to-meaning relationships (Remsen 2016). We review the scienti...
Article
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Evolutionary conceptions of species place special weight on each species having dynamic independence as a unit of evolution. However, the idea that species have their own historical fates, tendencies, or roles has resisted systematic analysis. Growing evidence from population genomics shows that many paradigm species regularly engage in hybridizati...
Preprint
Full-text available
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 shou...
Article
Full-text available
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 shou...
Article
Full-text available
Centralized biodiversity data aggregation is too often failing societal needs due to pervasive and systemic data quality deficiences. We argue for a novel philosophy for biodiversity data science that embodies the spirit of the Web ("small pieces loosely joined") through the decentralized coordination of data across scientific languages and communi...
Article
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The arguments I give here are different ways of getting at the idea that Leonelli’s framework, based on tracking data journeys, may in fact be more general and powerful if it is not predicated on taking a universally relational view of data. There is no question that the work of following data journeys across science provides an important counterba...
Article
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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 priori...
Article
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Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors 'at the source.' We show that this strategy falls systematically short of a full diagnosis of the u...
Preprint
Full-text available
Growing concerns about the quality of aggregated biodiversity data are lowering trust in large-scale data networks. Aggregators frequently respond to quality concerns by recommending that biologists work with original data providers to correct errors “at the source”. We show that this strategy falls systematically short of a full diagnosis of the u...
Article
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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 fruitf...
Article
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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 err...
Chapter
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I will argue that MLS theory does not provide a complete, self- sufficient approach to theorizing about evolutionary transitions. As a formal, mathematical theory about evolution within a population, it presupposes but does not address the material structure of the population that realizes the model. An MLS model might tell us whether a cooperative...
Article
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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...
Article
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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...
Article
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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 semanti...
Chapter
Full-text available
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 arg...
Chapter
How do the multitude of perspectives on explanation fit together, if at all? The “Modes of Explanation” conference was daring in the way it brought together scholars whose fields ranged from philosophy of science to narrative theory, crossed the analytic–continental divide in philosophy, and incorporated business practitioners interested in managem...
Chapter
Full-text available
What does it look like when a group of scientists sets out to reenvision 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 arg...
Article
Full-text available
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 di...
Article
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Protein structure prediction without using templates (i.e., ab initio folding) is one of the most challenging problems in structural biology. In particular, conformation sampling poses as a major bottleneck of ab initio folding. This article presents CRFSampler, an extensible protein conformation sampler, built on a probabilistic graphical model Co...
Article
Full-text available
We introduce a computational method to predict and annotate the catalytic residues of a protein using only its sequence information, so that we describe both the residues' sequence locations (prediction) and their specific biochemical roles in the catalyzed reaction (annotation). While knowing the chemistry of an enzyme's catalytic residues is esse...

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