Many Methods, Many Microbes: Methodological Diversity and Standardization in the Deep Subseafloor Biosphere

Darch, Peter T.

doi:10.9776/16246

Cited by 5 publications

(7 citation statements)

References 21 publications

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“…One component is building tools and instruments to collect data and metadata about samples and developing systems for accessing and interpreting these forms of information. Devising and implementing standards is also a critical part of building infrastructure (Edwards et al, 2013 ) and is often a site of contestation between domains and communities because competing options for standards often serve the interests of different domains in varying ways (Darch, 2016 ). The resolution of standards-making can result in some communities being disenchanted.…”

Section: Discussionmentioning

confidence: 99%

The core of the matter: How do scientists judge trustworthiness of physical samples?

Darch

2022

Front. Res. Metr. Anal.

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In recent years, research funding agencies, universities, and governments have become increasingly concerned with promoting the reuse of research datasets. Enabling researchers to evaluate the trustworthiness and fitness-for-use of research datasets produced by others is critical for facilitating the reuse of these datasets. Understanding how researchers make these evaluations is crucial for developing digital infrastructure and tools, such as data repositories and metadata schema, in a way that better supports researchers in making these evaluations. Physical samples such as rocks are critical for generating datasets in many scientific domains. Often, samples are collected on field expeditions conducted by large infrastructural projects. These projects comprise many human and non-human components that affect the quality and integrity of samples. However, little is known about whether and how prospective dataset users evaluate the samples' trustworthiness and sample collection processes underlying these datasets. Researchers‘strategies for evaluating sample trustworthiness are explored through a longitudinal qualitative case study (ethnographic observation, interviews (n = 66), and document analysis) of subseafloor biosphere research, an earth sciences domain. Domain researchers use rock samples collected on research cruises conducted by the International Ocean Discovery Program (IODP). Subseafloor biosphere researchers are primarily concerned about samples being compromised by microbiological contamination. Researchers vary regarding the components of IODP infrastructure they consider when evaluating sample trustworthiness. These components include methods to process samples, people handling samples, IODP policies and procedures, and IODP organizational politics. Researchers‘strategies vary according to their disciplinary background, with microbiologists employing more fine-grained judgments about methods; whether researchers have participated in IODP expeditions, with those who have employing more fine-grained judgments about people involved; and whether researchers have ever been involved in organizing cruises or serving on IODP committees, with those who have employing more fine-grained judgments about many aspects of cruises. Researchers who make less complex decisions may be prone to erroneously trusting contaminated samples; researchers who make more complex decisions may be prone to erroneously discarding uncontaminated samples. The paper concludes by considering implications for the design of digital infrastructures to support researchers in evaluating sample trustworthiness.

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Section: Discussionmentioning

confidence: 99%

The core of the matter: How do scientists judge trustworthiness of physical samples?

Darch

2022

Front. Res. Metr. Anal.

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“…The deep subseafloor biosphere community continues to evolve. Current pressures to standardize methods reveal the significant challenges in ensuring that this community can act as a single, strong, and united entity in negotiating access to shared infrastructure (Darch, 2016). Relationships between shared and domain-specific infrastructures should be studied across a wider range of scientific endeavors, as points of friction often reveal deeper truths about scientific practice (Borgman et al, 2015;Edwards et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

“…As explored in more depth in Darch (2016), some members view methodological heterogeneity as a key strength of the domain, with researchers from diverse disciplinary backgrounds bringing new methods to bear on research questions. A particular concern is that standardizing methods of this emergent domain is premature, and will foreclose possibilities for more efficient or reliable methods in the future.…”

Section: ''Nowadays They Won't Publish Your Work If It Has Molecular mentioning

confidence: 99%

Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere

Darch

Borgman

2016

PeerJ Computer Science

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Background. An increasing array of scientific fields face a ''data deluge.'' However, in many fields data are scarce, with implications for their epistemic status and ability to command funding. Consequently, they often attempt to develop infrastructure for data production, management, curation, and circulation. A component of a knowledge infrastructure may serve one or more scientific domains. Further, a single domain may rely upon multiple infrastructures simultaneously. Studying how domains negotiate building and accessing scarce infrastructural resources that they share with other domains will shed light on how knowledge infrastructures shape science. Methods. We conducted an eighteen-month, qualitative study of scientists studying the deep subseafloor biosphere, focusing on the Center for Dark Energy Biosphere Investigations (C-DEBI) and the Integrated Ocean Drilling Program (IODP) and its successor, the International Ocean Discovery Program (IODP2). Our methods comprised ethnographic observation, including eight months embedded in a laboratory, interviews (n = 49), and document analysis. Results. Deep subseafloor biosphere research is an emergent domain. We identified two reasons for the domain's concern with data scarcity: limited ability to pursue their research objectives, and the epistemic status of their research. Domain researchers adopted complementary strategies to acquire more data. One was to establish C-DEBI as an infrastructure solely for their domain. The second was to use C-DEBI as a means to gain greater access to, and reconfigure, IODP/IODP2 to their advantage. IODP/IODP2 functions as infrastructure for multiple scientific domains, which creates competition for resources. C-DEBI is building its own data management infrastructure, both to acquire more data from IODP and to make better use of data, once acquired. Discussion. Two themes emerge. One is data scarcity, which can be understood only in relation to a domain's objectives. To justify support for public funding, domains must demonstrate their utility to questions of societal concern or existential questions about humanity. The deep subseafloor biosphere domain aspires to address these questions in a more statistically intensive manner than is afforded by the data to which it currently has access. The second theme is the politics of knowledge infrastructures. A single scientific domain may build infrastructure for itself and negotiate access to multi-domain infrastructure simultaneously. C-DEBI infrastructure was designed both as a response to scarce IODP/IODP2 resources, and to configure the data allocation processes of IODP/IODP2 in their favor.

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“…The first was in undersea science, where ocean drilling ships acquired rock samples (or, cores) for physical and biological research. This body of work builds upon our ecological studies of CENS, given the scientific commonalities, and on the astronomy research, given the large‐scale infrastructure required (Darch, 2016, 2018; Darch et al, 2015; Darch & Borgman, 2016). The second collaboration is biomedicine, where a distributed and multidisciplinary array of labs, in a hub and spokes model, shares data about craniofacial abnormalities.…”

Section: Open Science Data Reuse and Knowledge Infrastructuresmentioning

confidence: 99%

Collaborative qualitative research at scale: Reflections on 20 years of acquiring global data and making data global

Borgman

Wofford

Golshan

et al. 2021

Asso for Info Science & Tech

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A 5‐year project to study scientific data uses in geography, starting in 1999, evolved into 20 years of research on data practices in sensor networks, environmental sciences, biology, seismology, undersea science, biomedicine, astronomy, and other fields. By emulating the “team science” approaches of the scientists studied, the UCLA Center for Knowledge Infrastructures accumulated a comprehensive collection of qualitative data about how scientists generate, manage, use, and reuse data across domains. Building upon Paul N. Edwards's model of “making global data”—collecting signals via consistent methods, technologies, and policies—to “make data global”—comparing and integrating those data, the research team has managed and exploited these data as a collaborative resource. This article reflects on the social, technical, organizational, economic, and policy challenges the team has encountered in creating new knowledge from data old and new. We reflect on continuity over generations of students and staff, transitions between grants, transfer of legacy data between software tools, research methods, and the role of professional data managers in the social sciences.

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Many Methods, Many Microbes: Methodological Diversity and Standardization in the Deep Subseafloor Biosphere

Cited by 5 publications

References 21 publications

The core of the matter: How do scientists judge trustworthiness of physical samples?

The core of the matter: How do scientists judge trustworthiness of physical samples?

Ship space to database: emerging infrastructures for studies of the deep subseafloor biosphere

Collaborative qualitative research at scale: Reflections on 20 years of acquiring global data and making data global

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