Multilevel Research Strategies and Biological Systems

O’Malley, Maureen A.; Brigandt, Ingo; Love, Alan C.; Crawford, John W.; Gilbert, Jack A.; Knight, Rob; Mitchell, Sandra D.; Rohwer, Forest

doi:10.1086/677889

Cited by 54 publications

(7 citation statements)

References 91 publications

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“…That is, they involve integration of a mechanistic understanding of cell and molecular processes with "macro-" or "systems level" approaches. This distinction is helpful in that it illuminates how systems biological explorations of cancer are often multiscale, building "up" from biochemistry and cell and molecular biology and, simultaneously, moving "down" from structural or network models into the realizers of these patterns and their common features (for similar views, see also Fagan 2012;O'Malley et al 2014;Green, Fagan, and Jaeger 2015).…”

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confidence: 99%

What and How Do Cancer Systems Biologists Explain?

Plutynski¹,

Bertolaso²

2018

Philos. of Sci.

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In this article, we argue, first, that there are very different research projects that fall under the heading of "systems biology of cancer." While they share some general features, they differ in their aims and theoretical commitments. Second, we argue that some explanations in systems biology of cancer are concerned with properties of signaling networks (such as robustness or fragility) and how they may play an important causal role in patterns of vulnerability to cancer. Further, some systems biological explanations are compelling illustrations of how "top-down" and "bottom-up" approaches to the same phenomena may be integrated.

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confidence: 99%

What and How Do Cancer Systems Biologists Explain?

Plutynski¹,

Bertolaso²

2018

Philos. of Sci.

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“…It can therefore facilitate the acquisition of integrative understanding and underpin interdisciplinary collaboration across domains as diverse as molecular biology, physiology, development, and even ecology (Bevan & Walsh 2004). Model organism research is now a canonical example of multi-level research, which includes the ability to relate multiple conceptual, methodological, and explanatory perspectives to one another (Mitchell 2003) as well as the integration of causalmechanistic and mathematical models representing findings pertaining to different levels of organisation of the organism, ranging from the molecular to the cellular and developmental (O'Malley et al 2014).…”

Section: A Modelling Ecosystem: How Model Organisms Facilitate Integrative Understandingmentioning

confidence: 99%

Model Organisms

Ankeny

Leonelli

2020

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This Element presents a philosophical exploration of the concept of the 'model organism' in contemporary biology. Thinking about model organisms enables us to examine how living organisms have been brought into the laboratory and used to gain a better understanding of biology and to explore the research practices, commitments, and norms underlying this understanding. We contend that model organisms are key components of a distinctive way of doing research. We focus on what makes model organisms an important type of model and how the use of these models has shaped biological knowledge, including how model organisms represent, how they are used as tools for intervention, and how the representational commitments linked to their use as models affect the research practices associated with them. This title is also available as Open Access on Cambridge Core.

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“…Many gut microbes can be cultured, but their full diversity (especially of anaerobes), plus their interactions, were and still are not understood in detail. To develop this understanding, international research consortia began to treat the human body as constituting an ecological niche that with the gut microbiota forms a complex multilevel system (Turnbaugh et al 2007;O'Malley et al 2014). This ecological perspective began to influence an expanded interpretation of the term microbiome, which was often taken now to emphasize 'biome' and its ecological connotations rather than 'ome' and its more restrictive molecular interpretation (see Footnote 1 for terminological debates).…”

Section: Historical Background To Microbiome Researchmentioning

confidence: 99%

Methodological Strategies in Microbiome Research and their Explanatory Implications

O’Malley

Skillings

2018

Perspectives on Science

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Early microbiome research found numerous associations between microbial community patterns and host physiological states. These findings hinted at community-level explanations. 'Top-down' experiments, working with whole communities, strengthened these explanatory expectations. Now, 'bottom-up' mechanism-seeking approaches are dissecting communities to focus on specific microbes carrying out particular biochemical activities (e.g., choline metabolism pathways, Clostridium difficile suppression). To understand the interplay between methodological and explanatory scales, we examine claims of 'dysbiosis', when host illness is proposed as the consequence of a community state. Our analysis concludes with general observations about how methodologies relate to explanations, and the implications for microbiome research.

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Multilevel Research Strategies and Biological Systems

Cited by 54 publications

References 91 publications

What and How Do Cancer Systems Biologists Explain?

What and How Do Cancer Systems Biologists Explain?

Model Organisms

Methodological Strategies in Microbiome Research and their Explanatory Implications

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