Remaking yeast: Metaphors as scientific tools in Saccharomyces cerevisiae 2.0

Metaphors as design tools for microbial consortia: An analysis of recent peer-reviewed literature

Single engineered microbial species cannot always conduct complex transformations, while complex, incompletely defined microbial consortia have heretofore been suited to a limited range of tasks. As biodesigners bridge this gap with intentionally designed microbial communities, they will, intentionally or otherwise, build communities that embody particular ideas about what microbial communities can and should be. Here, we suggest that metaphors-ideas about what microbial communities are like-are therefore important tools for designing synthetic consortia-based bioreactors. We identify a range of metaphors currently employed in peer-reviewed microbiome research articles, characterizing each through its potential structural implications and distinctive imagery. We present this metaphor catalogue in the interest of, first, making metaphors visible as design choices, second, enabling deliberate experimentation with them towards expanding the potential design space of the field, and third, encouraging reflection on the goals and values they embed.

Words Are Essential, but Underexamined, Research Tools for Microbes and Microbiomes

Language constitutes an essential set of scientific construction tools, not only for communicating knowledge, but for conceptualizing the world. Metaphors in particular, as conventions that guide and reproduce analogical reasoning, merit attention that they largely do not receive. My research addresses this deficit by examining how metaphors for handling microbes shape possibilities for working with yeast and bacteria in synthetic biology, microbiome research, and other fields that reconfigure what microbes can be. Though poised to reexamine assumptions, these fields routinely rest on metaphors and other language tools that quietly embed ways of thinking that may work against wider aims-for example, imagining bacteria as imperfect machines that should therefore be rendered increasingly passive and controllable. Researchers, therefore, need to examine how language tools structure their observations and expectations so that the tools they choose are appropriate for the work they want to do.