Research: Digitizing Dirt

How does metagenomic sequencing change our knowledge of microbial life?

A science-as-process-art collaboration with artist, designer, and microbiologist Christina Agapakis.

Our exploration of new bioinformatic techniques for studying soil microbes was exhibited at the UCLA Art|Science Center in 2014. A partial capture of these representations is available at http://dirtmap.org, and some details follow.

Collecting Dirt on the PCT DNA Sequence Data

A single gram of microbe-rich soil can contain up to two billion bacterial cells and 18,000 unique genomes. New techniques for extracting, isolating, digitizing, and representing this microbial wilderness render the soil and its liveness in new ways.

In this project, we document an engagement with the techniques of scientific copying and inscription. We explore the ways that new digital techniques are reshaping the fundamental categories of biological knowledge, while also offering new opportunities to engage with the aesthetic dimensions of scientific practice and quantiative data.

Photos of the Dirt

We began with the collection of 62 soil samples from 22 different sites along the California section of the Pacific Crest Trail…

…and the extraction of RNA from that soil in a microbiology laboratory.

Lab Images

A series of novel visualizations explore the dirt, the RNA data, and the many transformations the dirt and data go through in becoming first a flat text file, and then a series of charts and graphs.

These representations make newly visible some of the ways that new technologies — and the information resources they offer — are reshaping the very same scientific knowledge and categories on which their design was predicated.

Ideas about species delineation, genetic transfer, the purity and sanctity of organism and ecosystem boundaries all begin to break down in this new data-driven view of microbial life.

Cluster plots of species diversity within each sample of dirt

Read More…

Artifacts & Outcomes

Short Writings, Talks, Presentations:

This recent project builds on my longstanding interests in scientific work. In the early 2000s, I was an ethnographer in biomedical engineering labs, as part of a research team studying cognition and learning, led by Nancy Nersessian and Wendy Newstetter at Georgia Tech.

** Note: Links for ACM publications go to the ACM Digital Library where you should be able to download the definitive version of articles free of charge. Please email me if you run into any problems with this service.

THANKS

This project was funded by a grant from UCIRA.