Data Sonification and Life Forms

One of the things we do as AS IF Center is to catalyze collaborations through Art-Science Matchmaking. I hope you enjoy this guest post by Judith Casseday about one such collaboration with Rob Dunn Lab.      – nl


I have a keen interest in data sonification that furthers our understanding of the data. This
blog post by Mark Ballaro and George Smoot increased my interest in exploring how modal/timbral shifts that are set in a familiar, well-tempered scale spectrum might illustrate data-driven relationships. Recently, I read a notice from AS IF about collaborating with Rob Dunn’s Lab on a project studying microbiology of sourdough. It felt like a dream! I have a two and half year old sourdough starter which is used to create 75% of the bread I eat, I recently studied cell biology and neurobiology, I have a deep interest in molecular chemistry about which I am just learning, and I am looking for a data sonification project. I sent the Dunn Lab an inquiry, they checked out my sound work, and I was invited to participate.

First I met with the sourdough folks at Rob Dunn’s Lab — Erin McKenney, post-Doctoral Fellow in Microbiome Research and Education and a research lead on the sourdough project, and Lauren Nichols, Dunn Lab Manager. I learned that the sourdough project is looking at the ecology of sourdough starter communities as relates to yeast and bacteria growth in flour when exposed to water and the local microbial environment. I attended a Dunn lab staff meeting and learned about the amazing research they are doing. All the projects are basically looking at how the smallest phenomena impact much larger phenomena and vice versa, the micro to macro to micro feedback loop. They keep finding that diversity is the key to sustainable growth and a healthy environment. I left the meeting excited and inspired! Next stop will be the AS IF Center in October, for a retreat with some of Rob Dunn’s collaborators on the sourdough project.

I wanted to sonify some data to prepare for the sourdough meeting, so I reached out to the Dunn Lab folks, and Erin McKenney sent me a data set to try my hand at. The data, from Erin’s dissertation study, is about nine lemur babies belonging to three different species, and enumerates how the microbial colonies in their guts evolve from birth to weaned. We have identifiable parameters that can be orchestrated to show changes over time. Perfect!

The lemur microbial data is on a massive spreadsheet with lots of terminology I don’t know… yet. This will be an interesting process as we work out exactly what the sonic illustration will depict. I sense that certain data will lend itself to sonification and that is the part I do not yet know. After spending some time studying the spreadsheet, I asked Erin how we can cluster some of the microbial data together, and she sent me the data sheets for the bacteria, classified at the phylum and class levels. The phylum-level data became my focus as there were only 35 phyla as opposed to 95 classes and 255 strains of bacteria. One of the lemur mothers had triplets so I decided to put together phylum-level profiles on this small group. Culling through the data for these specific individuals narrowed the number of phyla down to 24, then I made an arbitrary cutoff point of >.00 density for each phylum (Erin said this was fine and is actually a tool scientists use to declutter data). Now I was down to 15 phyla – a manageable number for timbral illumination.

The microbes were collected from the three lemur babies at six time points, from birth to nine months old. These time points were birth, nursing, introduction of solid foods, regular consumption of solid foods, and two times as they were weaning. Microbes were collected from the mother when she gave birth. Erin had the brilliant idea to have the mother’s phylum-level profile (which represents the stable adult community, and does not change over time) be a drone under the babies’ phylum-level profiles in the sound illustration. This allows you to hear when the profiles diverge and when they converge.

The sonic substance for all this is a phyla megachord that stretches from G1 to G5. Each phylum is voiced by a single pitch, so, for example, Protobacteria is G1. Since there are only thirteen pitches in a chromatic scale, some of the phyla would land on the same pitch, different octaves. There were five phyla that tended to have the highest presence in each sample, so I made them the Gs, and all the rest had separate, distinct pitches. I used amplitude to render the amount each phylum was present in each sample.

The next question was how to voice the individual profiles in order to hear the data as clearly as possible. After much experimentation, I decided to represent the mother’s voice as a woodwind with steady, slightly pulsing tone throughout. I chose bell-like voices for the three lemur baby profiles, letting each phase ring out four times over the mother’s profile. The idea is to listen and compare the mother’s profile with the babies’ profiles. Listen for the change (or lack of change) as the each stage rings in four times. What you hear is a uniformity of tone at birth that becomes more dense and dissonant as the phyla diversify with the babies’ diversifying diet. Then the final wean profile settles into more consonance with the mother’s profile.

You can listen to the lemur data sonification project here, and soon I’ll begin experimenting on sonifying data from the sourdough project.

-Judith Casseday

 

The American chestnut returns to AS IF Center

If you were to walk among the forests of the eastern United States over a hundred years ago, you would likely be walking in the shade of Castanea dentata,  the American chestnut. It’s estimated that there were about 3-4 billion of these majestic trees in the east, possibly making up a quarter of the trees in the Appalachians.

Original range of the American chestnut

The trees could grow to a massive size and provided food for wildlife, domesticated animals,  and people. The wood was incredibly rot-resistant — historic cabins with chestnut siding still stand in our mountains today, especially in the Great Smoky Mountains National Park. The chestnut seemed indestructible, until the first half of the twentieth century when chestnut blight arrived on imported Asian chestnut trees, wiping out entire forests all across the east within a period of about 40 years.

American Chestnut trees destroyed by chestnut blight, Chattahoochee National Forest, north Georgia, 1930. Photo courtesy of ChattOconeeNF.

Yet a few of the trees persist. Miraculously, the roots of some of the trees have stayed alive, producing shoots that leaf out and grow for about a decade, then when the sapling reaches reproductive age, it gets the blight and dies back, only to leaf out again a few years later. One of the most optimistic sights in the southern Apps is encountering one of these everlasting chestnut saplings on a summer hike.  You reach out to touch them, and you’re touching a sacred remnant of our past.

But you might also be touching the future. Is it possible we could restore our American chestnut forests one day? For over 90 years, there have been efforts to restore this beloved tree species, often using the genetic material of those brave saplings that persist in our woods. In 1983, The American Chestnut Foundation (TACF) was founded to continue restoration efforts, and has been using a backcross method with Chinese chestnut species to develop blight-resistant American chestnut trees. They have developed genetic lines that are fifteen-sixteenths American chestnut, with one-sixteenth Chinese chestnut for blight resistance.

To support the TACF research and restoration effort, and as a gift to High Cove community and to Carol Jacobsen & Marc Poland whose land and facilities make our art-science center possible, AS IF purchased chestnut trees to be planted in our community this spring.

The seeds arrived in late winter and sat dormant in the fridge for a few weeks, little treasures packed in moist sphagnum moss, sealed in plastic bags. As the spring weather approached, several community members gathered at the Yellow House to select planting sites that would be optimal for chestnut — dry ridges with loamy, well-drained soils. Lucky for us, a geologist happened to be in our midst (thank you, Kaye Savage!) who got out her soil maps and advised us about site selection.

At the Yellow House, selecting optimal sites for our chestnut babies. L to R: Olga Ronay, Carol Jacobsen, Richard Martin, Kaye Savage

We had a late spring this year. It snowed, it stayed cold, it rained cold rains, then snowed some more. And then it snowed. And again. When spring finally came, it lasted about a week — then suddenly it seemed summer would be upon us. So we waited and waited for the right moment, then a week later, we were in a hurry — time to plant! One hot late spring/ early summer day, Olga and I geared up to plant our seeds. To keep voles and other small mammals away, we cut the top and bottom out of a beer can and created a metal sleeve for the seeds, burying them about halfway into the ground. To protect for deer, we made cages of goat fencing. Such a lot of hardware for one little seed!

Olga adjusts the deer-proof fencing around our chestnut seed.

We also planted a couple of seeds in pots that we will be tending throughout the year — when they are strong, we will plant the saplings next to their sister trees. Wish our little seeds good luck!

Good luck, little seed!

Addendum: Read this article from the Washington Post about biotechnology and the American chestnut, also featuring an image of a giant chestnut tree from our county in 1914!

American chestnut tree in Mitchell County (where AS IF Center is located) from 1914.

 

 

 

AS IF resident artist Joe Bigley will explore effects of small organisms on big ecosystems

Curious about what’s going on at Art + Science In the Field? Please join us Saturday, May 19 at 4pm for a presentation by resident Joe Bigley followed by an Open House at AS IF Center studios. The presentation will be held at High Cove Firefly Lodge; after the talk, join us at AS IF Center’s Yellow House garage and studio facilities, where we will serve light eats. BYOB. A mere two dollars per person will help us cover the rental fee for use of the Lodge.

Joe Bigley is an assistant professor of art and sculpture at Spelman College in Atlanta. He received an MFA from Alfred University and has taught at the university level and lived abroad. His creative practice is typically a form of social commentary. He works in various sculpture processes, site specific installation, painting, collage, kinetic works, performance, and digital video.

Conglomeration #8, wood, copper, brass, stone, gut. 16” x 7” x 5”

At AS IF Center, Joe will focus on two different projects. First, he will continue progress on a 100-work series of collages that incorporate various scientific principles into the text and imagery. Second, he will work on a project in response to present invasive pest species that affect our local forests. He will conduct research on forest ecology, including collaboration with the US Forest Service. The end result of this project will include large scale semi-permanent sculptures installed at High Cove. The installations will highlight the widespread impact of unseen forces on expansive ecosystems, focusing on small organisms such as the Emerald Ash Borer Beetle, Hemlock Wooly Adelgid, or Phytophthora ramorum spores which cause Sudden Oak Death.

Product placement (2017), Site-specific Kinetic Installation. Trees (21), Motion Sensor, Motors, Microcontroller, Mixed. 16′ x 18′ x 60′ (Eyedrum Gallery. Atlanta, GA)

To get to AS IF Center, follow the directions to the Firefly Lodge. If Lodge parking is full, go back onto Rebels Creek, take a right, then in just a few meters take the first right at Castanea Street (at the black studio under construction). Park at the pullout areas off Castanea Street, near the black studio and community garden on the left, or near the barn on the right, then walk past the pond and the Lodge driveway. For questions, please contact us.

Reflections on Art as a Pathway to Effecting Change

This is a guest post from AS IF Center resident Cynthia Reeves, who was the Art of the Climate resident in March.

The biggest takeaway from the first annual ClimateCon held in Asheville March 19-21 was how climate change affects every facet of society—from major considerations such as protecting the global food supply in the face of increasing threats caused by climate change to more minor considerations such as how climate affects day-to-day consumer choices. The conference attendees represented every sector of society—business, government, NGOs, non-profits, the arts—all responding proactively to climate change. I was especially impressed by how many corporations have established sustainability departments not only to burnish their reputations as good actors on the global stage but also to bolster their bottom lines. Participants effectively dispelled the myth that mitigating climate change impacts increased costs. The opposite is true.

The conference, hosted by The Collider, has as its mission to deliver a “collaborative experience with a wide variety of business and science professionals who come together to advance the development of data-driven products and services.” Thus, it wasn’t surprising that the arts were not a significant presence. As a writer whose current work incorporates the science of climate change, networking with scientists, business people, innovators, public sector sustainability professionals, academics, and NOAA and NCEI data managers did provide me with a wealth of information to use in my fiction. Scientific facts alone, however, aren’t enough to convince climate change skeptics; art can be used to communicate on a human scale how climate change affects us all. Translating those facts into “story” and characters grappling with a world in which climate change exists may help motivate a skeptic’s change in thinking.

Cynthia Reeves writing upon landing in the Arctic Circle

Likewise, during my residency at AS IF, I had the opportunity to reflect on art’s role in providing a pathway to effecting change by presenting a talk—“Of Ice Floes, Whale Bones, and Abandoned Mines”—about my experiences aboard the tall ship Antigua as a participant in the 2017 Summer Solstice Expedition to Svalbard (Norway). The Arctic Circle sponsors this artist-scientist collaborative residency. The talk focused on the otherworldly beauty of the Svalbard archipelago and how it has inspired my fiction. As part of that presentation, I had the privilege of screening “Moving Image Study of Smeerenburg Glacier,” a six-minute film of a massive glacier calving set against the quiet, sculptural splendor of an ice field. The British cinematographer and filmmaker Adam Laity—one of my fellow Arctic travelers—created the film from footage and sound captured by him and others as we witnessed this spectacular event.

The talk was a study in juxtaposition: the Arctic’s pristine natural landscape contrasted with the human imprint upon this fragile environment. I wanted to emphasize the positive: that we can preserve this environment. The talk reflected that positivity—but also the inherent contradictions—of life in the Arctic now. At the very least, I hoped for the audience to be awestruck by nature and (possibly) nature’s ability to heal itself. Given the audience’s reaction as the film unfolded—the gasps and wonderment and even tears it provoked—I believe the talk succeeded.

-Cynthia Reeves

Very, very cool: A writer shares insight from the Arctic Circle Summer Solstice program

On Sunday, March 17, AS IF Center writer in residence Cynthia Reeves generously shared her time, expertise, and passion for writing with the Toe River Arts community, by way of two events – a workshop in using science research in writing fiction, and a talk about her experience in the Arctic Circle Summer Solstice Expedition.

For the three-hour workshop called Making the Leap from Fact to Fiction, Cynthia prepared readings, gave writing assignments, and offered expert writing guidance to nine workshop attendees, three of whom traveled from Asheville in order to participate. Cynthia challenged workshop participants to think about character development and point of view while weaving science facts into the writing.

 

Following the workshop, in a talk entitled Of Ice Floes, Whale Bones, and Abandoned Mines: Close Encounters from the Arctic Circle Summer Solstice Expedition,  Cynthia regaled us with tales of her adventures to the Svalbard archipelago in the Arctic. She took us to abandoned coal mines taken over by noisy flocks of Kittiwakes, shared grief for a beach piled with remnant whale bones from the archipelago’s heyday as a whaling center,  and concluded with this arrestingly beautiful short video of a calving glacier, filmed by fellow resident artist/ shipmate Adam Laity. 

As we shook off the winter chill and yearned for spring, we were reminded of melting glaciers and other meteorological dramas unfolding on remote parts of our planet. Thank you, Cynthia, for sharing your writing insight and Arctic adventures with our community.

These two events were brought the Toe River Arts community through a partnership with AS IF Center and Toe River Arts Center. We are grateful to TRAC for offering their space and helping us host these two events.  

 

 

 

We begin.

Sunrise from the Yellow House porch

Sunrise from the Yellow House porch

This is not really the beginning, it’s a continuation of many art + science collaborations, some that have grown over many years and some that lasted only a few days… with many artists, scientists, visionaries, educators, explorers, innovators, crazy people, scholars, children, neighbors, ancestors. It’s just that now, we have a PLACE.

We are glad you are here in our virtual place. We hope that you will find inspiration in these pages, but above all, that you will come to this physical place, the AS IF Center, and help shape a think-and-do community of art-science creativity, play, scholarship, and exploration that will grow for generations.

Let us know what you think! Email us with feedback. Write with questions, comments, constructive criticism, suggestions for events and workshops, contact info for art-sci people we should know.

Hope to see you soon! Come have coffee with us on the Yellow House porch, watch the sun rise, and begin your day of art + science inspiration.