Duke University Science and Society sponsors a number of programs to foster the interdisciplinary exchange of ideas. One of these programs, SciComm Lunch and Learn, will be the host for Listen to Your Gut, a presentation on baby Lemurs, gut microbiomes and the sonification of data. Dr. Erin McKenney will present her research on changes in the gut microbiomes of baby Lemurs from birth to wean. (Dr. McKenney’s research was done at the Duke Lemur Center!) I will present the Baby Lemur Gut Microbiome Song, which is a sonification of those changes, and talk about how to “listen” to the data.
The program, originally scheduled on campus last March, will happen over Zoom on October 14, 2020. This means that you can all come!!! Here is the link to RSVP- this is necessary in order to get the Zoom link:
In addition, we will share about the Sourdough Project, which Dr. McKenney and I worked on through the Rob Dunn Lab at NC State. I hope to have a section of The Song of the Sourdough ready to present on October 14th. These two studies/sonifications illustrate different approaches to sounding out data. I am grateful to Dr. McKenney for sharing her research and being game for explorations in sound! Another big gratitude goes out to Dr. Ariana Eily and The Art of the Scientist for taking an interest in the idea of sounding data!
On Friday, March 20th, Dr. Erin McKenney and I will present our work on sounding the data from her doctoral dissertation, which focuses on changes in Lemur baby gut microbiomes as their diet changes from birth to weaning. (See this post for further information: https://wp.me/p5yJTY-tD ) We will also preview some of the findings and sounds from the Sourdough Project through the Rob Dunn Lab at NC State.
Our presentation is sponsored by Duke University Science and Society, and is one of a number of talks and presentations presented by this department. The program is open to the public and a pizza lunch is served. You can register at this link: https://scienceandsociety.duke.edu/engage/events/upcoming-events/ Scroll down the March calender to our event, click on it, scroll down and register.
A major soundscape creation for 2019 is to sonify data for the Sourdough Project. The Rob Dunn Lab at NCSU, the Ben Wolfe Lab at Tufts, and the Noah Fierer Lab at the University of Colorado are collaborating to further the study of microbiomes in sourdough starters. The Sourdough Project has gathered starters from many parts of the world in order to study the bacteria and yeast interactions that create the fermenting acids and leavening gases necessary for the creation of sourdough bread.
In October 2018, the Sourdough Project Team and two artists met at the As If Center in Bakersville NC. The As If Center (Art and science In the field) is the burgeoning vision of Nancy Lowe, who is keenly interested in exploring this fertile collaborative area.The other artist was Ferne Johannssen, freshly graduated from college, and off to see what life outside of Vermont has to offer. Ferne is a visual artist/printmaker. [Interestingly, Ferne made a print on a scoby (symbiotic colony of bacteria and yeast) which grows and ferments in kombucha tea.] The purpose of our meeting was to seed an artistic and scientific direction for sharing the data from the Sourdough Project. All three labs were represented and we spent most of our time sharing information and structuring the research paper that will come from this study. Here is a description of the study from the Rob Dunn Lab website:
There are millions of kinds of bacteria and fungi on Earth. We have found several thousand species in human belly buttons alone. Yet if you mix flour and water, the community of organisms that colonize the resulting concoction is almost always composed of a small handful of organisms that are able to leaven bread, yielding a sourdough starter. How this happens is one of civilizations great mysteries, a mystery at the heart of the bread making (and, for that matter, traditional beer brewing). Yet, while bakers understand how to make starters, the underlying biology of the species in these starters remains mysterious. Starters can produce similar effects on bread (and similar flavors), despite being composed of different species, a key different ingredient. Conversely, starters composed of the same species sometimes yield different flavors. Then there is the issue of what happens to starters over time. The organisms in starters are hypothesized, by some, to stay the same over time—an old growth forest of miniatures—even if their living conditions change. Few ecosystems are so (apparently) stable. Then again, starters can change through time, sometimes suddenly. Starters are, if anything, predictably mysterious. But not for long. We aim to understand the biology underlying the differences among starters and the changes (or lack of change) in starters through time.
The last sentence of this description is what I honed in on. My current sense of how to render data as sound is that it would be most effective with data changes (or lack of) across a timeline. The other word that caught my eye is biology. What is biology? The science of living matter in all forms and phenomena, with special reference to origins, growth, structure, behavior and reproduction. The bases of biology are macromolecules (proteins, lipids, nucleic acids and carbohydrates), cells, and evolutionary changes creating phylogenic families across species. With sourdough starters, we are at the microbial layer of life. On the microbial level, diversity rules and it may have something to teach us. That is what I hope!
The Sourdough Project team had a conference call a few weeks ago, where we saw some of the data analysis of the samples, and received updates from each of the labs. Patterns are starting to emerge as the data is narrowed and focused into categorical relationships. This is the crossroads where it all comes together in the question: What do I want from this data? This most interesting question was posed our first night at As If Center, as we sat around an outdoor fire: what is your currency? what do you want from this project? I can’t remember ever having been asked that before.
The bakers who sent in samples want to know the microbiotic fingerprint of their particular starter. The scientists want to discover some new information about the ecologies of sourdough starters in general. The artists are interested in translation, transposition, representation of the discoveries found in the fingerprints. For myself, I am looking to identify a timeline and voice the bacteria-yeast exchange that is fermentation and leavening. Here is a diagram of a potential time frame:
which give rise (the timeline but also a phase within the process)
to VOCs (Volatile Organic Compounds) aroma
To my ear this begins with the very lively interaction of the organisms that changes over time into a lighter, gaseous state. There is an alchemy that takes place and we are trying to hear and understand that.
Still looking at TRIC (Terry Riley’s In C) as a template for orchestrating interesting timbral relationships in this context. Pattern 35 is a possible frame for rise which seems to be the name of this piece. Pattern 35 jumps to a start with an eighth note run. This is the organism interaction phase. Then the mid section is where the rise happens with more space and elevation in tone. Then the aromatic texture is very open and light and unfinished.
What other sound elements might lend to this soundscape? There are likely real live sound samples to be had from this process. Another thought is what if each starter could have its own microbiome sounded out? To do this, I need to see more deeply into the data then I have to this date.
Data sonification is a burdgeoning area of sound design that is quite amazing in its depth and flexibility. I have a keen interest to sonify data in a way that furthers our understanding of the data. I would love to create a sonic pie chart for example. While a visual pie chart is a snapshot, a sonic pie chart would be more like an animation. A chemical reaction could be sonified by assigning particular voices to different parameters of the reaction: as the reaction proceeds, the voices would change from “reagent” voices to “product” voices. Consonance and dissonance couid illustrate the changing relationships amongst the components of the chemical reaction. One possible way to sonify, in my mind.
Then at Moogfest 2018, a workshop introduced me to the world of SuperCollider and MaxMSP as instruments for creating sonic pie charts. Mark Ballora of Penn State University (Please check out his work at http://www.markballora.com) has been working with sonifying data for decades. He was doing it when no one was paying attention. Mark uses SuperCollider to create sonifications of tidal changes and the movement of hurricanes. This type of sonic representation of data illustrates how a group of parameters changes over time, and when you listen, you hear all of the changes happening over time. Voila! A sonic pie chart! Attending Mark’s workshop, shifted my soundsense, as I realized I do not want to learn computer programming (at this time). This blog post by Mark Ballaro and George Smoot (https://www.huffingtonpost.com/mark-ballora/sound-the-music-universe_b_2745188.html) helped me understand that my interest is in exploring how modal/timbral shifts that are set in a familiar,equal-tempered scale spectrum might illustrate data-driven relationships. What I am interested in is more a sonic illustration, than a map or a pie chart.
Just before Moogfest, The Dance DL, a Durham dance listserve sent this announcement:
Rob Dunn’s lab at NC State University explores microbiomes of some of our most familiar places. The sourdough project studies sourdough starters from around the world, including some really ancient ones that have been passed down for generations. Seeking an artist working in any media with an interest in microbiology, bread baking, making the invisible visible, and/or communicating complex science through art. Help us bring the awe and wonder of science–and the microbial world– to the world.
As I read this notice, it felt like a dream! I have a two and half year old sourdough starter which is used to create 75% of the bread Trudie and I eat. I have recently studied cell biology, neurobiology and have a deep interest in molecular chemistry about which I am just learning. And I am looking for a data sonification project. I sent them an inquiry, they checked out my sound work, and I was invited to participate.
First step, meet with the Sourdough folks at Rob Dunn’s Lab. On Friday June 15th, Erin McKenney, post-Doctoral Fellow in Microbiome Research and Education and a research lead on the sourdough project, and Lauren Nichols, Dunn Lab Manager, met me in the lobby of the David Clark Labs (home of the Dunn Lab). 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 lab staff meeting and learned about the amazing research being done here. 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. And 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 Penland, NC in October.
The only other preparation I would like to do is to try sonifying some data. I reached out to the Rob Dunn Lab folks, and Erin McKenney sent me a data set to try my hand at. The data is about nine lemur babies from three lemur species, and how the microbial makeup in each baby’s stomach evolves as changes are introduced to their diets. (This is Erin’s dissertation study!) We have identifiable parameters that can be orchestrated to show changes over time. Perfect!
The data is on a massive (to me) spreadsheet with lots of terminology I don’t know…yet. This will be an interesting process as we work out exactly what the sonic map 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 class and phylum data sheets. Phylum became my focus as there were only 35 phylum as opposed to 95 classes and 255 strains of bacteria. One of the lemur mothers had triplets so I decided to put together phylum profiles on this small group. Culling through the data for these specific individuals narrowed the phyla divisions 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 was down to 15 phylum – a manageable number for a timbral illustration.
The microbes were collected from the three babies six times from birth to nine months. The timeline for the samples was birth, nursing, introductory solid foods, regular 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 profile (which does not change over time) be a drone under the babies’ phylum profiles in the sound map. 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 phylum 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.
Then there was how to voice the individual profiles in order to hear the data as clearly as possible. After much experimentation the mother’s voice is a woodwind with steady 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. You will probably need to listen closely several 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 profiles settle into more consonance with the mother’s profile. So very interesting!
When I sent this to Erin, she said, “The patterns you’ve detected and sonified are exactly what I published.” Yes! This is the sketch I will use to create a soundscape of the Lemur Data. From this exercise, some tentative questions have emerged that will help when we start working on the sourdough project:
How is the data organized/catagorized?
What is being measured?
What are the signifigant changes and time frames within the data collection process?
What are the researchers interested in hearing from the data?