Listening to Bioluminescent Bacteria
by Ritwik Kaikini
Ritwik Kaikini (MA’ 18) and Brian Merlo (BE’ 19) presented one of the iterations of the project, which is now leading its research pathway into diagnosing a bacteria’s life cycle phase just by listening, instead of seeing. During the presentation, Ritwik explained that Woody Hastings—who was one of the founding fathers of the field of circadian biology—during his experiments with bacteria Aliivibrio Fischeri and Vibrio Harveyi, concluded that these bioluminescent bacteria “made light only when they had high cell density, they made no light when there was low cell density.” Pursuing research to determine why this happens, Dr. Bonnie Bassler, a molecular biologist, discovered that the time of light generation and the phenomenon of bioluminescence is closely related to genes. She explained the concept of quorum sensing, where each bacterium votes based on their nutrient availability and depending on the votes, these bacteria decide to manifest genes into certain forms of behaviors like bioluminescence, virulence or bio-film formation.
(Listen to Dr. Bassler’s talk on quorum sensing here: youtube.com/watch?v=saWSxLU0ME8)
Students in the ArtSciLab presented Micro Lux Chants, a collaborative project from the lab, at the 2018 Research Art and Writing (RAW) conference held by the Department of Arts and Humanities. The panel was chaired by Dr. Sabrina Starnaman, a clinical assistant professor teaching history, philosophy and literature at the department of Arts and Humanities.
Brian explained that Dr. Jeremiah Gassensmith had approached the ArtSciLab, initially in the interest of understanding what phase of the life cycle, the bioluminescent bacteria (Aliivibrio Fischeri) is in, by listening instead of visualizing the growth. Every bacterial cycle has four phases, namely: lag, log, stationary and death phase. The goal of the second phase of the project was to ‘sonify’ the rate of change of the population growth of bacteria. Sonification is the process of translating any data change into sound outputs for the user to be able to understand and absorb information just by listening.
Auditory perception in everyday life
Humans use auditory perception in everyday life.
Brian went on to explain one such example: “Imagine yourself searching for water inside a dense forest during a hike. When we try to navigate or search for running water, we listen for the sound of water. This sound is built so strongly in our memory, that we know it is the sound of running water somewhere in the distance. As we walk closer to the river, the sound begins to change and evolve in terms of its frequency, amplitude or pitch”. We are able to locate the source of water using just our ears. Similarly, we can study or identify stages in a phenomenon having data changes using our ears.
Data Capture and Patch construction
The team conducted iterations of time lapse photography of the bioluminescent bacterial growth from August to December 2017. The bacteria were observed over a life cycle period of 5-6 days, and images were captured every 5 minutes. These images were compressed to form time-lapse videos which were roughly 1-minute long.
In January 2018, the team wrote a patch (a block of visual code) to demonstrate the concept of ‘listening to a rate of change’. The visual time lapse video footage of the bacteria is fed into this patch, which converts it into a binary footage (only black and white). The blue bioluminescent spots are converted to black spots on a white canvas. This helps us determine the number of blobs of bacterial colonies and their degree of growth over a period of 5-6 days.
Metaphor of the Maraca
Brian came up with the idea of using the maraca, a traditional instrument filled with pebbles and used as a shaker or a rattle. Each bacterium can be treated as a pebble inside the maraca and as the bacteria grew in number, so did the intensity of the rattling of these pebbles inside the maraca. Ritwik also explained that we could treat each bacterium as a coffee bean inside an empty coke can and shake the can. Once the bacteria grew in number, then number of coffee beans inside grew and the sound changed.
Q&A Video Link: https://www.youtube.com/watch?v=xLWJLDoj-Rk
The audience listened to this ‘sonification’ and we had a variety of reactions from different people. A biology student asked how this project can lead into cancer research. Ritwik explained that these bacteria are like indicators of health within various regions of the body. Bioluminescent bacteria can indicate whether the regions of our body have been attacked by cancer cells or not, depending on their characteristic of giving out light. If they give out light, the region is healthy, if the light dies out the region is infested with cancer cells. He gave the analogy of the colonies of bacteria being like an army or a civilization that lives managing nutrients for the entire colony. Once the civilization is thriving in a healthy condition with sufficient nutrients, they are able to make light. At this point, Roger Malina and Sabrina Starnaman brought up the point of the anthropocentric nature of explaining concepts in science and how it sometimes makes the concept more familiar to understand, though ethically debatable. Another member of the audience also pointed that the sounds reminded him of the lost musical genre of ‘blip-hop’.
The presentation ended with a holistic discussion of how the field of art-science is evolving and reaching a realm where art informs science through its experimental unorthodox ways and science informs art through its own disciplined methods. In the process of striking the equilibrium between the two fields, there’s a vast array of research areas to be explored and new innovative solutions to be found.