Thesis Musings

I’m at the beginning of my dive into thesis research. We officially began our thesis class at ITP 2 weeks ago, and were asked to write a little bit about what was on our mind.

Prompt: Write a short blog post on the big concept or passion or interest or questions you want to tackle (not the technology).

Yogurt is a food. Yogurt is alive. Yogurt was an accident. Yogurt is intentional. Yogurt is recursive. Yogurt is an archive.  

A spoonful of yogurt might sound like nothing more than an occasional breakfast snack; but what if I told you that within that yogurt, we can find questions and answers touching on everything from experience design to metaphysics; systems architecture to the future of computing?

Yogurt has been in the human diet in various parts of the world for thousands of years. We know it as a tangy, smooth-textured dairy product that is in a distinct class from cheese, milk, kefir, butter, and the rest. We know how it’s made now, too — heat milk, let it cool, add a bit of previous yogurt, give it time, and voila– you’ve got yogurt. But it wasn’t always this simple. 

Yogurt likely began as an accident. It probably went something like this: milk was left outdoors in a hot environment near some plants, where lactobacillus — a lactic acid producing bacteria — was crawling around. That bacteria found its way into the milk and metabolized the lactose in the milk to produce lactic acid. That lactic acid lowered the pH of the milk. The hot environment “cooked” the milk, changing the shape (denaturing) many of the proteins in the milk. The more acidic environment and the denatured proteins encouraged a re-formation of protein networks in the milk. Those new networks of proteins created a firmer texture, and the lower pH gave the milk its tangy taste. Some brave soul took a bite of that substance, liked it, maybe even felt good rather than sick, and perhaps tried to recreate it. Over many centuries and experiments, we now have a relatively reliable way of making yogurt. 

The mechanics of the inner workings of yogurt, which I can go to in much more detail, are ripe for analogy to the ways that human systems form, de-form, transform, and re-form. Bookmark “resilience in networks,” and “transformation” as topics of interest, and yogurt as a lens through which to look at these topics. 

Also bookmark “experience design” as a practice of interest, and the cultivation of spoiled milk into a repeatably delicious product as something that we can analyze as an act of intentional design, and extend into other food and non-food design processes.

As I mentioned above, yogurts are created from previous yogurts. They don’t have to be done this way, but in common practice, they are. In that sense, yogurts are recursive. A piece of the whole begets the next whole; the “next” is dependent on the “previous.” In Indian households it is very common to make yogurt at home, and yogurt starters are often an important item to bring along when moving from one place to another, or to share with family and friends when they come to a new place. We can trace lineage through yogurt — where did it come from, where did it branch, how did it transform? We can tell stories of migration, of immigration, through yogurt; both through people and through bacteria. 

There are a few ways we could go about tracing the lineage of yogurt. One of those ways would take advantage of recent dramatic improvements in our collective ability to understand the biological makeup of the world around us. Genome sequencing has become orders of magnitude cheaper, with handheld DNA sequencing tools now available to hobbyists, with room for further improvements in hardware and cost well within reach. The study of genomics coupled with the techniques of bioinformatics, among other related fields, are giving us new information about both the “hardware” and “software” of life, and allowing us to identify specific species of invisible microorganisms in our environment. We even have the ability to “program” some genes. We’ve figured out ways to store information in DNA, and we’re beginning to understand the possibilities of using DNA instead of bits as the basis for computing. Taken together, we are starting to learn techniques that may give us new infrastructure-level tools to reimagine the ways in which we build the materials around us — both physical and digital. The uses of these technologies will not be neutral; we have to imagine and execute the uses of the technologies that we want to see exist. 

It’s possible that yogurt already is a kind of archive in itself; I would like to explore whether we can use the bacterial makeup of yogurt as a way of identifying its ancestors in ways that are roughly similar to how we are able to identify our relatives using DNA. I’d also like to explore using DNA storage to embed oral histories of the Indian community in New York — my mom’s family was part of the early batch of Indian immigrants to arrive in Queens in the 70s — in the DNA of lactobacillus, and use that lactobacillus to make yogurt. I’d then want to demonstrate the ability to read out those files from the yogurt DNA.

Zooming out — I am trying to weave together a variety of interests and questions through an exploration of yogurt. It is possible that I’ll narrow in on one specific area: resilience in networks, transformation, lineage, stories of the Indian-American community’s roots, the future of biology and computing, infrastructure technology versus end uses, Vedic philosophy. It’s also possible that all of these can be refracted through one prism. Let the journey begin…

My Microbial Companion: Nukazuke

Assignment:

Start a microbial culture that you will keep as a companion for the rest of the semester.

Idea:

Nukazuke are Japanese rice-bran ferments. They’re made by first preparing a bed of rice bran, salt, water and additional ingredients like mustard powder, kombu, dried red chili flakes and garlic. Other add-ons can be used instead of these. After mixing together the ingredients, bury a vegetable, chopped if necessary but with skin-on, in the rice bran bed. The salt in the rice bran bed functions just like salt in a lacto-ferment; it promotes healthy lactobacilus growth and inhibits other pathogenic bacteria that can’t survive in higher-salt concentrations. The rice bran supplies sugar for the naturally occurring bacteria in the air, and the buried vegetable (especially its skin) often carries a lactobacilus biome that will help begin culturing the rice bran bed.

Each day until mature, swap out the vegetable in the bed. This helps promote a more diverse microbiome in the rice bran bed. I’ve been tasting the pickles each of the last two days; they are noticeably transformed from their normal state, slightly sweeter and saltier, but still very young for a nukazuke. I expect that within a week I will have a mature bed.

Once the bed is mature, I’ll be burying vegetables or ~12 hours or more to get the fermented final product. I’ll try different vegetables, and eventually I may take some of the mature culture to

I followed this recipe, and also learned a lot from The Art of Fermentation by Sandor Katz.

Scaling Intuition

Assignment: Capture relationships between objects at different scales.

The motivation behind this assignment was, in part, to build an intuition for size, scale and relationships between objects and space. We will need to hold onto this intuition when shrinking down to micro-scale. Something I found interesting while doing this assignment, which I suspect will return when we study bioinformatics techniques: as the scale between objects increased, I began approximating the density of objects in a given area rather than precisely measure the relationship.

Initially, at 1:10 scale, it was easy to measure an exact relationship between my chosen objects, books, to one another. As I moved to a sewer grate grid, I could count the rows and columns, calculate the number of rectangles in the grid, then find the relationship between one rectangle and the whole grid.

But once I got to the tiles in the ITP foyer with irregularly-shaped specks as their building blocks, I began approximating the number of specks in a given area (a rectangle), then approximating the number of rectangles in a tile, then counting the number of tiles in the foyer before arriving at a calculation. When scaling bacterial activity from a sample to a real location, I imagine we will need to do something similar.

In the realm of counting

1:10 // Height of 1 book : Height of stack of books

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1:600 // 1 rectangle in this Brooklyn sidewalk sewer grate : ~600 rectangles in the entire grate

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In the realm of approximation

1: 1000 // 1 oval in on the back of a chair in an ITP conference room: 1000+ ovals in the entire mesh

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When I refer to “specks” in the next two examples, I mean one of the light-colored irregular shapes in the tiles below.

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1:100000 // 1 speck : 9 tiles

I counted ~100 specks in a rectangular area, then approximated the number of rectangles in 1 tile. I estimated that there were ~16,000 specks per tile. So roughly 1 speck in 1 tile compared against 6.25 floor tiles would give a 1:100000 relationship.

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1:1000000 // 1 speck in 1 tile: ~63 tiles (there are 320 tiles, so 1 speck: whole floor is about a 1:6000000 relationship!)

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