Nature of Sensing

001 Beyond Vision, Sensing takes on the physical

Working in hardware and software for the last decade has opened up my curiosity and interest about sensors and what they have enabled our everyday inanimate objects to be, creating layers of data, giving things new ways to interact with. While these sensors continue to become smaller and faster, the limitations for the types of interactions they provide remain wide. When we look at human sensing capabilities, it is quickly apparent that our sensory interactions with the world span far beyond vision. We can smell, taste, proprioception, comprehend ambiently, sense peripherally and sense in a group.  When I look outside of the human and turn to other living things — the plants and insects I see on a hike in the California desert, the microorganisms in my fermented foods, my neighbor’s cat who wanders in the neighborhood - I see how crude our sensing technologies in hardware and software are. Comparing a car to termites reminds me to stay humble.

At the molecular level, how do living things sense and interact with the chemical world? The foods and toxins that organisms are attracted to and repelled from? Smells, flavors, hormones are chemicals. They are molecules occupying space. Sensing these molecules is a physical interaction, and biology becomes crucial aspect of that design, uniquely able to detect molecules with incredible sensitivity and precision.

I began my residency with this frame of mind and many questions:  what does it mean to sense biologically? Is “biosensor” an actual sub category of the sensors I was familiar with from hardware? What is a biosensor made of?  What kinds of things could it sense? I jumped into the deep end.

002 A Biosensor Anthology | Making the Invisible Visible  

The first few weeks I spent at Ginkgo involved me asking the question to many scientists “So, what is a biosensor exactly?” I knew that they were not like the little electronic sensors I was familiar with and I was sure I wouldn’t be able to hold it in my hand and play with it. Biosensors are invisible to the naked eye. Because their scale is so small, they require scientific apparatus to view, capture, and interact with.

As a curious person embarking in new territories in design, I made it an important part of my process to be openminded, to listen, and to share my way of understanding with someone who might be using a different language to communicate something similar. To my surprise, the language around software was easily understood and provided an easy parallel in the two fields of computing and synthetic biology:

inputs / triggers / sensing
outputs / feedback / reaction 

While I am a critic of this kind of cross-over for reasons I will mention later, I found it a fast way to build trust and communicate clearly what I was interested in doing. As I continued having conversations with scientists and engineers at Ginkgo, I compiled a BioDesign Dictionary, a place where I would store new terminology I came across.

I took notes vigorously, listened, and reiterated the conversation to understand the language used around biosensors. We established among ourselves that we are not referring to electronic and hardware devices that sense biological data like heart rate monitors or the readily available glucose sensors. We were talking about biological bits that sense biological things.

Anticipating the parallels of input and feedback, I expected that sensing is one side of the story. What happens after something is sensed is navigated by a biological mechanism, called “reporter”, which would produce the output. As a designer, I was eager to learn about what I could work with, and what tools I could explore. From my conversations with scientists, I learned that while there are a large variety of sensors used in synthetic biology, as well as many methods for tuning already existing sensors to be sensitive to other molecules or different concentrations, I was surprised to find that  the reporters available were quite limited. For instance, sensors may range from detecting caffeine, pheromones, light, taste of fish, a wide range that could open up designing interactions in different contexts. Still the outputs would mostly limit to color change or fluorescence. While these outputs are sufficient for a scientists to detect with naked eye a microbial interaction, from a design perspective it is limiting to visual interaction. I am eager to evolve this area of feedback in biology to open up experimentation for unique interactions as diverse as sensing.

As I began to list, write and research, I discovered that most often biosensors are proteins that sense a chemical molecule. Although there are other types of biosensors that sense physical changes such as pressure, changes in the cell wall, or movement, I decided to focus on biosensors that can detect chemical molecules.

“If there is a chemical in nature, there is a biosensor for it in nature.” Ginkgo’s Head of Selections and Strain Improvement ,Nikos Reppas, told me. I felt excited but very quickly realized that even if it is possible to discover or engineer a new sensor, it doesn’t mean it is possible to do so in the short time frame of my residency. Instead, I began to explore the scientific literature about biosensors, and learned to work with biosensors that Ginkgo engineers already used in the foundry. As I collected scientific papers and worked with the Ginkgo scientists, I began to make an inventory of biosensors, a short taxonomy from a perspective of a designer who is interested in sensing.

3D topology of the TRPA1 Responsible for Sensing Itch, Irritation and “Spicy”. The video shows the complexity and the nature of physical dimensionality of a biosensor.  

Now that I knew many biosensors were proteins, I wanted to understand how they sense molecules. The reason for this was powerful and important: the way a protein senses the presence of a molecule is by them fitting in to one another - like a key and lock. The geometry and topology define the interaction. Sensing in this case means for a molecule to fit into a protein.  

I was inspired by the tools that scientists use to view, modify and ultimately work with proteins, partially because it was the interface for interacting with such invisible things, but also because I could visualize my anthology by manipulating what parts to view on the surface reconstruction of the proteins in digital space.  I learned basics of PyMol and worked with the folks in protein engineer teams to give form to these intricate topological shapes. Although this exercise felt more like gathering and collecting, it helped me understand how intricate, detailed, and unique each sensor is.

“If there is a chemical in nature, there is a biosensor for it in nature” was often on my mind as I continued my explorations. The types of biosensors felt endless. As one might feel in a large library, inspired and lost in the rows of books, I felt inspired and dedicated myself to learning about the libraries of biosensing. The back and forth process of speaking to scientists and referencing scientific journals helped me curate a set of unique sensors for designing novel interactions. I was able to categorize a few areas of interest from the perspective of designing environment, body and interactions, and decided to focus on sensors for Smell, Taste, Hormones and Toxins.

003 Paper as Interface | Material Intelligence

It was important for me from the first day to embody the biosensors through a medium that was familiar. I researched various materials and found that paper was interesting to work with for several reasons. Paper absorbs water - in life sciences water matters. Paper can be flat packed and shipped. Paper is lightweight and affordable. Paper comes in various colors, thicknesses, and textures. But more than its material properties, paper has cultural and scientific historical significance that felt relevant in sensing and perception. Paper is a material we have used to sketch ideas on, externalizing ideation. Paper is used to write on, to embed knowledge, to carry our ideas. Instructions, stories, agreements, paper serves as a cultural vessel that builds societal exchanges of thought for instructions, stories, and agreements. From a scientific historical perspective, paper has a legacy for “sensing”. Paper has been used as a tool for diagnostics, sensing disease, Universal pH Tests, Urine Tests, and Pregnancy Tests.

Through my research I discovered several experts who have been working with paper based biosensing diagnostics. Keith Pardee and a team at the Wyss Institute for Biologically Inspired Design at Harvard had been working on cell-free methods to embed genetic machinery in paper, including biosensors that can act as diagnostics or other useful low-cost sensing devices. I was inspired by the concept of cell-free sensors, which enable designers to take the paper embedded with biosensors outside of an enclosed laboratory, since cell-free meant that there is no living organism. It also meant that all someone has to do to “activate” the sensing interaction is to “just add water”.

While most paper diagnostics come in a form of of a strip, held on one side, dipped on the other, I was eager to explore new affordances and interactions in this space. And turned out, both the Wyss and the Pardee Lab were excited about that as well.  

I made a trip to the University of Toronto to visit Keith and we discussed several ways I could work with paper and explore biosensing. I also visited the Wyss institute and talked to experts in synthetic gene networks and paper intelligence.

As I gained knowledge in the area of intelligence, I began to prototype intricate affordances for wearable paper sensors. This was something I could sketch without embedding the sensors in yet, to explore interaction and form at the human scale.

004 Micro Organism with a Nose | Smell Biosensor

As I continued sketching affordances for interaction, I felt distant from the biological process. One of my biggest findings has been that Lab work and Design sketching may have similarities in process,  but they have very different spaces. and I had to split my time between being in the lab with safety attire, and in the studio where I could sketch object interactions rapidly. It was at this phase where I understood that time scales in biology were are wildly different than that of computing. Life takes time - living things sleep, eat, grow. And there are not that many shortcuts to accelerate that process, than a few standard practices.

In the lab I wanted to see biosensing in real time and, in action. To do this, we embedded two different biosensors in living organism. This was the fastest and easiest way for me to experiment with sensing biologically.

I worked with Joshua Dunn, Ginkgo’s Head of Protein Design and Creative Residency Mentor, along with and other scientists to create a microbial interaction. We worked with a strain of yeast that Ginkgo engineers designed to biofabricate and produce a specific aroma. By feeding it the food that it likes the yeast was able to produce the smell after two days. On the same Petri dish we grew an strain of E. coli harboring an olfactory biosensor, giving the bacteria the capability to smell — a “nose”, if you will. The smell biosensor would specifically sense the presence of the odor we asked the yeast to produce.

On our microbial interaction petri dish, the E. coli was designed to “output” the color blue once it sensed the smell. On this plate, the two newly designed organisms — smelly yeast and sniffing E. coli — shared a sensing interaction.

Experiment in designing smell-producing yeast and its distance spatial interaction with E-coli bacteria on same plate. *Click for Link to Full Res Image*

Ecoli with embedded biosensor turns blue on the left upon sensing the odour produced by yeast on the right.

005 Museum of Sensing | Collective Sketches for Social Dreaming

As the field of Designing for Biology matures and evolves, the area that I continue to find most important is the process. The creative process and the scientific process both need—just as bacterial growth—the right conditions to flourish:  a supportive environment, good nutrition, plenty of water, etc. The conditions for sketching creative prototypes, ideation and futures for biology is one that allows for collaboration, ambiguity, and openness to fun. The nutrition for sketching biology is passionate minds coming together, expression of what is an invisible idea in the mind to a visible sketch, be it physical, digital, flat, volumetric, interactive, or simply performed... when we can share our thoughts we allow the ideas to grow and take place in reality.

I shared with Ginkgo scientists two workshops, and in them two methodologies for cultivating collaboration: Brainstorm and Critique.

Brainstorm is a judgement-free space that allows everyone of all backgrounds, ethnicity, seniority or position in the company to contribute and have a voice through making. It was surprising for teams to find through the languages of sketching that they knew so little about their coworkers: some draw, some make objects, others act it out. We established that when we don’t criticize or judge the ideas at their infancy, they can become sketches and breathe into them an expression. Sometimes what seemed impossible became possible later on, or led in to new thinking directly or indirectly. All ideas were to have a space to be sketched - desired or undesired, good or bad.

The second workshop I shared with the team was a Design Critique,  where they were encouraged to constructively share feedback with suggestions and considerations. This space was about gaining perspective, checking for bits overlooked, and also about diversity of experiences and thought. Our upbringing and the environments we are situated in often define our point of view, but if we are designing for the greater world, then it is helpful to get perspective and feedback often, especially in a field that will affect not only humans but all parts of life. Here we had space to talk about why an idea is desirable and undesirable, why it is good and bad, why it might make me afraid or make me fall in love.

As we got in to groups and sketched ideas together, we began the process of social dreaming. When we think about biological sensing, what do we want collectively on our planet? What do we expect in our communities and as individuals? What biosensors are desired? And what kind of sensing is undesired? Our hopes and fears take on a shape to be visible in this space.  

One way to capture these sketches of biological designs was to put them in a museum. I gave each Ginkgo member a tag where they would write about their newly sketched tools and what it sensed. As they gave the tags back to me I stamped them “ARCHIVED”, officially confirming their contribution to “The Ginkgo Museum of Sensing”.

From the objects they brought initially from their homes tagged as 2019, to the objects they sketched for 2039, Ginkgo scientists’ visions and ideas were documented in “context of their body” as wearable and later mounted at Ginkgo Bioworks HQ as a collective memory of the biosensors to come.

006 Axioms + Provocations

This sort of thinking about critique and questioning the how, why, and who of decisions made about new technologies is an important part of my work on sensing technology. When it comes to biosensors and what is designed, deployed, and measured, Who decides? how is it decided? and how does the idea evolves from sketch to the complex socio economic world that is never devoid of political boundaries, geographically or otherwise? As I explored biosensing in the scientific literature and in the lab, I developed a set of guiding Axioms and Provocations about Biosensing throughout my time at Ginkgo Bioworks Residency:


I shared it presented my Axioms and Provocations in biosensing at the Biofabricate conference in 2018. You can find my talk **here**

Coming from a background of Platform Design, I wish to open up the biosensing technologies as tools of expression, connection and communication. I work with sensing technologies to reimagine the way we perceive the world and as I continue my learnings and work in biosensing, I am delighted and privileged to have spent 3 months in the lab around scientists at Ginkgo Bioworks, not only working with some of the world leaders in biosensors but also diving deeper in this emerging field to recognize the opportunities and challenges first hand.

Three months not only flew by, but it felt like only an intro to biosensors, a taste of working at the biological time scale and with living systems of nature that we are still understanding and learning to not use, but work with.

The most profound exercise at the residency was not focusing on design, or one of science, but rather of the in-between space that cultivates both. My terminology is now: Sketching in Biology, Brainstorming Ecology, Designing Lab Experiment. This in-between space provides potential for multiplicity of viewpoints, nurturing a collective notion of thinking about the future. It’s a hazy border that cultivates healthy disagreements and ways to come to understanding, one that involves humans and other species and opens the door for plural thinking in design and science and ecology.