After passing quals at the end of my first year, I TAed Justin Bois's class on data analysis in biology. I’d taken it the previous year and appreciated how it forced me to think like a scientist, translating my experiments to equations and calculating the probability that random chance would lead to the same observations. I hoped TAing it could reinforce that mindset (and my coding background could be put to good use helping introduce students to coding best practices and packages well suited to scientific analysis and plotting).
During our fall lab retreat, a discussion about how hard it was to manually connect microbial data back to the environmental conditions where samples were collected led me to design a relational database for the Orphan lab — a system to link measurements and microbial community data to their sampling context integrating with the spreadsheets typically used in the field on cruises (not the cushy experience you are imagining).
That fall I also met Helen Wexler, a bioengineering graduate student working on making bricks and other products out of algae. Our work and personalities meshed well and over winter break we entered the Bill Gross New Enterprise Competition together (along with another graduate student Alex Johnson). We were selected as finalists and worked with a mentor, Calum Chisholm, to refine our pitch and business plan. While we didn't win the pitch contest, we walked away with $10k and something better — Bill was particularly impressed that we were thinking at the correct scale.
In the winter I began thinking more practically about how to implement the directed evolution and community selection methods in a way that closely matched the conditions I expected the microbes to experience in the ponds, and allowed me to exert selection pressure based on the metric I cared about, yield. To that end I began designing tall columns (2 meters) lined with ports and sensors to inoculate with my starter communities. Getting the first columns watertight took the better part of the summer. I went through round after round of marine epoxy and failing leak tests.
Eventually I realized it would be easier (and the columns would be cheaper) if I put the HOBO loggers (light and temp) on a stick and put that into the column rather than drilling holes in the column and then trying to make it water tight. For sampling, I tried a variety of lure locks and holes but eventually landed on a solution inspired by anaerobic work in the Orphan lab. I drilled small holes in the column and then inserted thick rubber septa, letting the compression do the sealing. Simple, but it took more than three months of failures to get there.
That spring, Victoria and I applied for a Rothenberg Innovation Initiative (RI2) grant to explore the directed evolution of microbial communities for application in a carbon capture company. In the summer we learned that we had won the grant and I began planning for LOTS of columns.
After getting back into the habit of thinking like a scientist in year 1 (and passing quals), I used my time in year 2 to survey the landscape — figuring out what I actually needed to build during grad school to set the company up for success. The business side of that happened over the summer. Helen and I did an internship at Caltech's Office of Technology Transfer and Corporate Partnerships, along with an undergraduate, Gabo Zhang, they brought on to help us. Our goal was to further refine our business plan: updating my techno-economic analysis with better-cited numbers, benchmarking it against comparable models in the literature, and integrating Helen's cost estimates for clamshell packaging production. We also set out to apply for an ARPA-E grant.
We weren't approved to submit the final grant, but the process pushed us to flesh out a plan for scale up and build a connected TEA centered on using algae to make cosmetics packaging — our intended beachhead market. Calum continued as our mentor, helping us map other players in the carbon capture space and evaluate their scalability at the gigaton scale across energy, water, land, and metals use compared to our approach.
Check out what I did in my third year at Caltech here.