May 10, 2021

Scratching the surface of what’s possible with biology

Zymergen VP of Operations Jed Dean offers his perspective on using biology to scale discoveries into global solutions

By Jed Dean

Coastline of Monterey

The wild and beautiful Monterey coastline, as terraformed by the planet’s greatest technology: biology. Photo by Ryan Sepulveda on Unsplash

Editor’s note: This is among the first in a series of new perspective pieces from the leaders of Zymergen, aimed at sharing more personal insights and deeper perspectives on the ideas that matter most to us.

4.5 billion years ago, our planet began as stardust. Today, it is host to a complex, interdependent web of life. Biology has terraformed the planet: revamping the atmosphere, reconfiguring the chemical composition of the oceans, generating massive amounts of new minerals and rock layers, covering the landmasses. Biology is the beauty of a field of wildflowers, the power and magnitude of the carbon cycle in a rainforest, and the atom-scale precision of proteins, the molecular machines within each of our cells. For me, there can be little doubt that biology is the most powerful technology on the planet.

As a scientist, I’m fascinated by this feat. In many ways, my job at Zymergen is to replicate it on a tiny scale. By tapping into nature’s diversity as well as its molecular machinery, it is my goal to create biological systems with speed, consistency, and predictability. If that sounds easy, well, here are a few lessons learned through our early years:

1. We don’t know all that much about biology. 

There are thousands of biology labs in the world, and tens of thousands of academic publications on biology topics most of us have never thought about. Yet, we are only scratching the surface of what there is to know about biology. It’s not just the individual parts but also the complex interactions between parts and the environment.  Think of biology as all of Central Park on a pitch-black night — science has cast but one small streetlight of knowledge thus far. We are building a better fundamental understanding about biology, and we must learn as we go. 

2. Scaling is tough. 

And the difference in scale here is enormous. We’re engineering both at the molecular scale (cells can be one quadrillionth of a liter) and at the scale of industrial processes (large scale fermentors can be hundreds of thousands of liters). We make precise changes in the genes of a single cell, and then grow those cells into literally tons of biomass to make a product. The tools and expertise we use to engineer systems across this scale are radically different, and require intense creativity and collaboration to have success in bringing products to market.

Image of a sapling in a forest

Forests are just one example of how nature scales itself to produce tremendous materials. We imagine scaling cells to produce a forest’s worth of high-performance material.

3. Data is everywhere to be gathered and used. 

Data is everywhere, but to collect, store, and access the right data requires real thoughtfulness. The measurement tools of science enable us to gather enormous amounts of data, but the signal within that data can often be very weak and washed out by the noise. To unlock new insights about biology, we need to understand the experimental designs of researchers in addition to the data itself. That can be very difficult to capture routinely and accurately. But if we can address these two problems then we can use algorithms to engage at the level of complexity of the biological world around us.

We have made tremendous strides on each of these challenges, even as we are just scratching the surface of what’s possible. We see a bright future at Zymergen, and we know we have an obligation to create planet-scale solutions to the large problems that face humanity and the planet. In future posts, I’ll share more about my origins, ideas I’m thinking about, and the future as I see it. Everything from pulling back the curtain to share learnings from Zymergen to spotlighting tremendous work by others. I’m looking forward to the conversation.

Jed Dean is Vice President of Operations and Engineering at Zymergen. He designs and builds automated workflows for genome engineering and high throughput screening. Previously, he developed technology and automation for life sciences at Amyris and at the Stanford Genome Technology Center. He earned his bachelor’s degree in molecular biology from Purdue University and has a PhD in biochemistry from the Stanford University School of Medicine. When he isn’t with his team in the lab, you can expect he is with his family deep in the backcountry of the High Sierra.

Jed Dean, Vice President of Operations and Engineering