Why the Future of Synthetic Biology Needs a Platform

SynBioBeta San Francisco 2017: Why the Future of Synthetic Biology Needs a Platform

Today, the Ginkgo team and I are attending the 6th annual SynBioBeta conference in San Francisco—an annual meeting that brings together leaders in the synthetic biology industry. I’m kicking off the day discussing why biology is the most powerful and advanced technology on the planet and Ginkgo’s mission is to make biology easier to engineer.

We’re witnessing an exciting shift in the biotech world. Companies big and small across a variety of industries—from enzymes to fragrances to agriculture—are realizing the power of biology as a better way to make everyday ingredients and products.

Last month, we partnered with Bayer to launch a new company—along with a $100M Series A investment—to improve plant-associated microbes, focusing on nitrogen fixation. Nitrogen fertilizer is a significant contributor to greenhouse gas emissions and water pollution, and we’re proud to be at the forefront of solving such a major problem with biology.

We hope this partnership serves as a major indicator for synthetic biology’s potential: big companies are looking to solve big problems with this technology. But more importantly, we believe the potential for biology doesn’t have to come with a $100M investment. Smaller companies are also rethinking manufacturing through biology, and we’re committed to being a platform that’s accessible to companies of all industries and all budgets.

Today we have three announcements that help cement our vision for being a universal and accessible platform for the biotech world:

• We’ve long-admired Transcriptic’s mission to make lab work less expensive and faster thanks to the power of automation. Today we’re investing over $10 million to bring their software into our foundries, to further improve our automation processes.
• We’re teaming up with Geltor, an 8-person company creating texturizing proteins for foods and cosmetic products, to help it make products faster and more efficiently. With our foundry, Geltor’s team can focus on product design and development, and more importantly make biotech timelines compatible with business cycles in the CPG markets.
• To support our growth, we’ll be purchasing one billion pairs of synthetic DNA from our longtime partner Twist Bioscience. It’s a historic purchase, and ensures we’re ready to support the needs of today’s customers and tomorrow’s partners.

I’m incredibly proud of what our team has built so far. We’ve designed a platform that powers  big and small customers, while allowing partners to build on top of our technology to create something even greater.  At the same time, I’m humbled by what lies ahead. We’re looking forward to meeting other consumer biotech companies this week at SynBioBeta to learn about their roadblocks and hope that Ginkgo can play a role in contributing to their success!

2017 So Far:  Growing our Technology & Our Team

2017 So Far:  Growing our Technology & Our Team
Jason Kelly, Ginkgo Bioworks co-founder and CEO

The first half of 2017 has been nothing short of incredible for Ginkgo. We acquired Gen9 in January to bring their DNA synthesis capabilities in-house, and last month announced successful commercial-scale fermentation of an ingredient with our partner Robertet. Both of these were significant milestones in our work on continuing to scale our technology, but we know there’s more work to do.

Today, we’re officially announcing two new additions to our team here at Ginkgo who will play a huge role in our ability to continue to scale: Ena Cratsenburg, our chief business officer, and Will Schroeder, head of metabolic engineering. Ena has over a decade of business development experience in biotech, but also spent more than five years with Pixar.  She’s already brought that mix of practical experience and outside-the-box thinking to her role overseeing new partnerships and the commercialization of our tech and products. You can read more about Ena’s day-to-day experience at Ginkgo here, and how she found her way from Pixar to biotech.

Will serves as our new head of metabolic engineering, managing the teams of organism engineers designing the microbes that produce cultured ingredients for our customers. He comes to us from ADM and spent 12 years at Cargill. Both of these companies are partners of ours, and it’s great to have Will’s unique understanding of the industry and incredible expertise in enzymes (he’s the author or inventor of 16 publications and patents in the areas of microbial fermentation, molecular biology and enzyme catalysis!).

Please join me in welcoming Will and Ena to the team! You can read more about our commitment to diversity in our hiring practices here, and see open job recs here.

2 steps toward open DNA parts

Biological engineering today is increasingly built on a foundation of standard biological parts that engineers can use to build their systems.  These are the basic subroutines in our programming language.

It’s important that the parts that provide core functionality be free of restrictive IP rights and a couple recent developments deserve to be celebrated:

(1) Last week a district judge interpreted certain natural gene sequences to be primarily information rather than chemicals and hence not patentable.

Rob Carlson wrote up a nice summary and you can also read coverage from NYTimes and Genomics Law Report.  The ruling only applies to natural sequences, but it means that biological engineers can be a little more comfortable using  the massive amount of new DNA sequence that is added to GenBank daily.   Also nice to see the law catching up with the 60-year old realization that DNA is information.

(2) The  BIOFAB: International Open Facility Advancing Biotechnology (BIOFAB) was launched in December by the BioBricks Foundation with an initial bolus of funds from the National Science Foundation.

I heard the BIOFAB gang speak at the recent SynBERC conference in Berkeley and was excited to see the progress they had made.  The fab is set up to be an industrial-scale part production facility for generating open (IP-free), high quality biological parts.  The parts will hopefully be released under something similar to the the BioBrick Public Agreement that is a sort of GPL for biological parts.

Here’s hoping for more steps toward open parts in the future.

Pearl Biotech Open Gel (Un)Box(ing)

pearlgelbox

Just received our gel box in the mail today.  Pearl has added a great tweak to the standard gel box with an illuminator that fits snuggly under the box.  The illuminator apparently does a good job of exciting SYBR Safe DNA stain so you can watch your DNA running in real time.  The design is open sourced and it would be great to see someone design a camera mount for the gel box to make a cheap gel imager.   All in all, the box looks solidly built and it’s exciting to see people innovating on tools for biological engineering.  Looking forward to seeing more from Pearl in the future.

Bacterial Edge Detector

One of Ginkgo’s favorite biological engineers – Jeff Tabor, has just published his latest engineered biological system, a bacterial edge detector, in Cell Magazine.

edge-detector1

The edge detector is a great example of combining different biological parts (light sensors, cell-to-cell signaling molecules, reporters, and logic gates) to make a complicated engineered biological system.  In the final system, the engineered E.coli are spread in a lawn on a petri dish and light is shown on the dish in a particular shape.  The bacteria at the edge of the shape detect that they are at the interface between light and dark (this is the really amazing bit that requires communication between neighboring cells and some genetically-encoded logic) and express a reporter protein creating an outline of the shape.

This project was actually begun by Jeff and the UT Austin iGEM team in the 1st iGEM competition in 2004.  During the 4 months of the competition they didn’t manage to get the edge detector working, but they did build the first bacterial photography system (“Coliroid“) which was later published in Nature.

Hopefully Jefff’s success with the edge detector will be an inspiration for this year’s iGEM teams to go after ambitious projects!

George Church on de-extincting

Well, time for me to make an appearance on the blog.  Now that Barry has added authorship, my delinquence has become obvious.  Just wanted to flag a New York Times article about bringing back Mammoths.  One of my favorite synthetic biologists – George Church has some interesting comments in the article.  On a side note, I recommend catching one of George’s talks if you have a chance – be sure to look out for the spinning tRNA (if you don’t see it at some point in the talk, you might be watching an imposter):

 

The approach George recommends is starting with the genome of a close relative of the Mammoth such as the African Elephant and then making the necessary changes to convert the elephant genome to match the recently sequenced Mammoth genome.  The elephant/mammoth egg could then (possibly) be brought to term by an African Elephant.  Development is a pretty robust process, so maybe it would work.

He also describes a new technology out of his lab that might be able to automate the large number of genome changes needed to pull off such a feat.  I suspect he’s talking in part about the good work described in this patent application by one of his graduate students (and another of my favorite synthetic biologists) Harris Wang.  

George also mentions that making zoos better isn’t as high on his list as addressing major world problems like the energy crisis.  I agree with that, though I have to say that de-extincting species isn’t too far down there.