ENGAGE THE HYPER-DRIVE. Is everyone’s organism for making fuels, chemicals, materials, foods, flavors, fragrances and therapeutics — beautifully and slowly — heading for rapid obsolescence?
“Everyone wants to make it faster,” notes Kytopen co-founder Cullen Buie. “Over the past 18 months, we discovered there’s a huge market for speed.”
That’s one of the reasons why, if you open an unmarked door in Emeryville, California, about 900 synbio company co-founders fall out like a scene out of A Night at the Opera. There are more speed freaks in synthetic biology these days than you’ll find in the pages of Hot Rod.
Say goodbye to artisanal design in synbio, for sure — the days of mysterious alchemists and alchemy. Now it’s about huge throughput, fast, cheap. Foundries for casting new metabolic pathways into a organism’s chassis at Warp 10. Speed, speed, speed.
The reason is not hard to figure out. There are 2.3 million times more biochemical reactions to engineer in a microbe than there have been seconds in the life of the universe.
“The number of potential combinations is something on the order of a septillion. That’s a one with 24 zeroes after it,” said Matt Lipscomb, CEO and co-founder of DMC. “Even with the recent significant advances in lab automation, computing power and machine learning algorithms, it’s impossible to experimentally explore the entire design space.”
Think advanced design. Banks of high-throughput servers enslaved to the process of exploring new metabolic pathways. Optimizing existing pathways, or investing novel ones.
The stakes are high because fast is getting faster, that’s the takeaway from news pouring out of the advanced materials and the bioeconomy sectors this week via Ginkgo BioWorks, Twist Bioscience, Arzeda, TeselaGen, Kytopen, and Volkervessels.
Ginkgo supersizes its Twist order: A billion base pairs of DNA, fast
From Silicon Valley and Boston, we heard that Ginkgo Bioworks and Twist Bioscience Corporation expanded their already gargantuan synthetic DNA supply deal — now, it’s one billion base pairs, including genes up to five kilobases in length.
Ginkgo’s technology platform is bringing biotechnology into consumer goods markets, enabling fragrance, cosmetic, nutrition, food companies, and more to make better products.
Ginkgo intends to use the one billion base pairs of synthetic DNA for work in its newest automated foundry for organism design, Bioworks3, opening in November 2017. The third foundry will be used in part by the new company that Ginkgo and Bayer recently launched with $100M in Series A funding focused on nitrogen fixation for sustainable agriculture. This supply of synthetic DNA will also fuel Ginkgo’s continued expansion into new industries for a wider breadth of companies to leverage the power of biology in their lines of business.
Twist Bioscience has been supplying synthetic DNA to Ginkgo Bioworks since November of 2015, when the companies announced an agreement for Twist Bioscience to deliver a minimum of 100 million base pairs of synthetic DNA over the course of 2016 — a quantity equal to approximately 10 percent of the total DNA synthesis market in 2015. Ginkgo is the largest consumer of synthetic DNA globally, and with this supply expansion, it is expected to order approximately one third of the global supply of synthetic DNA.
“An increasingly diverse scope of companies are looking to tap the power of biology to rethink traditional manufacturing, and demand for synthetic biology is at an all time high,” said Jason Kelly, CEO and co-founder of Ginkgo Bioworks.
Twist CEO Emily Leproust commented, “Pairing Ginkgo’s tremendous organism design capabilities and Twist Bioscience’s core DNA synthesis scalability, showcases the growth of the bioeconomy.”
Arzeda, TeselaGen expand to accelerate the design-build-test cycle
Meanwhile, from San Francisco and Seattle we note that Arzeda will license TeselaGen’s proprietary cloud-based informatics solution and collaborate to extend TeselaGen’s state-of-the-art biological design automation platform.
TeselaGen builds enterprise quality software platforms for designing, building and precision editing DNA, enabling the development of vaccines, biologic medicines, and sustainably sourced chemicals. TeselaGen uses its Synthetic Evolution technology for efficient rapid prototyping and editing of recombinant molecules.
Arzeda creates innovative cell factories that can transform or supplement current chemical production methods. One, design novel metabolic pathways employing the necessary enzymatic building blocks to process feedstock to final product the same way that wheat ultimately turns into beer. Two, integrate these novel pathways in a cellular chassis and optimize them to reach the desired level of yield, concentration and purity.
“TeselaGen has created a unique solution for DNA assembly design,” said George McArthur, Ph.D., Research Scientist at Arzeda. “As an Alpha Access Program member, we have already significantly improved the efficiency of our genetic design-build workflow using TeselaGen’s genetic engineering CAD software. With this collaboration, we are looking forward to scaling our workflow even further.”
“TeselaGen’s industry-leading software tools complement our own technology stack. With the deployment of TeselaGen’s software tools at Arzeda, we will improve our protein design pipeline throughput. ” stated Arzeda CEO Alexandre Zanghellini. “These tools will accelerate our design-build-test cycle, which will enable us to get products to market faster,” he continued.
TeselaGen CEO Michael Fero said, “Our hypothesis is that biotechnology is essentially an information technology. Improving the flow, handling and interpretation of information is a tremendous accelerant for biotech product development.”
Kytopen: Delivering DNA to bacterial cells 10,000 times faster
We haven’t written about Kytopen before — one of the newer entrants.
As co-founder Cullen Buie observes:
“One of the main bottlenecks during genetic engineering is the actual delivery of the DNA into the cell. As it stands, a highly trained person inserts DNA into cells one sample at a time, which is a manual and labor intensive process. Kytopen has invented a continuous flow process for delivery using electricity in microfluidic devices to zap bacterial cells as they’re flowing inside microscale channels. This is the new wave of genetic engineering, delivering DNA to bacterial cells up to 10,000 times faster than current state-of-the-art methods.
“Initially we believed that the industry would be interested in engineering new types of microorganisms, but they are far more interested in speeding up the whole process,
The plethora of applications enabled by low-cost DNA synthesis and sequencing, engineering, and analysis have allowed scientists to make jet fuel, cure chronic diseases, and develop synthetic leather. Imagine what’s next. “The bacteria are amazing, marvelous little creatures,” Cullen says affectionately. “What’s fascinating to me is how much potential there is. To the extent that we can unlock that diversity with our creative engineering, this is a tremendous opportunity.” When Cullen describes their entire journey as market-driven, Paulo agrees. “We’re operating in an industry that has huge potential and you see it everywhere,” says Paulo.
1 septillion reasons Dad’s CRISPR-Cas9 may already be Toast
In the rapid-fire tech and political world of 2017, a day feels like a month, a year is like a generation, and sometimes it feels like 90% of the population hasn’t heard of a technology wave before it is swamped by the next tsunami, and that may well be the case with the first wave of CRISPR-Cas technology — and we looked at it in 1 Septillion Reasons your Dad’s CRISPR-CAS9 may already be toast.
It was voted “Breakthrough of the Year” in 2015 by AAAS and big companies are just now taking big licenses. It’s a hyper-specific, gene level version of what any gardener does with a pair of pruning shears, yet takes the system of improving genomes, using the set of DNA that Nature gives us to work with, to another level. But it’s been slooooow.
One more thing: Volkerwessels’ 100% recycled plastic road is gaining viral visibility
The idea has been around for some time — what is racing in this case is social media, which is to say the visibility of this idea.
It’s lightweight design, a fraction of the construction time, virtually maintenance free, and three times the expected lifespan. PlasticRoad, which consists of 100% recycled material, is the ideal sustainable alternative to conventional road structures.
PlasticRoad features numerous advantages compared to conventional roads, both in terms of construction and maintenance. Plastic is much more sustainable and opens the door for a number of new innovations such as power generation, quiet road surfaces, heated roads and modular construction. Additionally, the PlasticRoad design features a ‘hollow’ space that can be used for cables, pipes and rainwater.
You can see an animation of the idea, here.