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From five-cent synthesis to Martian DNA: Synbiobeta 2014

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Synbiobeta 2014-2By Jean Peccoud
PLOS Synthetic Biology Community Contributing Editor

Synbiobeta San Francisco 2014 is wrapping up this morning with a networking cruise in the bay that I won’t be able to join because I need to head to the airport in a few hours.

This was the first time I could attend a Synbiobeta conference. The event has a very distinctive flavor to it. It’s certainly very different from the science fair spirit of iGEM. It’s not as academic as the SB series of conferences. It’s very business-oriented, fast-paced, to the point, and focused. A few hundreds people attended the event, about twice as much as last year.

Craig Venter’s Keynote Lecture

Craig Venter gave the keynote. He took advantage of the opportunity to aggressively promote his latest book: “Life at the Speed of Light: From the Double Helix to the Dawn of Digital Life”. His talk moved at the same speed.

After reminding the audience of his previous achievements, he started sharing his vision of the future. He showed few slides on “biological teleportation”. At a high level, the idea is that you may be able to transfer “life” through digital communication instead of shipping samples. One extreme version of this idea is to send DNA sequencers to Mars to stream sequencing data back to earth where Martian DNA could be reconstituted. He is testing the concept by putting a sequencing lab in a truck and sequencing DNA found in soil samples collected in the Mojave Desert. Another potential application of the idea would be to develop a worldwide network of DNA fabrication facilities that could be mobilized very quickly to produce DNA-based vaccines to prevent the development of epidemics before they are out of control.

As much as I want to find these ideas inspiring, a side of me cannot refrain from questioning some of the underlying hypotheses. Reproducing Martian DNA on earth is exciting but last time I checked we were still looking for evidence of life on Mars. A world-wide network of DNA manufacturing facilities for emergency response sounds great but would that make any difference when you keep in mind that making DNA is only one step in a complex process that also involves producing the vaccine out of the DNA, delivering the vaccine to a large fraction of the world population, and allowing people to develop protective immunity after vaccination. Synthetic DNA used to make the vaccine could be shipped overnight anywhere in the world. Would the 12 hours saved by sending DNA sequences digitally have any impact on the efficacy of the response? I am not sure.

One of his last slides was about genome redesign. He is currently working on redesigning a synthetic genomes by making it smaller and reorganizing it. I would have loved to hear more about this as I can see all sorts of problems and questions arising out of this work. For instance, when you refactor a genome, how do you define what should go where? How do you define functional blocks? So many genes have multiple functions that it is somewhat difficult to assign many of them to a single functional block. What is the optimal organization of a genome? I don’t know and he did not really provide much information.

I could not keep up with Craig toward the end of his talk. I summarized this in a tweet that captures pretty well the feeling:

Main sessions

All the presentations were short. The format was more like an investor or a sales pitch than the longer format that you would find in an academic event. A detailed program is available online at http://synbiobeta.com/event/san-francisco-2014/.

The topics of the sessions were Designer molecules, BioCAD tools, Gene synthesis, Genome Editing, and Waste carbon management. In addition, a session called News and Views consisted in a series of short company presentations. The program concluded with an investor roundtable.

Synthetic Genomics announced the release of an instrument automating Gibson assembly of DNA fragments. Interestingly, Craig Venter mentioned that this instrument includes a tamper-proof biosecurity screening system to make sure it is not used for illegitimate applications. I was very happy to hear this as I have long been advocating that embedding biosecurity in the hardware would provide a very effective level of protection than a stand-alone software application. I am wondering if this example could inspire Illumina and other providers of sequencers to do adopt a similar strategy.

Cambrian Genomics stated their ambitious plan to provide DNA synthesis services as cheap as DNA sequencing. They are about to start providing DNA to select customers at a rate of 4 to 5 cents per base pair. I guess, we have to start thinking about how to use gene synthesis in our experimental workflows when the price of synthetic DNA will drop below the symbolic threshold of 1 cent per base pair.

DNA2.0 gave a presentation summarizing their work on optimization of gene expression using machine learning algorithms. They also gave us an insight in the various software applications that they have released over the years to help the community design synthetic DNA sequences.

Still in the software area, Genome Compiler announced a new version of their application that now includes automated annotations of genomic sequences. This development is somewhat similar to the software offer of Synthetic Genomics. The convergence between genomics and DNA synthesis is noteworthy. Tesalagen gave a live demo of their suite of software by designing a pathway in front of the audience and computing its assembly protocol. The demo was a little too fast to really understand the details of what was going on but a live demo that goes smoothly is always impressive.

An interesting development is the launch of Ryffin, a company founded by Tim Gardner to provide software solutions to increase the reproducibility of experimental work in biology. The motivation comes from the experience Tim gained improving the stability of Amyris processes. I completely understand the needs and I applaud the vision but I will need to hear this talk a few more times to understand how he intends to solve this challenge.

Wishes

Since John Cumbers invited the audience to provide feedback in order to help shape the next issues of the conference, I will finish by sharing a few ideas:

The bulk of the program consists of presentations given by fairly young and small companies. It would be interesting to have a broader representation of the synthetic biology market. I’d love to learn about the synthetic biology strategies of large companies who are the customers and partners of many synthetic biology startups. It would be interesting to hear the perspective of companies like Exxon, BP, DuPont, Novartis, and other Fortune 500 companies who have made significant investments in this space. It would be useful to hear about the success stories but also about the disappointments, about the promises and the challenges they faced. Their presentation could bring maturity and market experience in the program to balance the youthful exuberance of startups. The perspective from the end of the value chain would provide a reality check that would help synthetic biology companies refine their value proposition.

Even though a significant fraction of the attendants came from academia, there was only one presentation from someone with ties to an academic institution. Many innovations in synthetic biology have their roots in academic research. Many tech transfer offices struggle understanding the market potential of synthetic biology inventions. It would be interesting to learn the details of successful technology transfers from faculty or technology transfer offices. These examples may help people struggling getting synthetic biology intellectual property protected or licensed. It could also help market existing intellectual property and negotiate new licensing deals.

Speaking of deals, I heard several people regret that the conference had not provided more efficient networking channels. The organizers encouraged participants to download the Bizzabo mobile app only but a limited number of them did, and the app did not help people meet each other. In such a small community, many people know each other and it is easy to spend all the break time catching up with the people they already know making it difficult to meet new people. Furthermore, there was no space allowing the privacy necessary to discuss any kind of business deals. It would be useful to know ahead of time who is going to the event. This could be achieved by creating a private LinkedIn group for instance rather than having to download yet another social app. Conference participants could be added to the group by the organizers as soon as they register. It would be great if private meetings could be scheduled ahead of time with select leads. Providing such a service would make the return on the investment of coming to the event easier to quantify.

The next Synbiobeta will take place in London on April 22nd, 2015. Save the date in your calendar like I did.

I am aware that my report is biased by my own interests. Let me know if I missed something important, I will add it to the report later.

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