ADVERTISEMENT
  About the SA Blog Network













Oscillator

Oscillator


Notes, thoughts, and news on synthetic biology.
Oscillator Home

Glowing Futures

The views expressed are those of the author and are not necessarily those of Scientific American.


Email   PrintPrint



Back in 2010 I was a teaching fellow for a group of undergraduates competing in the International Genetically Engineered Machines competition (iGEM) with a project on “personalized” genetic engineering of plants. We designed genetic modifications that would alter flavor, color, vitamin production, and the presence of allergens, so that a gardener could customize seeds to suit his or her whims and needs. As a proof of principle, we built BioBrick plasmids and transformed the model plant Arabidopsis with the gene for miraculin and genetic constructs that could theoretically decrease the expression of allergen genes. We also designed a prototype genetic engineering kit, the iGarden, that future gardeners might use to optimize seeds using genetic parts from the iGEM registry. These prototypes, in the form of genetic constructs, lab experiments, and nonfunctional kits also served as design provocations meant to ask questions about the way that biotechnology works now and could work in the future. Could plant genetic engineering be done outside of the current industrial model? Could genetically modified plants be open source, less resource intensive, educational, fun? What would it take to build and distribute such a kit, beyond the DNA sequences to transform the plants? How might such a system deal with unintended consequences?

We were just one team of many hundreds who have participated in iGEM since it began almost ten years ago, each with a unique project proposing a different application for synthetic biology, building on the open source designs and data of previous teams to develop increasingly ambitious projects. iGEM has captured the imagination of thousands of students, leading to many provocative questions about the future of biotechnology and how it will be taught, practiced, regulated, and sold.

In recent months, a proposed synthetic biology project has again captured the imagination of thousands of people, sparking new conversations about how biotechnologies are funded, designed, made, and distributed. Genome Compiler’s “Glowing Plant” project has raised over $425,000 on Kickstarter so far, promising rewards that range from stickers and t-shirts to engineered seeds and a kit where, like with our iGarden, you can theoretically genetically modify your own Arabidopsis plants at home with genes from bioluminescent bacteria.

Genome Compiler Corp Glowing Plant Project

The support, media coverage, and financial backing for the project has been overwhelming and largely positive, reflecting a wider enthusiasm for the potential of crowdfunding and open source technologies in many industries. In its design and in its success, the Glowing Plant project is providing access not only to the sequences of (already available) bioluminescent gene constructs but also openly highlighting some of the evolving tensions in the ways that innovation, regulation, intellectual property, and commercial interests intersect. Like much of the work in synthetic biology that the Glowing Plant project builds on, this is a project that is about much more than the direct applications proposed, prompting critical reflection and debate about topics ranging from government oversight to technological hype.

Engineering Bioluminescence

The genes that make fireflies and some bacteria luminescent have been used in molecular biology experiments for decades as visual reporters of gene expression. Unlike the more commonly used Green Fluorescent Protein from jellyfish, which requires input of blue light to fluoresce, the luciferase protein produces light as long as its substrate molecule luciferin is present. The 2010 iGEM team from Cambridge University focused on engineering biobricks for the expression of luciferase in E. coli along with pathways for the metabolic recycling of luciferin. Without having to externally add luciferin to the system, the bacteria engineered with these BioBricks were brighter than typical luciferase expression systems, visible after a few minutes of adjustment to a pitch black room (for more details on their project and a perspective on the Genome Compiler Project, check out this excellent post from one of the team members).

Cambridge iGEM 2010

While the team worked with bacteria due to the time constraints of the iGEM competition schedule, they were inspired by the possibility of one day being able to make luminescent plants as streetlights, modeling some of the efficiency requirements that would be necessary for such a system to be feasible and producing a mock-up architectural drawing of glowing tree lined streets. At the iGEM Jamboree that year our teams talked excitedly about the potential of future iGEM teams combining the Cambridge team’s luminescence genes with our BioBrick expression system for plants.

Cambridge iGEM 2010 E. Glowli

Of course many other researchers, artists, science fiction writers, and gardeners have been inspired by the possibility of glowing plants before. The first report of luciferase expression in plants was in a 1986 Science paper (PDF), demonstrating that luciferase could be expressed in tobacco plants “watered” with luciferin. The figure from the paper showing the cross section of the plant glowing brightly is beautiful and quite striking. However, the image also shows some of the challenges of using luciferase to make any significant light. The image is not a photograph, but made by placing the plant directly onto film in a darkroom. It’s unlikely that such a plant would be able to make a significant amount of light that would be as striking to the naked eye.

Ow et al. Science, 1986.

Excerpted figure from Krichevsky et al. PLoS ONE 2010. Photograph of glowing plant taken with a five minute exposure.

Since then, luciferase as well as other visual markers like fluorescent proteins have been used countless times in many plant species for a range of experiments in plant biology, using sensitive instrumentation that can quantify light output in very small ranges. Attempts to use luciferase for the production of glowing plants as decoration or lighting are much less common, but have also recently been developed by several groups. In a recent paper published in late 2010, just after we were speculating about glowing plants at the iGEM jamboree, a group of researchers from Stony Brook University reported having engineered tobacco plants to express luciferase and the luciferin recycling pathway, creating autoluminescent plants that could glow dimly without addition of luciferin.

So what’s different between these past glowing plants and the plants proposed by Genome Compiler? At a technical level, besides using their software to optimize the genetic code for a different host organism (the Genome Compiler team is using Arabidopsis, not tobacco), not much. But this project isn’t really about reproducing past work and trying to make cool plant night-lights. In fact, Omri Amirav-Drory, the founder and CEO of Genome Compiler, was quoted in the Wired UK article about the project saying “To be honest, it’s actually annoying that I have to do it. I wish that other people would do it–I wish that 100,000 people would use my software to to solve another 100,000 problems in the world.” This project isn’t about this particular genetic engineering project, it’s about the potential of all future genetic engineering projects.

Like the BioBricks foundation, iGEM, and the many projects and proposals of synthetic biology researchers, the Glowing Plant project is about exploring the potential for what might be possible if teams of biologists and engineers could build off of the open source work of others. It’s about exploring the limits of current technologies, economic and regulatory frameworks, and patent regimes, to make genetic engineering more effective and efficient, more fairly distributed, and as safe as possible. However, there’s one important difference between the work of students and academic researchers and Genome Compiler: this project is about more than simply inspiring others, it’s about inspiring people to use their product in future genetic engineering projects. It’s about selling the idea that open source synthetic biology can solve problems and that you should use their closed source software to do synthetic biology.

Selling a story

Amirav-Drory continues in the Wired interview saying, “We chose Kickstarter for a reason — we’re trying to sell a story more than anything.” The story is a triumphant one of the future of open source synthetic biology, crowdsourced design and crowdfunded production solving big problems, doing “something that people on the street would consider science fiction,” designed using the Genome Compiler interface and printed by their DNA synthesis partner company, Cambrian Genomics. This is about using Kickstarter as a marketing platform not for a product but for an idea, an idea about “democratizing the tools of creation” with a proprietary software tool. The imagery and rhetoric of the Kickstarter campaign and of Genome Compiler’s product intentionally blurs the old and the new, the proprietary and the open, the technologically feasible with the technologically “innovative,” science fact and fiction, to create this story and to garner significant attention and crowdfunding.

A Slide from Genome Compiler CEO Omri Amirav-Drory's Solve for X presentation

The image of the glowing plant from the 1986 Science paper that the team is using as the logo of their campaign combines many of the tensions present in the design and marketing of the project. First of all, the image is a direct copy of the work of past researchers, copyrighted by Science, and used with ambiguous citation in promotional materials, proposed Kickstarter rewards like t-shirts, advertising and branding on their website and their software. The use of this copyrighted image to raise funds is a symptom of a larger issue with how intellectual property is being dealt with in this story (more on that later), but more importantly the image provides the team both credibility in terms of feasibility of the project as well as in terms of “wow”-factor. The image of the glowing plant shows that this is technology that has been around for a long time–nearly 30 years!–but is also misleadingly reminiscent of the science fiction plants from the movie “Avatar,” which are frequently cited as inspiration.

Demonstrating that something is technically feasible (and that you are competent enough to do it) while still being innovative and working on more than an incremental improvement to what has been done before is the key challenge when asking for money, whether in a grant proposal to the NSF or to the wider “crowd” on Kickstarter. The Genome Compiler team cites the previous work of others on glowing plants and the open-source luciferin recycling pathways from iGEM on their site as proof of concept and then briefly discusses some possible experiments they could do to make the plants brighter, with some of the possible designs available in the “cloud” through their software interface. With the level of funding they have received, they will be able to synthesize and test many version of the design and will likely improve incrementally on previous work on bioluminescence in plants.

As with many cases in biotechnology, however, patents and intellectual property raise complex questions about what levels of openness are best for incremental advances and true “innovation” in this story. Do patents stifle innovation, blocking others from making progress with lawsuits and expensive licensing? Or do patents protect innovative people, allowing them to be fairly compensated for their work when it is used by for-profit corporations? Can there be a different model where sharing is incentivized with different structures of attribution, compensation, and innovation? Is biotechnology and the patenting of DNA sequences or living organisms a special case?

In general I don’t agree with biotechnology patents and I support the efforts of the BioBricks foundation to explore different arrangements and licensing schemes. It is difficult to tell what the role of Genome Compiler will be in the long run of the debate about intellectual property in biotechnology, and it’s difficult to tell what role patents will end up playing in the Glowing Plant story. The language of the kicktarter campaign and of the Genome Compiler software is language of the open source movement, emphasizing sharing and “democratization” over profit. However, while Genome Compiler cites the PLoS ONE paper from the Stony Brook team, they fail to mention the fact that this group has started a company, BioGlow Inc., to produce and sell ornamental glowing plants, and that this company holds a broad patent on bioluminescent plants (there are a number of other patents on transgenic bioluminescent plants as well). Does the power of the story of openness on the part of Genome Compiler trump the previous work of the BioGlow group? What or who is being democratized, who is being protected or infringed on here? Do crowdfunding “rewards” infringe on patents the same way that a product for sale would?

Genome Compiler Corp. has gotten into patent trouble before, not over uses and applications of their software, but with the actual software itself. The DNA synthesis company DNA 2.0 has a patent on their version of “drag-and-drop” synthetic biology design software called Gene Designer, and has sued Genome Compiler for infringement. Fortunately, many other options for this kind of software exist, including some well developed open source options that allow you to edit, build on, and contribute to the future development of the software itself rather than just releasing your designs to a corporation’s “cloud” so that they might one day decide to do a Kickstarter about your idea too. These include programs like Clotho or TinkerCell to name just two of many, as well as a host of much simpler DNA viewing tools that allow users to design small-scale plasmids, not to mention the open and completely free databases of genetic sequences that anyone can access like the National Center for Biotechnology Information or the iGEM Parts Registry.

Same as it ever was

In an email exchange with the Marketing Manager of Genome Compiler Corp. about the patent situation, the company stated that “[We] initially thought of doing some kind of defensive patent, but we decided not to in the end. Genome Compiler was built with the thought of democratizing creation and we would be thrilled if someone wanted to use or alter the design. The design is already up for anyone to see on Genome Compiler in the cloud. We were not concerned with other patents since we were using a different method.”

But how different is it, really? When people have raised concerns about the uncontrolled release of genetically modified seeds and DIY Agrobacterium engineering kits to backers according to the Kickstarter rewards structure, the team’s response has been to emphasize similarity over difference, claiming: “We are using the term ‘synthetic biology’ in its most general sense, the technology we are using is functionally the same as that which has been used in the creation of many other biotechnology products over the last two decades.” (PDF) While distinguishing themselves from BioGlow, Inc. when it comes to patent regulation, they claim significant similarity and overlap when it comes to government oversight and regulation so that the conditional USDA approval of BioGlow’s product (PDF) might cover the Genome Compiler Glowing Plant as well.

So is it the same or is it different? While aggressively selling themselves as something new and something inherently moral and democratic, Genome Compiler is unfortunately acting out a very familiar story. They are a for-profit corporation trying to wedge themselves into a crowded market of DNA-based services that has many viable open source alternatives, exploiting the ideas, work, and the enthusiasm of idealistic people excited about the potential of synthetic biology, overpromising and overhyping the potential of the technology in the short term in order to market their derivative, proprietary software tools and themselves as leaders in the future of the field.

Like the provocations of iGEM designs and prototypes, this project asks many more questions than it answers. Amirav-Drory says that the Glowing Plant project is “so obviously beautiful, and non-dangerous and legal and ethical,” but there’s nothing obvious about the future of synthetic biology, especially when we’re talking about where these technologies will go in the future, when 100,000 people will be working on 100,000 projects. Will we someday have glowing plants lighting our streets, “solving” the problem of electricity use for lighting? Probably not. Will corporations continue to try and exploit others and their ideas to make a profit? Unfortunately yes.

Christina Agapakis About the Author: Christina Agapakis is a biological designer who blogs about biology, engineering, engineering biology, and biologically inspired engineering. Follow on Twitter @thisischristina.

The views expressed are those of the author and are not necessarily those of Scientific American.





Rights & Permissions

Comments 8 Comments

Add Comment
  1. 1. 100ideas 4:10 pm 06/3/2013

    Thank you for writing such thoughtful article. The hype meter is in the red for this project and it’s very refreshing to see it more broadly contextualized.

    Link to this
  2. 2. CitizenScientist 4:15 am 06/4/2013

    You have left out a critical aspect of the Glowing Plant project which taints your perspective providing some false impressions to your readers. The
    Kickstarter campaign grew out of a citizen-science maker movement organized at Biocurious, a community-driven synthetic biology lab, in the Bay Area. We’ve been working on the engineering for over a year and have educated dozens of non-scientists in the process. We share a common passion for science and open collaboration and have been enthusiastic supporters of the opensource movement. While iGem is only open to a few, our lab makes the science available to anyone. I am pleased to see the success of the Glowing Plant Kickstarter as it helps open the door to a future full of hope and promise.

    Link to this
  3. 3. Christina Agapakis in reply to Christina Agapakis 10:36 am 06/4/2013

    @CitizenScientist

    Thanks so much for your comment. The ways that the project is connected to Biocurious beyond using the lab space were not very clear to me from the materials or reporting available online and Biocurious was not mentioned directly in email communication with the company about the design and motivation of the project. The press release from the company says: “The introductory work was done at Biocurious, a community lab in Sunnyvale, but we’ll be renting our own garage once the kickstarter is complete as there is less risk of someone messing with our experiments.”

    If anything it seemed that mentioning BioCurious would be in the context of another example of how this company is taking advantage of the maker movement and community science labs in general. They are exploiting the availability of low-cost lab space at Biocurious when it was convenient and exploiting the enthusiasm for open science as part of the PR push. Can you clarify how Biocurious has been involved in the engineering and design of the project? If the project was more connected with the community lab why is the Kickstarter project not sponsored by Biocurious itself or some other non-profit affiliate?

    Link to this
  4. 4. antonyevans 6:18 pm 06/4/2013

    I’m the project lead for the Glowing Plant project. This project came together out of the Biocurious Bioluminescent meetup on Monday evenings. People like Kyle, Raymond, Cameron and Patrik (plus many others) have been integral to the success of the project. We would like to continue working out of Biocurious’ lab space but they have a policy of not releasing organisms created in the lab which is in conflict with our goal of putting a glowing plant in the public’s hands.

    The first goal of this project is to educate and inspire the public about the potential of synthetic biology. As we discuss in this update, every single output from the kickstarter campaign will be released open source: the DNA designs, the methods we use and the parts which we synthesize:
    http://www.kickstarter.com/projects/antonyevans/glowing-plants-natural-lighting-with-no-electricit/posts/469999

    The iGem parts are not available to the DIY Bio community, we hope our synthesized parts will become the foundation of the equivalent of Biobricks for DIY Biologists.

    The second goal is to create trees which we can use to replace street-lights. This is a Big Hairy Audacious Goal, but by creating publicly available parts we hope to accelerate that journey by encouraging more groups to collaborate and innovate in the space and big goals are widely recognized as the way to achieve that. The best open source projects involve a collaboration with industry as they work well when there are multiple incentives to participate. I was at Maker Faire a few weeks ago and it was amazing to see the innovation taking place around 3D printers, triggered by the same kind of basic open source components: we hope to create the same kind of ecosystem around glowing plants.

    Rather than accusing Genome Compiler of exploiting the DIY Bio movement we should thank them for supporting the community and putting resources into making this project happen. The future of this industry, as the costs to participate drop and knowledge becomes more available, will be small groups working out of community labs and garages – this is where innovation comes from and hopefully more companies will start to recognize this and get involved themselves.

    Link to this
  5. 5. Christina Agapakis in reply to Christina Agapakis 9:48 pm 06/4/2013

    Antony-

    Thank you for responding. It’s been interesting to see how much enthusiasm your project has generated; you have certainly succeeded in your goal of inspiring people!

    It has also been interesting to watch how “open source” has been discussed in the context of this project, and how that has evolved over time. While the designs have been freely available on the Genome Compiler interface since the beginning of the project, the discussions of whether or not to apply for defensive patents and how to commercialize or license any future seeds has been illuminating and informative about how an open source biotechnology company may navigate these complexities in the future. Your commitment to maintaining the openness of future outputs is commendable. I’m interested to see how things will play out in the future in terms of access to sequence data vs. cloned DNA vs. seeds etc.

    But my critique is not really about whether or not the outputs of this particular project are open source “enough” or whether this kind of approach will one day get us to glowing trees. My point is that “open source” does not mean ignoring copyright and patents when it is convenient for your story and selling copyrighted propriety software when it is not convenient for your business plan. You have not addressed my concerns about other companies’ patents and other researchers’ copyrights or the fact that Genome Compiler’s product itself is not open source. I’m not arguing a case for patents in biotechnology, rather I’m making a case about how this rhetoric and ideology is being used in ways that are not always as open and clear as they seem.

    I’m also curious about the maker kit you are offering to some of the backers. You’re not using agrobacterium to produce the seeds you might send to backers because of the USDA regulations around plant pests. What sort of regulations are there around sending agrobacterium in kits to backers so that they can engineer the plants themselves?

    Link to this
  6. 6. PatrikD 3:05 am 06/5/2013

    It is also important to point out that the Glowing Plant project is NOT run by Genome Compiler. Your article makes it sounds as if Genome Compiler is running the show, which is definitely not the case.

    Genome Compiler is contributing some resources to the project, because they consider it a great way to show of the capabilities of their software. But the fact that the Genome Compiler software is not open source has nothing whatsoever to do with the open source nature of the Glowing Plant project.

    Link to this
  7. 7. Christina Agapakis in reply to Christina Agapakis 12:13 pm 06/5/2013

    PatrikD-

    The relationship between the kickstarter project and Genome Compiler has never been particularly clear and press materials about the project have all come from the Genome Compiler marketing team (who refer to the Glowing Plant as “our project”). If you look at the other comments, it’s clear that many different groups of people consider themselves involved in this project (from Genome Compiler the company to Biocurious the lab space to DIY Bio the “movement”), and all of these groups have somewhat complicated relationships with “openness,” regulation, and synthetic biology.

    My argument here wasn’t aimed at deciding once and for all whether the Glowing Plant project is truly “open,” because things are more complicated than that. What openness means when you have a variety of groups interacting with a variety of regulations, all of which are currently in states of flux, is an open question. My point is that synthetic biology is oriented towards particular visions of the future, involving things like the wide availability of genetic engineering “kits,” novel regulatory schemes, and glowing tree streetlights. Often these future-oriented visions neglect some of the current realities of the field, assuming that problems which may be insurmountable (e.g. the physics of photosynthesis and bioluminescence) will simply resolve themselves, through “innovations” by other people. It is the ambiguities of this project more than its specifics that highlight some of these complex challenges. I’m interested here in how we talk about and how we might one day design for the complexities inside the cell and outside, how synthetic biology is and will be practiced, marketed, and sold.

    Link to this
  8. 8. CitizenScientist 3:20 pm 06/5/2013

    Christina,
    So now the conversation has begun and can continue…torn from the ivory towers into the public space where it belongs. ALL parties here should be commended for driving this.

    Link to this

Add a Comment
You must sign in or register as a ScientificAmerican.com member to submit a comment.

More from Scientific American

Scientific American Dinosaurs

Get Total Access to our Digital Anthology

1,200 Articles

Order Now - Just $39! >

X

Email this Article

X