Genetic Constructor: An Online DNA Design Platform
Maxwell Bates†, Joe Lachoff†, Duncan Meech†, Valentin Zulkower‡, Anaïs Moisy‡, Yisha Luo‡, Hille Tekotte‡, Cornelia Johanna Franziska Scheitz†, Rupal Khilari†, Florencio Mazzoldi†, Deepak Chandran§, and Eli Groban*†
† Autodesk Life Sciences, San Francisco, California 94111, United States ‡ Edinburgh Genome Foundry, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, U.K. § Radiant Genomics, Emeryville, California 94608, United States
Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.
More informations in the report produced along the process.
I imagined an activity composed of cards that allows participants to ‘create’ personalised engineered ‘thing’. They first would have to choose an ‘organism’ and then create a sequence in order to modify it; and finally explain the story behind their creation. Encouraged to reflect on the implications and outcomes (positive and negative) of such creation, it would give both insights of what the general public inspirations for synthetic biology are and a vision of the hopes and fears of the society. Moreover, it would introduce the basic grammar of DNA and its visualisation.
The aim of this activity is not only to inform participants about the processes of DNA design but also to invite reflection on what it means to design through living organisms.
I have conducted a series of interview with biologists to determine what how they would communicate the DNA design process to the general public: how to keep the process simple but accurate and what could be an interesting interaction to understand the principles of synthetic biology (the same interviews helped to develop the ‘Dominoes’ project).
The final design is a set of cards composed of 25 organisms cards (plus 15 blank ones), 8 promoters, 15 coding sequences (CDS) (plus 15 blank ones) & 8 terminator, as well as 53 story cards, allowing the participants to explain the story behind their creation.
In total I collected: 36 stories, 10 new CDSs and 5 new organisms.
There is no clear tendency in the answers, same range of fantasy story (8%) than proposal for health (7%). Being able to gather more data would help to identify a trend (if there is one). I could imagine developing a webapp, where users could create in the same way (with drag and drop) sequences and write stories link to them. Then, they could share them on social media.
In addition, it would allow to collect thoughts, reactions from the comments and like section. A very small questionnaire after the activity could also help to gather the data from the type of story produced, allowing live data analysis.
Half of the stories are human-centred, while only one quarter would modify human. It suggests that most of the modi cation imagined would be beneficial for humans even if an animal or a plant is the target of the modi cation.
Even though I encouraged to reflect on the consequences (advantages, risks…) on the story card, only 3 stories have a sentence about it. To get more insight on this aspect and encourage broader reflection, designing a longer activity would be necessary.
The sequence and the story would be the first chapter, then the participant of the workshop could have to spot what are the elements part of the ecosystem of this organism and relations with some aspects of human society: cultural effects, group behaviour, social change, social trade-offs, political and economic systems, social conflict, global interdependence… It would be asked to reflect on these connections and establish where could be the potential risks, dangers, uncertainties but also advantages, benefits or values. Each group could analyse the sequence of other groups. From that – chapter 3 – they would come back to their original design and have to change it, taking into consideration the observations from chapter 2. A second iteration of
the second chapter and a third iteration of the sequence could be considered. It would help to illustrate that each choice creates new conditions and entanglements with other factors which result in more constrains in the design.
The aim would be to emphasise the interconnectivity of ecosystems and human society, and how synthetic biology could become an important source of disturbance and that each new design should be carefully considered.
In order to allow to reflect on some of the stories already created, promote the project and share the ideas, I have decided to illustrate some of the cards. We could imagine a series of ‘postcards from the future’ as a series of illustration, promoted on a dedicated website or in an exhibition during a scientific conference, where these stories could be the starting point to discuss public opinion and ideas on synthetic biology as well as the implications of the discipline in human society and on natural ecosystem.
The next step in the development of this project would be to redesign the cards and create a game. Some aspects have already been explore with the help of Erika Szymanski, Research Fellow, Science, Technology & Innovation Studies at the University of Edinburgh.
Slime mould is an informal name given to several kinds of unrelated eukaryotic organisms that can live freely as single cells, but aggregate together to form multicellular reproductive structures. Slime molds were formerly classified as fungi but are no longer considered part of that kingdom.
… I developed a kind of obsession with these ‘creatures’.
They feed on microorganisms that live in any type of dead plant material. They contribute to the decomposition of dead vegetation, and feed on bacteria, yeasts, and fungi. For this reason, slime molds are usually found in soil, lawns, and on the forest floor, commonly on deciduous logs.
Within each protoplasmic strand the cytoplasmic contents rapidly stream. If one strand is carefully watched for about 50 seconds, the cytoplasm can be seen to slow, stop, and then reverse direction. The streaming protoplasm within a plasmodial strand can reach speeds of up to 1.35 mm per second which is the fastest rate recorded for any micro-organism. Migration of the plasmodium is accomplished when more protoplasm streams to advancing areas and protoplasm is withdrawn from rear areas. When the food supply wanes, the plasmodium will migrate to the surface of its substrate and transform into rigid fruiting bodies. The fruiting bodies or sporangia are what we commonly see; they superficially look like fungi or molds but are not related to the true fungi. These sporangia will then release spores which hatch into amoebae to begin the life cycle again.
When a slime mold mass or mound is physically separated, the cells find their way back to re-unite. Studies on Physarum have even shown an ability to learn and predict periodic unfavorable conditions in laboratory experiments. John Tyler Bonner, a professor of ecology known for his studies of slime molds, argues that they are “no more than a bag of amoebae encased in a thin slime sheath, yet they manage to have various behaviours that are equal to those of animals who possess muscles and nerves with ganglia – that is, simple brains.”
Atsushi Tero of Hokkaido University grew the slime mold Physarum polycephalum in a flat wet dish, placing the mold in a central position representing Tokyo and oat flakes surrounding it corresponding to the locations of other major cities in the Greater Tokyo Area. As Physarum avoids bright light, light was used to simulate mountains, water and other obstacles in the dish. The mold first densely filled the space with plasmodia, then thinned the network to focus on efficiently connected branches. The network strikingly resembled Tokyo’s rail system.
“Biologists first brought the slime mold into the lab more than three decades ago to study the way it moves—which has a lot in common with they way muscles work on the molecular level—and to examine the way it reattaches itself when split. “In the earliest research, no one thought it could make choices or behave in seemingly intelligent ways,” Reid explains. That thinking has completely changed.”
“The single-celled brainless amoebae did not grow living branches between pieces of food in a random manner; rather, they behaved like a team of human engineers, growing the most efficient networks possible. Just as engineers design railways to get people from one city to another as quickly as possible, given the terrain—only laying down the building materials that are needed—the slime molds hit upon the most economical routes from one morsel to another, conserving energy. ”
I am thinking to develop a political art installation using a series of Winogradsky columns.
They illustrates how different microorganisms perform their interdependent roles: the activities of one organism enable another to grow, and vice-versa. These columns are complete, self-contained recycling systems, driven only by energy from light.
Invented in the 1880s by Sergei Winogradsky, the device is a column of pond mud and water mixed with a carbon source such as newspaper (containing cellulose), blackened marshmallows or egg-shells (containing calcium carbonate), and a sulphur source such as gypsum (calcium sulphate) or egg yolk. Incubating the column in sunlight for months results in an aerobic/anaerobic gradient as well as a sulphide gradient. These two gradients promote the growth of different microorganisms such as Clostridium, Desulfovibrio, Chlorobium, Chromatium, Rhodomicrobium, and Beggiatoa, as well as many other species of bacteria, cyanobacteria, and algae.
The Biodesign Challenge offers art and design students the opportunity to envision future applications of biotechnology.
This semester I am part of the teaching team of the Biodesign Challenge course at the School of Design – University of Edinburgh. We are part of this international competition, were master and undergrad students are going to develop projects involving biology concepts in group of 3/4 around the theme ‘Communication’. The course is lead by Larissa Pschetz and Bettina Nissen, Naomi Nakayama & Eric Thorand.
Picture by Larissa Pschetz
Picture by Larissa Pschetz
Picture by Larissa Pschetz
The Biodesign Challenge offers art and design students the opportunity to envision future applications of biotechnology in a competition that highlights student work. Our organizers connect classrooms with a team of biologists and experts to guide the students as they develop their ideas.
At the end of the semester, the winning teams are invited to New York City to showcase their designs in front of members the academic, industrial, and design communities at the Biodesign Summit in June 2016.
The paper especially written for the conference with Larissa Pschetz, will be available soon.
Recent advances in biology and intersecting areas of research have brought a renewed interest in engaging with living materials. BioDesign is becoming increasingly popular, and has included diverse proposals, ranging from products that incorporate microorganisms as new, often considered more sustainable materials, to speculations on future impact of synthetic biology. In this paper we present three objects that incorporate living organisms as a way to reflect on the design process. We discuss how engaging with living materials could be considered a shift in traditional design practices, and the challenges of integrating design in current biotechnology development.
Synthetic biology is the science of designing biological systems.
The term “synthetic biology” has been used during the past century to describe a wide range of projects that bring an engineering mindset to biology.
The science of biology and the practice of engineering (knowing and making) are especially connected in parts-based synthetic biology, where many engineers and scientists seek to “build life to understand it” through the assembly of standardized genetic modules. Many synthetic biologists take inspiration from a statement left on Richard Feynman’s last blackboard at Caltech in 1988: “What I cannot create, I do not understand.” This line captures well the exchanges of “reverse transcription” between science and technology that characterizes much of the current research in synthetic biology: synthetic biologists take apart and rebuild biological networks in order to better understand them.
Edinburgh Genome Foundry
I had to learn about Synthetic biology as I have been for the past year a research associate at Design Informatics , as well as working at EGF : The Edinburgh Genome Foundry, a research facility specialised in the assembly of large DNA fragments using a highly automated platform.
In EGF, I mostly do UI and UX design for their different system, web site as well as Graphic Design to determine the identity of the facility. As a start, I researched different design tool for biologists, analyse the interface and understand the different representation they use to work with DNA: the circular view called plasmid view the linear view with the ACTG they use to design primers for example.
Before understanding that I had to come back to the basics of biology, DNA… watching for example Once Upon a Time… Life the series from the 80s, I had long discussions where biologists where explaining / teaching me how DNA works, what are the steps and basic grammar. I made interviews…
I had the great opportunity to collaborate with Autodesk Bio/Nano Research Group, to help designing Genetic Constructor : a high level web based design tool for Synthetic Biology. I had the immense privilege to work under Joe Lachoff (Senior Principal User Experience Designer) supervision. Genetic Constructor simplifies sequence design by organising DNA constructs into composable blocks. This keeps the interface clear and friendly even for complex projects, and makes it effortless to re-use parts between projects or to define c.ombinatorial libraries. The aim is to change the way DNA is designed and the methods employed to do it.
From that I had the idea to develop Dominoes (you can see on the front page of Genetic Constructor on the picture above) : a prototype of physical interface for biologists to design constructs, trying to encourage scientists to think about the design and less about the sequence. The next stage would to get picture of the design and import it in Genetic constructor, where it would be possible to upload the sequence afterwards. It could also be used as a game to learn the grammar of synthetic biology.
With Design Informatics the research part of my job started with mapping interests related to biology, the relationship between the different actors, the kind of projects made with synthetic biology : the scientific ones, the one made from iGem (an international competition for undergrad students interested in the field of synthetic biology), critical design, speculative design, product design, art projects… in order to create connection between the disciplines.
With Larissa Pschetz we had the idea of what we called Biological clocks. As designers start to consider materials that evolve through time and as part of complex ecosystems. This idea explores ways for design to employ synthetic biology in order to promote less anthropocentric views of time. We are interested to create biosensors and raises questions of how microorganisms can be designed to communicate issues that are important to a particular ecosystem – e.g.: plates of modified bacteria installed in the urban environment who would change colour in relation to the level of the pollution. Most importantly, it puts the ecosystem at the centre of the equation, helping to reflect on issues of time, design, and coordination beyond the social.
We also questioned the connection between Synthetic biology and human body. While scientist already think to create tattoo allowing to monitor your vitals signs, we are trying to imagine how our body could become an interface: what could we display and what are the ethical questions that will have to be raised if such technology was coming on the market.
I spend a lot of time in the lab to experiment and get familiarise with the living materials, bacteria and yeast, filming the growing process, experimenting to grow microorganisms from my hands, near a trash, on a wall… pick some colonies to get specific colours, duplicated them… playing around with living things.
We organised a workshop with scientists/ biologists / design and social scientists to explore how synthetic biology may affect and be influenced by design. How could access to biological materials be facilitated to artists and designers? What changes when we consider living organisms as a material for design? We interviewed some of the participants asking them about their vision of Synthetic biology and Design, their hopes and fears, how they see the future…
From this workshop and some previous ideas we developed an installation living with living things . In this work we explore what it means to live and design for a world where things have a live of their own, and where the lives of things become integrated with human practices constructing new everyday rituals.We present three concepts, of a) a fabric that evolves according to seasons and human care, b) a knife that is augmented with biological material to support consumption of specific foods and c) a sink that, as a clock, signalises when a particular action is needed. The three concepts reflect on the role of living things for our future lives as a) actively integrated in human routines, b) passive producers of contents for consumption and finally as c) commensal co-habitants of the human environment.
The following section is going to present a condensate of what I find interesting/fascinating in Synthetic biology.
Designing with living organism means two different things:
– you engineer a living organism to make it produce a substance (e.g.: creating milk by modifying yeast to produce the right protein to get milk)
– you engineer a living organism and use it as a product, this means you need to take into consideration new aspect when you are designing such as you need to feed whatever you are using with appropriate nutrients otherwise it would died (e.g.: modifying plants by incorporating fluorescent gene to make them glow).
Keep in mind that most of the work currently made in synthetic biology consist of building the tools of synthetic biology, it is still at an early stage. Most of the crazy idea we can have are still not feasible as working with living organism is very complex. Another thing we have to consider as designer are : how do you design using ‘invisible’ material ? Design with life ? Design against or with evolution ?
More over, there is this different categories of complexity around synthetic biology we should not minimise:
Discipline and data: we can read it, understand some of it, but we still don’t know why some parts of the genomes are important (can be yeast, bacteria… it gets even more complicated with the human genome), or how and why some parts relate to each other…
The heterogeneity and complexity of these relationships means that we may not be able to fully understand, predict, and control the function of synthetic biologies79 in a changing social and natural environment. Instead, we should approach the design of biological systems with more humility and with design principles that are more biological, emphasizing not control but adaptability, not streamlining but robustness, and not abstraction but complexity. Agapakis, C. M. (2013). Designing synthetic biology. ACS synthetic biology, 3(3), 121-128.
Experiments: genetic material is not easy to work with, need special temperature condition at different stages, you do your best to control these conditions but DNA design is about trials, error and assumption.
Until now, virtually every project has been a one-off – we haven’t figured out how to standardize the genetic parts that are the build- ing blocks of this new field. Researchers produce amazing new parts all the time, but much like trying to use someone else’s house key in your own door, it’s been difficult to directly reuse parts across pro- jects. (Biofab, 2013)
Complex boundaries between positive outcomes of the research and dangerous usage: Should we slow the research process because of fear of the unknown and miss important opportunities? Should we not take risk to avoid misused ? How to define boundaries ? It is difficult to see the bigger pictures and have predictions on how the research will be grasped by the industry or to assess the long-term effects.
About the ambivalence of Synthetic biology the early bio-artwork by Eduardo Kac, ‘Genesis’ (1998–9). Tac translated a bible passage into Morse code, and translated the Morse code into DNA base pairs and then finally genetic sequences, which he implanted into bacteria. He placed the genetically altered bacteria in a petri dish under ultraviolet light, which in-person and online viewers could activate. If a viewer disagreed with allowing humans to have dominion over nature as the quote from the Bible suggests, then in order to destroy the manifestation of the idea she could turn on the UV light which would cause mutations in the genes, thereby altering the statement; but in doing so, she would also be asserting her own power over nature. In both early and later artworks, human dominion over the natural world is ambiguously convoluted, since the human-made and the natural are increasingly co-existent and mutually constitutive.
Moreover, synthetic biology blur the distinction between species: using one species gene to modify another specie.
Indeed, while synthetic biology’s bioengineered generation and modulation of living matter has complicated how and what we determine as life, as the boundaries between living and nonliving, natural and artificial, organic and inorganic are becoming increasingly convoluted, we still cannot really say how these conflations and manipulations will fare, impact each other, or evolve in variable contexts, through multiple encounters and exchanges on micro to macro scales. Johung, J. (2016). “Speculative Life: Art, Synthetic Biology and Blueprints for the Unknown.” Theory, Culture & Society 33(3): 175-188.
This is also in relation with a contrast science fiction art projects around synthetic biology and scientific goals: some art and design projects will emphasise on the creation of creepy/monstrous creatures (see picture bellow), while scientists goal is to make more perfect creatures. One is concentrating on the worth case scenario and how the scientific research can become out of control when release from the lab. The other one tends to look only onto the short term, the academic aspect of the research or the bright side.
I will finished by this ‘letter’ for the Open Call Exhibition – For an exhibition titled: Yours Synthetically in the Ars Electronica Center, where they explore “current dialogue with biology, tackling the complex ideas, systems, models and unpredictable realities, in which the results will be long lived, as any changes to the planets biome will be, forever Yours.”
We have to talk.
Let’s just say that our relationship has been a bit challenging lately. We’ve had some ups and downs for sure, the ups of global temperatures and carbon in the atmosphere, and the downs such as the variety of species still sharing our planet.
As you know, I’m a bit concerned about our future. Take this whole area of synthetic biology for example. You say that you understand, that you care, but just because you’ve sequenced a few bits and pieces doesn’t mean you can read me like an open book. Sometimes it feels like I’m just another one of your machines. Is that it? Do you just want to engineer me?
These “synthetic” organisms you’re playing with, what are they going to be when they grow up? A bit of give and take wouldn’t hurt sometimes, not always you you you. My clock is ticking and I really need some commitment from you, what’s your long term plan? Do you even have one?
Yours Synthetically, Life on Earth Open Call Exhibition – For an exhibition titled: Yours Synthetically in the Ars Electronica Center, in Linz Austria, 2013.
I had the honour to be invited by George Cao on Nov 8 (2016) to give a talk at the Autodesk Shanghai Designer November Meetup. 20+ designers attended, I presented my work as a researcher and a designer @ Edinburgh University and @ EGF, and particularly about my contribution during the collaboration with Autodesk Bio/Nano Research Group working on Genetic Constructor. Most of the content of the talk can be found in this other blog post : biodesign talk.
“In her inspirational talk around the topic of “Designing with Living Things”,
Anais guided designers to get a glimpse of Synthetic Biology and how to design user-friendly tools for this domain. Designers were fascinated both by the complexity of Synthetic Genomes technology and how Anais translates it into a modernized and easy-to-understand application UI with the design thinking behind the scene. She also showcased some of her works of conceptual design & art which are futuristic and pretty inspiring.”
It was such a pleasure to meet with the all team of designers, being able to discuss with the people who are conceiving and developping some of my favourite app (sketchbook on iPad, AutoCAD…). I hope I will be able to see everyone again soon. Thank you again.
On 12th July 2016, we (Larissa Pschetz and I) organised the Design meets Synthetic Biology workshop, where we invited biologists, engineers, designers, artists and social scientists to design domestic artefacts through the lenses of synthetic biology, also considering issues of representation, access and perception of this emerging field.
Recent advances in synthetic biology, together with a renewed interest in engaging with living materials, have motivated designers to question traditional ways of carrying out and understanding their practice. As designers start to consider materials that evolve, through time and as part of complex ecosystems, issues of form, function, user needs, as well as ideas of modernity and progress start to lose their traditional centrality. To explore novel design methods we invited biologists, engineers, designers, artists and social scientists to participate in a workshop to discuss issues of representation, access and perception of synthetic biology. We were particularly interested in exploring how synthetic biology could be affected and influenced by arts and design.
Our initial questions were : How could access to biological materials be facilitated to artists and designers ? What are the abstractions and models adopted in synthetic biology, and how do they influence materials, access and new designs ? Could artists and designers contribute to create new representations of synthetic biology ? What are the narratives and facts in synthetic biology and how do they influence design and art practice ? What changes when we consider living organisms as a material for design ?
We divided the workshop into 3 sessions. The first one was a series of Pecha Kuchas from participants representing the different disciplines. It was meant to allow everybody to grasp the multidisciplinary facet of synthetic biology, open new perspectives and discussion on synthetic biology and give scientific insights to participants not familiar with the subject.
It was followed by a first exercise called: Representations and Processes. We asked the participants to discuss and sketch the process they would go through when designing from DNA to a ‘thing’. They were encouraged to think about appropriate tools, models, collaborations at different stages of the process. We wanted to identify and define what we called ‘black boxes’: the steps which are too abstract when you don’t have specific scientific knowledge, when the key of complex mechanisms have not been discovered yet or when you don’t have the appropriate tools to design living organism.
The second exercise was a design challenge. We asked the participants to redesign three objects: a knife, a blanket and a clock using synthetic biology and following a design process: brainstorming on attribute and function of the object, sketch and prototype with provided craft material. Going through this iterative process on different objects and with different partners we wanted to extend the potential outcomes and encourage discussions between the different participants. We were expecting the participants to grasp the challenge of designing with life, which also means dealing with evolution, to explore what it means to live and design for a world where things have a life of their own, and where the lives of things become integrated with human practices constructing new everyday rituals. We also wanted to observe if the interaction with the surrounded environment and broader impacts on the ecosystem would be taken into consideration or if the debate would stay around the design of the object, as well as is the morning discussions would have an impact on the design process they will go through.
The first observation would be that as we did not particularly emphasise that to make a link between the morning exercise and the afternoon one, and as the groups were different we did not noticed an obvious link between the two. Moreover, by asking to redesign common everyday object using synthetic biology we constrained the participants to add value to something which has been designed and re-designed for centuries. We made this decision to avoid frustration of not coming up with new concepts, and to give a starting point for discussions. However, at the same time we prevented to come up with innovative design ideas. It was a safe choice, nevertheless we have to open to the idea that what synthetic biology is going to bring to society brand new concepts and products that have not been developed yet and not only going to add value to existing concepts like it is currently (cheese made from engineered yeast, biosensor, fuel…). To arrive to this stage we will have to develop innovative ways to design, new tools and methods. Design with this invisible material which is DNA is not something which will come intuitively and we have to accept to go beyond traditional methods.
This field at the intersection of engineering and biology is opening new perspective and practice in term of new material: engineering a living organism such as yeast to make it produce a new substance, or engineering a living organism and use it as a product. Consideration of environment, nutrition, evolution, waste management… would have to be taken into account. Again, by asking during the workshop to re-design every-day life objects we tend to concentrate on the traditional form and function and forget about broader issues tied up to working with life.
Genetic material is a complex material to work with, experiments are complicated and our limited knowledge of genomes make positive outcome difficult to get. DNA design is about trials, error and assumption which make it currently only accessible to biologists. This is why some expert in the field see in robotics and computing the way to go in order to democratise synthetic biology: control of the optimal condition, experiments can be reproduced easily, combinatorial is made available at lower cost enabling to try large combinaisons of design in order to find the most effective one…
One of the concern raised during the closing discussion was that the design proposal where again using synthetic biology to tackle the symptoms of problems instead of the roots. The participant was reacting to one of the ideas developed by a couple of different teams: blankets for homeless people. She rightly noticed that design would often be developed to improve a bad situation without resolving the core of the issue. A good usage of synthetic biology might be to tackle the core of issues instead of addressing symptoms.
Finally, another concern was about the trendy topic since the Human write project has been announced: are we ready to design humans? Are designer going to be involved in the process ? And if yes, as we have already product design, web design, interaction design… is a new field going : human design ?