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.