Category: Technology

Design meets Synthetic Biology Video @ BLACK BOX in Newcastle

“Design meets Synthetic Biology”  has been selected to be part of the session “Futures” during the BLACK BOX Pop-up Cinema event @ Bio-Medicine West Wing Foyer, Newcastle upon Tyne,  from 4 Feb – 1 Mar 2019.

Thank you to Louise Mackenzie for giving me the opportunity to show this Video clip I made while I was a Research associate @ Design Informatics in 2016. 

It was the first time this video was publicly shown, and even thought I could not attend the screening, I am very proud and happy that this creation finally made it out from my computer 🙂 

 

 

On 12th July 2016, in Edinburgh, during ‘Design meets Synthetic Biology workshop‘, biologists, engineers, designers, artists and social scientists were invited to discuss issues of representation, access and perception of synthetic biology. 
We asked them to share their vision of the future synthetic biology, their hope and fears…
This video aims to represent the voices of a range of practitioners gravitating around the discipline but disconnected from each other. Far from a single united vision, it depicts the complexities of working with living material (working and understanding living materials, prediction of long term effects, ethic concern…) and paradoxical opinion surrounding the discipline (complex boundaries between positive outcomes of the research and dangerous usage…).

 

Dominoes

More informations in the report produced along the process.

The Dominoes have been designed as a concept of a tangible interface for biologists to sketch DNA constructs. The interface consists of a series of pieces representing different DNA parts, using Synthetic Biology Open Language (SBOL).
By manipulating these pieces and snapping them together biologists can sketch DNA sequences. Then, the aim of this project would be to be able be transferred into Genetic Constructor (Autodesk CAD tool for DNA design) to insert the sequences into the sketch blocks and test the validity of their design.
It could then be send to be assembled by Edinburgh Genome Foundry (EGF), a facility at the University of Edinburgh that offers a unique robotic platform to synthesise DNA.
 


 
I have conducted a series of interview with biologist to determine what are the needs: how do they currently design DNA, how they would use them, where, when, what symbols or shape they are using most, do they need different kit depending the organism they are working with (yeast, mammalian cells, plants…) …
It also allowed me to discuss their projects to determine what could be potential future needs. I am currently in the process of designing the fist set of prototype to be tested in different labs at the University of Edinburgh.
 

 
In addition, during these interviews, we discussed 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. It resulted in another project ‘Tales of Synthetic Biology’ presented Here.

From these interviews I have designed a kit of general blocs and 3 different options for the EMMA kit.

Design – general blocs
  • Use of 5 different colours for the coding sequence (promoter – CDS – terminator) to visualise 1 transcription unit. It will be useful when one transcription unit is will be to be express in the bacteria for the duplication (antibiotic resistance for example) and others will be expressed in the plant/yeast…
  • Blank pieces with directional arrow for projects where the direction is crucial at the early design stage.
  • Larger pieces for Transcription Unit (containing promoter – CDS – terminator) for high level sketch.
  • Small pieces for localisation signal, tag… to annotate some aspect inside a block
  • Two different proposals to visualise the strength of a promoter.
  • Two special set to design sequences for Golden Gate of Gibson assembly, in-order to determine the ending and connecting sequence of the blocks.
  • Each type of block is done with a speci c colour + a symbol to give the maximum visual markers, helping to design a sequence.
Design – EMMA kit

One kit where the colours correspond to type of the blocks, one where they correspond to position of the blocks and finally to the type of the blocks and they are numbered for the position.
 

Tales of Synthetic Biology

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.

I have tested them during 5 sessions (more than 20 people from designers, artists, biologists, engineers, technicians…) and twice during Louise Mackenzie ‘Transformation – Thinking Through Making With Life transgenic bio-art’ workshops at ASCUS lab Summerhall as part of Edinburgh International Science Festival 2017.

 

 

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.

Biodesign Talk

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.

Design Informatics

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.

Interests

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.”

 

Dear Humanity,
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.

Revealing map (project proposal)

For this idea I also looked into the concepts of ‘creating your own border’ and ‘staying in your confort zone’, however, this time on ow to expend our territories and encourage to reflect on all the place we will have to discover in our life.

For that, I want to create a mobile app: it will be a white page when you start using it for the first time, then the map will reveal itself when you went somewhere physically.
I tried to make a visualisation of my idea in this short animation:

In my head it is quite a simple idea (coming from a person who don’t have any experience in coding yet 🙂 but we already told me that it is not as simple and I am worked I will not be able to make it on time for the 13th of december.
One way I think it might be possible is to make a reverse heat map: instead of having colours appearing on a layer on top of the map, it would make transparent the white layer.

The second stage of this project (depending how difficult it is to do the ‘simple’ idea), would be to make the map appearing in different shade of colours: for exemple the area you use all the time (’your territory’: going to work and back home for example) would be tinted in red, whereas the one you visited only once would be blue.

Looking @ ‘to be disconnected’

On my last post about the different topic I was looking I developed the one on borders.

Since few days I was looking at ‘to be disconnected’ in relation with happiness (the border theme also have a connection with happiness in the way I see it). I looked at the fact that when you work you are expected to answer an email promptly, or the time spending on social media in comparaison with ‘human’ (see this post).

On this topic I am interested in making the ‘invisible’, ‘visible’ (same ideas with the borders, I guess happiness and make the invisible visible are the commun aspect in both cases). Visualise all the data surrounding us all the time.

I am asquint the question: is there a correlation with being more connected? If you are in an environment with less radiation would you spend less time on your mobile?

For that I would like to measure:

• the level of radiation corresponding with location and to see if the person is more connected when there is more waves around (link GPS tracking and, data transfert and level of radiation).

• how much data transferred on a location (link GPS tracking and data transfert) and superpose with the map of coverage

• the number of word exchange with a real person in comparaison with number of word with social media (or time speeding corresponding verbally and on social media)

I guess it is maybe less interesting than the ‘border’ theme, as a lot of people are looking at the subject currently with these app helping to disconnect: Freedom, I Off You, Antisocial, Forest or the wall paper which block radiations, and the WiFi cold spot.

I read that problems linked up with hyper connectivity are more a society issues (we use technology to respond to what is expected from us… ) and not a technical issue. Create more technology to not use technology seems not the right things to do, it is “the cat biting its own tail”.

I don’t think I can come with anything to change today society, because it means to solve a question of hierarchy (have the power, to be disconnected against society expect me to be connected all the time), also job organisation and planification, and  finally todays life style (teenagers hyper connected…).

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