Tag: Synthetic Biology

Publication about Genetic Constructor

While I was working as a research associate in EGF and DI, I have been working with Autodesk Life Sciences on a new software: Genetic Constructor, developed to support synthetic biologists to design DNA, creating a “new visual language that focuses on functional parts abstracted from sequence”. A paper about it was published at the end of last year in ACS synthetic Biology and I am one of the author, making it my second academic publication after Designing with Living Organisms for RTD.

 

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

ACS Synth. Biol., 2017, 6 (12), pp 2362–2365
DOI: 10.1021/acssynbio.7b00236
Publication Date (Web): October 11, 2017
Copyright © 2017 American Chemical Society

ABSTRACT

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.

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.

Videos from Design Meets Synthetic Biology Workshop

More informations in a blog post I wrote few months ago and this published bog post from innovate UK.

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. 


I created two video clip from the individuals interviews we made of some of the participants during the workshop. We asked them to share their vision of the future synthetic biology, their hope and fears… The result gives an overview of the range of practitioners gravitating around the discipline. The long version (18m10s) is aimed to be used as an exhibition piece. The shorter version (6min14s), is to publicise the workshop, be shown during lectures and presentations.

 

 

“Designing with Living Organisms” at Research through Design (RTD) conference 2017

I had the chance to present “Designing with Living Organisms” at Research through Design (RTD) conference  2017

Research through Design (RTD) conference  hosted at the National Museum of Scotland
22nd – 24th March, 2017
Collaboration with Larissa Pschetz
Edinburgh, Scotland 2017

The paper presented the process I went though and the issues I had to face when designing and exhibiting living organisms.

 

ABSTRACT

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.

 

 


 

The knife piece has been chosen as Provocation #1 during the Museum Panel session to discuss how do museums go about selecting which of today’s objects need to be preserved and why? How do they use these to map the lineage of our material culture, and how important are museum collections in giving rise to the new? What are the curatorial processes in place to achieve this? More precisely the role of the museum to ‘kill’ artefacts in order to collect or to keep artefacts alive.

 

 

From Twitter

 

Workshop Design meets Synthetic Biology

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. 

Published bog post HERE (shorter 😉 )

 

 

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 ?

The outcomes of this workshop inspired a dedicated exhibition called “Living with Living things” taking place at the Edinburgh Art Festival and Edinburgh Digital Entertainment Festival from the 4th to the 28th August on George Street. It will be part of the the exhibition  “Living with Data: Design Informatics” hosted in the the Pavilion commissioned structure by Pierre Forissier from Biomorphis Architects houses.