Category: Science and art

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

 

Slime Mould

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.

 

From How Brainless Slime Molds Redefine Intelligence by Ferris Jabr:

“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. ”

Other links

http://www.pnas.org/content/109/43/17490.full
http://www.bbc.co.uk/nature/19846365
http://www.wired.co.uk/article/slime-mould-art
https://www.theguardian.com/science/grrlscientist/2015/feb/09/slime-mould-and-researcher-set-to-play-piano-duet

Winogradsky Columns

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.

 

 

Useful links

https://en.wikipedia.org/wiki/Winogradsky_column
http://www.sumanasinc.com/webcontent/animations/content/winogradsky.html
http://archive.bio.ed.ac.uk/jdeacon/microbes/winograd.htm
https://www.scientificamerican.com/article/bring-science-home-soil-column/
http://www.personal.psu.edu/faculty/j/e/jel5/biofilms/winogradsky.html

Biodesign Challenge

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.

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.

from Biodesign Challenge Website

Research Through Design 2017 Conference

I will be presenting the project ‘Design with Living Things’ (previously ‘Living with Living Things’) at the Research Through Design 2017 Conference hosted at the National Museum of Scotland (NMS) in Edinburgh between the 22nd and 24th of March 2017.

The paper especially written for the conference with Larissa Pschetz, will be available soon.

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.