Stress-o-stat


Dr. Howard Boland
Director, C-LAB, University of Westminster, School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK
Email: howard@c-lab.co.uk 
Web: http://c-lab.co.uk
Reference this essay: Boland, Howard. “Stress-o-stat.” In Leonardo Electronic Almanac 22, no. 2, edited by Senior Editor Lanfranco Aceti, and Editors Candice Bancheri, Ashley Daugherty, and Michael Spicher. Cambridge, MA: LEA / MIT Press, 2017.
Published Online: January 15, 2018
Published in Print: To Be Announced
ISSN: 1071-4391
ISBN: Forthcoming
https://contemporaryarts.mit.edu/pub/stress-o-stat

 

Abstract

Stress-o-stat is a living artwork that visually captures stress in bacteria as light. The work explores convergence between life and machine, where the machine becomes lifelike and the bacteria, engineered through synthetic biology, machine-like. Stress-o-stat is a result of an immersive and independent laboratory practice using synthetic biology to develop new types of artistic expression. A special genetic switch involved in stress response was located and combined into a genetic construct to produce fluorescing proteins. Once implemented in bacteria, fluorescing proteins are expressed during oxidative stress, producing a yellow-green color in response to blue light.

Keywords

Synthetic biology, bio art, bacteria, stress, engineering behavior, genetically modified organisms

 


Final set-up of Stress-o-stat, 2011. Photograph by Howard Boland (C-LAB). © Howard Boland, 2011. Used with permission.
Final set-up of Stress-o-stat, 2011. Photograph by Howard Boland (C-LAB). © Howard Boland, 2011. Used with permission.

 

Background

Stress-o-stat employs modern biotechnology and genetic manipulation of living matter to create novel artistic expressions. As part of the doctoral research titled Art from Synthetic Biology, [1] it proposes that much like computational affordances (e.g. algorithms, databases, software, and hardware), synthetic biology through its material and methods may offer new potentials in the arts. The research impinges on biology and is informed by bio art practices using living matter as its media. Scientific evidence-based processes were used to design, develop, and analyze outcomes. The work provides an example of how artists may be able to independently develop and generate novel behavior by tapping into invisible processes in bacteria using genetic tools in synthetic biology.

Stress-o-stat utilizes recent standardization processes to expand the language and boundary conditions of art by reflecting on: (i) how art may help broker understandings of ‘life’ in non-human biological systems; (ii) what sort of interfaces we can build to enable such access; (iii) the questions that emerge combining programmatic logic with living matter; and (iv) the challenges faced when exhibiting such works (particularly in the UK).

 

Scientific Context

Synthetic biology introduces both new methods and material to molecular biology. Within (molecular) synthetic biology, three major strands exists: minimal genome [2] attempting to minimize (genetic) components needed to sustain life; orthogonal ribosome [3] expanding protein encoding systems to create new material possibilities; and ‘standardized parts,’ where this work is situated, aimed at developing standardization practices and methods to allow genetic manipulation and material to be more accessible. [4] Synthetic biology borrows, combines, and replaces natural biology in order to generate predictability in living systems by applying programmatic logic (e.g., assembly methods and behavior logic) to tap into novel properties and materials (of the living and its environment).

 

Artistic Aims

Stress-o-stat aims to draw out connections between inner biological processes and outer visual characteristics. Although bio art is understood as an art practice manipulating life processes on discrete levels, [5] as an ‘interaction’ (i.e. audience experience) it focuses on aesthetics, as well as performative, anthropomorphic, and ethical aspects. Stress-o-stat attempts to expand upon modalities by tapping into interactive cellular processes on a genetic level through synthetic biology and to allow these to be visualized. The need for artists to take into account biological meaning (e.g., what is being communicated) and knowledge processes has so far been overshadowed by cultural ideas and themes [6] that play little, if any, role on a biological or biochemical level.

Limited artistic practices investigate scientific methods and material on a molecular and genetic level. Overcoming these limitations requires artists working independently (i.e. outside collaboration) to acquire scientific knowledge, processes, language, and methods, and to situate a context in which to provide material and operational access. This research involves a lengthy, immersive laboratory practice, an appropriate method to undertake such work. Synthetic biology offers artists more structured methods for achieving outcomes through a programmatic approach that involves reducing genetics to components or parts that can be connected through assembly methods and form more complex devices or behavior. Much like electronics and computational technologies adopted by artists, synthetic biology, following a similar dialectic, is reformulating genetics into an approachable technology. For instance, could synthetic biology be assimilated by artists as computer programming was?

Despite shared symbolic connections between the virtual and biological, particularly through the concept of codes governing both forms of expressions, these systems have different ontological, epistemological, and material foundations, and cannot simply be reduced to the same category. Synthetic biology does however attempt to bring these ideas into proximity by producing greater behavioral predictability in biological systems. So while synthetic biology includes computational thinking, the material foundation of biology is such that a practitioner must learn how to handle this.

 

Preliminaries

Early stages of the research involved much learning, focusing on classic recombinant methods and molecular biology by observation of growth and colony development in Escherichia coli. While growth as a process can readily be explored by artists, my interest was directed toward behavioral changes, such as swarming and how bacteria undergo various phases during growth. In order to see differences in growth as behavior, initial questions asked: What genetic system could be built to visualise physiological states? And how can we go about connecting changes in behavior with expressions of proteins such as pigments or fluorescence?

It was understood that bacteria migrating in front of a colony would have more nutrients available than those in the center. As a result, the center would be more prone to oxidative stress since metabolic cycles are likely to destabilize under these conditions and accumulate radical oxygen. As conditions deteriorate, a known genetic and enzymatic stress reducing mechanism in bacteria enables the production of the enzyme catalase that reduces radical oxygen to water. By investigating components involved in creating the enzyme, a genetic system could be built. While genetic expressions are highly controlled events often involving multiple factors, by identifying a gene, katE, [7] responsible for encoding catalase, it became possible to locate a component known as a promoter that drives the transcription of this gene. In short, we may consider the promoter for katE to be a genetic switch capable of turning on the expression of a gene.

To develop a genetic solution, small circular pieces of DNA known as plasmids were used, as these can host genetic circuits, replicate, and co-exist with the genome. In general terms, the katE promoter could be used as an independent genetic part and promote the production of alternative proteins, such as green fluorescent proteins (GFP) expressed during stress. This potential of shuffling genetic components gives recombinant and synthetic biology a programmatic ability.

 

Material & Methods

The parameters, such as directionality and distance between katE and the promoter, suggested its sequence and location on the bacterial genome. [8] A physical product of the sequence was generated by synthesizing primers and using a polymerase chain reaction (PCR). Having registered with the Registry of Standard Biological Parts, [9] a physical library of genetic parts was available, and a standardized, green fluorescent reporter construct (BBa_E0840) [10] was selected. The final construct was made by digesting both the switch (promoter for katE) and the reporter construct with specific restriction enzymes making ends compatible, and then repairing these by ligating to connect parts into a final plasmid. Once introduced in bacteria, the switch would express GFP during oxidative stress, visualized as an iridescent yellow-green light.

Continuous growth made it difficult to differentiate oxidative stress and growth. To control stress parameters as light, the work employs a fermentation setup called a chemostat to maintain constant cell population using a three-tier system—a feed, a fermenter, and a deposit. It consists of tubes, vessels, and pumps connected in a functional manner to maintain homeostasis. With changing parameters (e.g., decrease in nutrient), the stress is visualized as fluctuating light.

The basic setup used two pumps, one providing fresh broth from the feed into the fermenter, and a second to remove surplus culture from the fermentation surface. By measuring cell density at intervals and regulating the flow, equilibrium was established. The installation uses light, filters, and a condenser to complete the stress-sensing device both functionally and as an experimental aesthetic of scientific parts. An external ‘window’ was created using a glass Graham condenser placed on the outside and connected with tubes, allowing culture from inside the fermenter to be flushed through. A blue transilluminator was fixed behind the condenser, and polarized orange filters blocked the blue light, leaving only fluorescence emitted by proteins.

 

Exhibiting Genetically Modified Organisms (GMO)

Whilst knowledge processes governing the production of such works involve a great deal of learning for artists, subsequent challenges follow when attempting to publicly stage these works. For instance, in the UK tissue culture has been exhibited on several occasions (e.g., the Wellcome Trust, GV Art Gallery, FACT), but exhibiting GMO is a relatively new activity, and it has been difficult to locate any previous example of such displays.

An important development was the event “Synthetic Biology: Machine or Life?” [11] organized by C-LAB and UCL iGEM at the Science Museum’s Dana Centre. It aimed at exhibiting two living GMO artworks, Stress-o-stat and Banana Bacteria. [12] In spite of prior agreements, my university requested these to be retracted after consulting the Health and Safety Executive (HSE), instead suggesting simulating Stress-o-stat using natural bioluminescent organisms such as Vibrio fischeri; we were rejected, thus postponing what would have been the first art exhibition of this kind in the UK.

In the past, several art exhibitions in the UK have seemingly featured GMO. For instance: Critical Art Ensemble’s GenTerra (2001) [13] supposedly exposed GMO bacteria to the environment at the The Darwin Centre, Natural History Museum, London; Jun Takita’s Light, only Light (2004) [14] had transgenic moss that was intended to be exhibited at Sk-interfaces, FACT Arts Centre, Liverpool, but was replaced with unmodified moss; and though not in the UK, Eduardo Kac’s Eduina (2009), [15] a genetically modified plant containing a gene from the artist, was exhibited at the Science Museum Dublin, though a PCR verification showed no traces of human genetic material. [16] Claims of exhibiting such material as art, at least in the UK, remain uncertain, and it is difficult for the public to verify such claims.

To establish a framework to overcome such challenges, discussions with HSE showed that it is possible to exhibit GMO by extending existing institutional GMO licensing to include external premises. In addition, an application was made to the university’s ethics committee which was endorsed. While it has yet to be put into practice, an agreement can be reached on exhibiting GMO in the UK. [17]

 

Outcomes

Given UK specific background, Stress-o-stat premiered in Mumbai, India (January 2012), and was the first public exhibition involving living molecular synthetic biology artworks. Setting up the work involved transportation of GMO material, growing material from small to large volumes, and reconstructing the installation. Since the lab work was performed by myself, access to a laboratory space and equipment was provided by the Biological Systems Engineering Laboratory at the Indian Institute of Technology, Bombay. [18]

Despite the complications of working in a foreign laboratory, the wet work for Stress-o-stat went as planned, much indebted to the researchers who facilitated their resources with limited time. Some of the material had to be sourced from the lab, and the final display is partly influenced by this. Like previous setups, it included a fermentation unit, pumps, a condenser, and a blue transilluminator. The system was transported from the laboratory to the exhibition and securely mounted. Despite bright light condition, visualizing fluorescence worked well as audiences were given orange filtered glasses to visualize the fluorescence, and this was further compensated for by using a UV light. The exhibition had over 90,000 visitors, and our space was often overcrowded, making any interaction with the displays difficult. We learned by speaking with the audience that Stress-o-stat was well received, but the exhibition highlighted a new set of challenges facing organizers wanting to include living, synthetic biology art.

 

Discussion

Synthetic biology often postulates a machine-like understanding of the living (e.g., devices, chassis, reporters, circuits), describing it as programmable. Nonetheless, by deconstructing and constructing new living systems, it also enriches perspectives of life. In opting for a tool language, it may seek to ease transitions of instrumentalizing life. Biology, understood through machine parameters, drafts life as a technology, making it accessible to a wider number of practitioners across disciplines. While digital technology’s movement toward simulating lifelike behavior suggests an expanded realm of the living (e.g., robotics, artificial intelligence, third order cybernetics), synthetic biology, in its adaptation of engineering structures, emulates an understanding of life as a machine.

Bio art has previously focused on mythical, ethical, and social perspectives of genetics. With synthetic biology, this ground is rapidly shifting toward a more detailed focus on constructing and developing bio matter situated on the borderline between machine and life. Stress-o-stat partakes in these ambiguities by employing a machine (the chemostat) to control the genetic program mediated through the living. In setting up the system, it also produces an organismic installation reminiscent of a life-support system by integration of pumps, tubes, cells, dripping liquids, and light. Operating between these layers, the work unfolds and connects two interfaces that allow biological signification to emerge. So, while the interplay between synthetic biology and the control apparatus accentuates hybrid notions of life and machine (i.e. life becoming machine-like and machine life-like), as a stress-sensing device it pushes further by undressing a small portion of a biochemical universe through genetic mediation. Art in this context is no longer situated only on the outside, but emerges and expands from within. The work playfully associates itself with instruments or devices such as thermometers and barometers used to guide our senses and read our environment. But rather than being a guide to our world, its invention deliberates ideas of extending our senses and exploring non-human worlds.

 

Conclusion

The work shows that scientific processes remain ramified, but it is possible for artists to develop an independent practice given institutional access. Exhibiting such works is challenging. In spite of having to postpone the exhibition of Stress-o-stat in the UK, at least one proposed framework has emerged; however, there remains a need for clearer regulations for artists to exhibit art involving GMO. While earlier stages of the work used classic recombinant methods, they benefited from the efficiency afforded by synthetic biology (e.g., material access, standardization methods, and characterization). Stress-o-stat involves building a two-part interface system: one layer that operates on a genetic level by tapping into oxidative stress by producing light, and a second layer to visualize and control parameters. In doing so, it begins invisible biological processes, opens up artistic possibilities, and deepens understandings of the living.

 

Glossary

Compatible ends: sequence ends or overhangs left behind when restriction enzymes cleave DNA

Digesting: a process of cutting DNA. Digestion is done by restriction enzymes

Enzymatic: a reaction whereby components are converted by enzymes

iGEM: The international Genetically Engineered Machine competition, an annual University competition spun out of Massachusetts Institute of Technology and organized by the iGEM Foundation

Ligating: a process of binding together compatible DNA strands; requires an enzyme (e.g. ligase) that repairs DNA ends

Oxidative stress: physiological stress caused by increase in reactive oxygen capable of destabilizing many cellular processes

Primers: short strands of nucleic acids (genetic sequences) used to start DNA replication; can be chemically synthesized and used to replicate DNA

Restriction enzymes: enzymes that cut DNA by recognizing specific sequences

Transcription: a processes of copying a sequence of DNA (creating a complementary sequence)

 

References and Notes

[1] Howard Boland, Art from Synthetic Biology (London: University of Westminster, 2013).

[2] P. E. Purnick and R. Weiss, "The Second Wave of Synthetic Biology: From Modules to Systems," Nature Reviews Molecular Cell Biology 10, no. 6 (2009): 410-422.

[3] W. An and J. W. Chin, "Synthesis of Orthogonal Transcription-translation Networks," Proceedings of the National Academy of Sciences of the United States of America 106, no. 21 (2009): 8477-8482.

[4] D. Endy, "Foundations for Engineering Biology," Nature 438, no. 7067 (2005): 449-453.

[5] Jens Hauser, "Bio Art—Taxonomy of an Etymological Monster" in Hybrid - Living in Paradox, ed. G. Stocker and C. Schöpf (Linz: Hatje Jantz, 2005); J. Hauser, "Biotechnology as Mediality: Strategies of Organic Media Art," Performance Research: A Journal of the Performing Arts 11, no. 4 (2006): 129-136; Eduardo Kac, Signs of Life: Bio art and Beyond (Cambridge, MA: MIT Press, 2007). 

[6] Eduardo Kac, "GFP Bunny," Eduardo Kac's official website, http://www.ekac.org/gfpbunny.html (accessed September 10, 2010).

[7] Catalase HPII, heme d-containing, NCBI Reference Sequence: NC_000913.2. NCBI.

[8] A. Zaslaver et al., "A Comprehensive Library of Fluorescent Transcriptional Reporters for Escherichia Coli," Nature Methods 3, no. 8 (2006): 623–628.

[9] iGEM, "Registry of Standard Biology Parts," the website of the International Genetically Engineered Machine (iGEM) Foundation, http://parts.igem.org/Main_Page (accessed March 10, 2014).

[10] J. Braff, 2004. GFP generator, BBa_E0840. Boston.

[11] C-LAB, "Synthetic Biology: Machine or Life?" the website of C_LAB, October 20, 2011, http://c-lab.co.uk/events/synthetic-biology-machine-or-life.html (accessed March 10, 2014).

[12] Banana Bacteria, Howard Boland, 2011.

[13] GenTerra, Critical Art Ensemble and Beatriz da Costa, 2011.

[14] Light, only Light, Jun Takita, 2004.

[15] Eduina, Eduardo Kac, 2009.

[16] John Michael Gorman (Science Museum Dublin), e-mail message to author, October 18, 2011.

[17] The author has since succeeded in carrying out in the first public art exhibition featuring living genetically modified microorganisms in the UK, which included the installation Stress-o-stat. This represents a milestone in bio art practices and highlights the challenges of putting such matter on display. The exhibition was hosted at the Royal Institution of Great Britain with a special evening event held on the 10th of April 2013. C-LAB, "Art from Synthetic Biology," the website of C_LAB, April 12, 2013, http://c-lab.co.uk/events/art-from-synthetic-biology.html (accessed March 10, 2014).

[18] C-LAB, "C-LAB Premiers Living Synthetic Biology Works at Techfest 2012," the website of C_LAB, January 8, 2012, http://c-lab.co.uk/events/c-lab-premiers-living-synthetic-biology-works-at-techfest-2012.html (accessed March 10, 2014).

 

Acknowledgments

Experiments were conducted at the University of Westminster, School of Life Sciences. I would like to express my sincerest gratitude to Dr. Tom Corby and Dr. Mark Clements. A special thanks to C-LAB’s Dr. Laura Cinti, members of the lab C.505, Dr. Anatoliy Markiv, Dr. Armaghan Azizi, and fermentation manager Neville Antonio.

The research was supported through a doctoral award from the Arts and Humanities Research Council and with support from the University of Westminster, School of Media Art and Design. Specialist material was kindly donated by Clare Chemical Research. Plasmid donated for preliminary research provided by Weizmann Institute of Science.

 

Author Biography

Howard Boland (PhD, MA Digital Practices Distinction, BSc Hons Software Systems for the Arts and Media, BSc Mathematics) is a multidisciplinary practitioner working across art, science, and technology. With strong technical and innovative creative skills, his experience spans from artistic and scientific research contexts to leading projects and teams in the interactive industry. Howard is the artistic director of the x-organisation C-LAB, specializing in biological art. His PhD (funded by the AHRC and the University of Westminster), entitled “Art from Synthetic Biology,” combined synthetic biology and art to produce novel visual expressions in bacteria, culminating in the UK’s first art exhibition featuring living, genetically modified microorganisms at the Royal Institute of Great Britain. He has extensive experience in the digital creative industry leading creative and technical teams to award-winning projects.