Computing the Microbiome: A New Network

What can we reveal about the Human Microbiome through speculative interactions between microbes and computers?

produced by: Danny Keig

This multimedia paper centres around the human microbiome, and explores the ways in which threads of art, science and technology interleave to create artefacts which critique the current modes of practice and thought. In delving into this topic, I aim to speculate about what a future interaction between the microbiome and technology might look like, good or bad, informed by aspects of ecology, or digital ecologies. Nature has played a predominant role in the history of computing thus far, from evolution inspiring genetic algorithms, to functioning of the brain inspiring neural networks in the field of machine learning, to think of nature as an informant to computational processes is to excite the non-living with traits of autonomy. In this paper, and through a series of digital artistic experiments exploring possible interactions between microbes and machines, I will put forward the case that speculation as an artistic process is vital to promoting new ideals through art.

In exploring a speculative interaction between the human microbiome and machines, there are certain facets which I hope to reveal and place at the forefront of its discourse, and by incorporating a Feminist TechnoScience framework my aim is to critique existing practices and thoughts. I hope to illustrate that the human microbiome may become a potential collaborator with computational processes, through inspiring technological frameworks, or by seeding or executing programs. I hope to explore ways in which the commodification of nature might impact our microbiomes, and the potential of this to stem from the interaction with computers.

Steven Shaviro, in discussing Whitehead’s philosophy of “the bifurcation of nature”, suggests that there is a great discrepancy between nature that is caught in our awareness, and nature that is the cause of our awareness (Shaviro, 2014). That is to say, what is visible on the surface, is philosophically juxtaposed with what we cannot see with the naked human eye. While it seems that Whitehead was initially referring to speculative physics by talking about components such as electrons and molecules, one could treat the world of the microbe as part of this category of nature which causes awareness. Not only does it contribute to our physicality, but schools of thought are arising that suggest bacteria is influencing brain function and decision making: “While psychological and physical stressors can affect the composition and metabolic activity of the gut microbiota, experimental changes to the gut microbiome can affect emotional behavior and related brain systems. These findings have resulted in speculation that alterations in the gut microbiome may play a pathophysiological role in human brain diseases, including autism spectrum disorder, anxiety, depression, and chronic pain.” (Mayer et al., 2014). Whitehead proposed that we treat the macro and the micro of nature with the same ontological status, and in this context the micro is likely to have macro scale effects (Shaviro, 2014). Shaviro discusses this notion of the world as being made up of processes and not things, and it is in this light that I would like to frame my discussion of the microbiome.

In speculating about interactions between microbes and computers, it helps to frame this discussion within the frame of digital ecology and networks, treating this subject not as two players, but as a process between them.

“Whitehead is deeply relevant to our contemporary concerns because he thinks about how novelty can emerge from selective repetition, how all the entities of the world are deeply interrelated and mutually dependent even in their separation from one another, and how nonhuman agents, no less than human ones, perform actions and express needs and values.” (Shaviro, 2014).

In gearing these thoughts towards arts practices, “A speculative method…would need to be sufficiently oblique, playful, under-determined.” (Michael et al., 2014). It appears that speculation can play the role of the questioner in critical discourse, and as Barone suggests,  “Good art...can be said to promote the enhancement of uncertainty.” (Barone, 1995).

Speculative approaches become multifaceted, encouraging communication and interplay between various layers of elements and can result in new ideals, “such methods are like ‘prepositional machines’ enabling the potential emergence of odd and unexpected relationalities.” (Michael et al., 2014). Not only do these speculative processes result in emergent properties, but the idea of digital ecology is built upon recognition that networks act in this same manner, “…each node can be perceived as a network itself and the ecological way of thinking focuses on understanding the emergent properties of a network.” (Raptis et al., 2014). In this light, to explore microbial communities and computation through speculation, it is highly relevant to treat this interaction as some kind of hybrid organic and digital network, “Ecology is networks... To understand ecosystems will be ultimately to understand networks” (Raptis et al., 2014). If we are to combine human and non-human networks, what are the repercussions? How do we define such a network?  

“Consequently, the fundamental difference between living and non-living ecologies is that a living ecology is autopoietic [13] because the patterns of organization emerge from the ecology itself through feedback loops and can even alter the structure of the ecology.” (Raptis et al., 2014)

In this sense, I would argue that this distinction between living and non-living ecologies will become increasingly hazy in the coming years with the rise of artificial intelligence. At what point will an AI become so independent that at no point does it need further human assistance past being powered on? The potential for autopoietic qualities in computational systems, or microbial computing, is both fascinating and ominous.

In the journal article titled Nature, Technology and Art: The Emergence of a New Relationship?, Ursula Huws delves into the complexities of computational art that is inspired by nature. Huws puts forward a compelling argument that the most inspiring model for nature focused computational art is one where the artist seeks not to imitate traditional art forms, but to capture the unpredictability of nature:

A small and largely neglected group of artists have chosen to use computers not just to imitate brush or camera, but to model or set in motion patterns of behavior that, by analogy or mimicry, can parallel those found in the natural world and give rise to the responses of surprise, insight, amusement or delight that are triggered by observing other (non-human) forms of life. (Huws, 2000)

Huws frames this argument in the context of a computer’s ability to crunch numbers with great efficiency, suggesting that the growth in artificial life technologies supports a growing movement of “emergent art” (Huws, 2000). Huws further explains this turn in a distinction between likeness and behavior, but what is noteworthy is the presence of simulation in both contexts. Emergent art can still simulate nature, but by moving away from representational portrayals, the pleasing unpredictability that Huws describes can be uncovered through a focus on behavior, “…in other words, (whether) it is possible to represent, comment upon or simulate nature in an artistic form not as likeness but as behavior.” (Huws, 2000). Norman White is one example of an artist working with robotics who can be placed in this field of emergent art.  

In surveying the current state of microbiome art, the most notable collection of human microbiome works is Invisible You, an exhibition at The Eden Project, Cornwall. Within this exhibition there is a huge variety of art practices and mediums, with a few computational practices also. Anna Dumitriu and Alex May’s work The Human Super Organism, features a touch screen on which the audience can place their hands and see microbes grow in an accelerated virtual petri dish. The piece encourages discussion surrounding the materiality of microbes and our physical makeup as consisting of at least equal parts microbes and human cells. Another exhibition in Edinburgh, Menagerie of Microbes, amongst other goals, sought to explore the ‘speculative possibilities’ of bacteria, slime mould and fungi. While these works are extremely important, concerned with making visible the scientific processes which are for the most part inaccessible to the public, to apply ideas of ‘emergent art’ to the microbiome suggests the potential for stepping beyond representation and utilising computation to explore microbial process.

Outside of the context of the microbiome, there are artists exploring process through bacteria. One example is the Brazilian-American artist Eduardo Kac. In 1997 Kac coined the term Bioart for his own works and discussed the concept of transgenic beings and artworks which exist as a blending of multiple entities (Kac, 2015). The Eighth Day by Eduardo Kac is a transegenic artwork consisting of a series of biological robots worldwide. The biobots house a bioelement of various cloned amoeba genes as their brain structures. When the amoebas divide, the robotic leg elements respond with complex movements. Movement in the biobot can be seen to be an embodiment of the amoeba activity (Kac, 2005).

Helen Pritchard’s Critter Compiler (2017), explores a speculative relationship of execution between a recurrent neural network and microbial algae growth. What is most inspiring about this piece is the symbiotic relationship formed between these two elements through temperature and efficiency, whereby heat generated by the neural network promotes algae growth, and algae growth cools the processor, impacting processing time on the CPU. Furthermore, Pritchard draws attention to a tendency of queer studies to explore injury, extending this phenomenon towards “more-than-human ensembles” through microbial computation (Pritchard, 2017, p. 241). This theory is highly relevant to microbiome research, as scientists are struggling to communicate to the public the injury that is being sustained through overuse of antibiotics, not only through prescription, but also through food sources (McKenna, 2017).

While the framework of the Anthropocene has provided the means for artists to enter into a political discourse regarding the natural world, Kayla Anderson suggests that it is speculative works which lend themselves to effective critique (Anderson, 2015). Anderson argues that even well intended art risks creating destructive narratives about the Anthropocene by proposing ‘solutions’ to complex problems. This is problematic as it further entrenches ideas of human dominance over the planet (Anderson, 2015) by enforcing practices of specieist and self-interested treatment of nature (Zylinska, 2014). As Joanna Zylinska puts forward, the Anthropocene is a “crisis of critical thinking”, and any improvements in our relationship with nature is going to stem from thinking (Zylinska, 2014). It is in this light that Anderson suggests that “Because critical making is a type of doing to facilitate thinking, works of critical, conceptual and speculative design may be best suited to addressing the Anthropocene.” (Anderson, 2015). From a Feminist TechnoScience perspective, this speculative approach is freeing from the dominant tendency of declaring solutions through art: “By focusing on propositions rather than solutions, artists and designers can challenge heroic, solutionist and masculinist narratives of the Anthropocene, instead provoking dark discussions and radical thought experiments.” (Anderson, 2015). This notion of course, becomes a leading ideal within my speculative approach when addressing the microbiome. The aims and questions shift from those which are geared towards conclusive answers and solutions to those that open up further thought-provoking discussions.

In the paper Probiotic Environmentalities: Rewilding with Wolves and Worms, Jamie Lorimer warns of the current cloud of hype which surrounds microbiome research,  “There is still a great deal of basic science to be done on the microbiome, and the discussion of translational applications is speculative and full of hype.” (Lorimer, 2017). In this atmosphere of hype, and with the human microbiome becoming a rapidly growing area of interest, IBM are funding a research project investigating links between the human microbiome and autoimmune diseases. Due to the masses of data that have been generated from gut microbe measurement and the computer power needed to crunch the numbers and make reliable inferences, using the infrastructure provided by the World Community Grid, volunteers can donate portions of their idle CPU to contribute to processing this data. Volunteers thus become a part of a new network, a node in a grand web, receiving inputs and processing outputs (World Community Grid, 2018). Again, it is the emergent properties of digital ecologies which highlight the importance of these interactions and demand that individual components should not be treated in isolation.

Diane Edwards, an artist dealing with the microbiome through her work, explores the relationship between microbes and humans through the lens of New Materialism in order to embrace a “non-anthropocentric consideration of the body…” and to explore the emergent properties which are revealed (Edwards, 2017, p. 7).

Through such intimate kinship relations, we hold a shared and combined genetic potential, gut bacteria having the genetic ability to produce certain molecules that we cannot and vice versa, which when combined allow for an enhanced genetic potential to survive, digest, metabolise and produce vitamins which otherwise would not be possible. (Edwards, 2017, p. 8)

Edwards critiques Big Data’s domination over microbiome research, such as in IBM’s case, due to the tunnel vision that arises when focusing on the virtual when she writes, “In medical sciences, the human is digitised to be added to vast comparison databases, this dematerializing of the body has now gone beyond the lab.” (Edwards, 2017, p. 20). The result of this is that microbiome science is being converted from biology to an information-science, passed on to mathematicians and computer scientists, and potentially making it subject to “computational storytelling” (Edwards, 2017, p. 21). Lorimer also discusses the Probiotic Turn, an approach to rewinding nature and reworming the microbiome after the suffocating effects from biosecurity which exist in the Anthropocene. The rewinding process is described as the (re)introduction of ‘keystone species’, leading to the development, evolution and experience of an ecology. Lorimer points to the possibilities of Big Pharma turning these keystone species into a commodified fix-all pill, which if distributed en masse could potentially decrease biodiversity and turn our microbial communities into a narrowband, purified ecology. These concerns with pharmaceutical companies, combined with their access to microbiome Big Data, provides a startling window into a future where our bacterial ecologies come under threat. Perhaps there is a need for artists to engage with microbial Big Data to speculate over some of these potential inferences and interferences.

In exploring these themes, my arts practice has been heavily inspired by modes of thinking such as speculation and the potential for emergent properties, fully recognising that they are both important conditions in any art that intends to connect (whether physically or metaphorically) with nature. In response, I have undertaken a series of experiments considering speculative interactions between microbes and machines. The results are a collection of works which attempt to establish a visual communication system, using computer vision to seed a computer program, the ambition was to not capture bacteria as a lifelike visual representation, but to portray the essence of their behaviours as understood and drawn by the machine. These experiments portray this concept in early stages of development, as a proof of concept, with a strong focus on the philosophical underpinnings to be applied within potential future works. They aim to explore ways of machine seeing in the microbiome, and the potentials for bacterial processes to become a part of an artistic digital ecology. Here the experiments are embedded, for each pair, the original bacteria appear on the left and the computational ‘translation’ on the right.

Source Video: Fresh water microscopy

Source Video: Microorganism from bog water at Sweetwater Wetlands, Tucson, Arizona

Source Video: Phenotypic mixing in bacteria

Using optical flow techniques, the complexity of the microbe movement is conyeved in overlapping segments.

This program looks for interesting features in the input image and creates a network of tracking nodes.

A sense of chaos is communicated through this lissajous, the motion of which is seeded by the microbes.
 

Given that the technological processes behind microbiome science are evolving so quickly, and the growing ability to detect and classify all of the different bacterial strands in a given sample, what will bioart look like when we know more about each of these bacterial forms and what they each contribute to human behaviour. In my ultimate speculation, which extends upon work done by artists engaging with microbial computational processes, I envisage an artwork based around an artificial intelligence system and a robotic manifestation of the bacterial ecology. If a bacterial sample was given to this system, and through big data, the contents were classified into all of the bacterial strands it possessed, could this robot provide some physical manifestation and embodiment of the microbial community? If each bacterial strand dictated a particular physical or emotional behaviour in this robot, could the sum of all of these parts create emergent properties which strongly communicated the bacteria’s effect on the brain? Could it even be possible to get a sense of personality from this embodiment, or better yet, to be able to pinpoint a specific individual’s personality in these movements?  

In surveying the state of microbiome art, it is pleasing to see that speculation forms an integral part to many existing practices. The fast-paced nature of microbiome research at present facilitates deep speculation on artistic and ethical planes and encourages artists in this sphere to keep up with scientific developments, critique practices and enrich public thinking. My initial artistic experiments with this topic have revealed to me a wide artistic and speculative scope. Ways of machine seeing have provided an environment to explore ideas of bacteria and computational processes forming a new digital ecology. To develop these ideas further, it is necessary to make emergence a fundamental topic of study, investigating the properties of this new ecology and creating speculative dialogues between computational and microbial processes which critique bacterial big data frameworks. For these concepts to truly come alive, a full circle system that incorporates bi-directional communication between living organisms and non-human processors would birth a thought-provoking transgenic being. It is clear that computation can benefit from a rich relationship with nature, whether through inspiration in the creation of new technologies or through direct interaction, and speculation is the perfect vessel for exploring this entanglement.

References:

Notes: Microscopic footage used under the Creative Commons License. Links provided.

ACUS Art and Science, 2018. Menagerie of Microbes | ASCUS [WWW Document]. URL http://www.ascus.org.uk/exhibitions/menagerie-of-microbes/ (accessed 3.14.18).

Anderson, K., 2015. Ethics, Ecology, and the Future: Art and Design Face the Anthropocene. Leonardo 48, 338–347. https://doi.org/10.1162/LEON_a_01087

Barone, T., 1995. Chapter 5 The purposes of arts-based educational research. International Journal of Educational Research 23, 169–180. https://doi.org/10.1016/0883-0355(95)91500-G

Kac, E., 2015. What if art could truly create biological life? | Eduardo Kac | TEDxVienna. URL https://www.youtube.com/watch?v=IS_5WJteCC8 (accessed 14.03.18).

Eden Project, 2018. Invisible You. The Human Microbiome exhibition - Eden Project, Cornwall [WWW Document]. URL http://www.edenproject.com/visit/whats-here/invisible-you-the-human-microbiome-exhibition (accessed 2.17.18).

Edwards, D., 2017. Making Kin with the Aliens Inside (Dissertation). Goldsmiths, University of London, London.

Huws, U., 2000. Nature, Technology and Art: The Emergence of a New Relationship? Leonardo 33, 33–40. https://doi.org/10.1162/002409400552216

Iv Ar, 2013. Fresh water microscopy (Bysjön) - YouTube [WWW Document]. URL https://www.youtube.com/watch?v=cM0hcwZAdZE (accessed 3.10.18).

Kac, E., 2005. THE EIGHTH DAY [WWW Document]. K A C. URL http://www.ekac.org/8thday.html (accessed 3.25.18).

Lorimer, J., 2017. Probiotic Environmentalities: Rewilding with Wolves and Worms. Theory, Culture & Society 34, 27–48. https://doi.org/10.1177/0263276417695866

Mayer, E.A., Knight, R., Mazmanian, S.K., Cryan, J.F., Tillisch, K., 2014. Gut Microbes and the Brain: Paradigm Shift in Neuroscience. Journal of Neuroscience 34, 15490–15496. https://doi.org/10.1523/JNEUROSCI.3299-14.2014

McKenna, M., 2017. Read this and you may never eat chicken again. The Guardian. URL http://www.theguardian.com/lifeandstyle/2017/oct/13/can-never-eat-chicken-again-antibiotic-resistance (accessed 12.02.18).

Michael, M., Costello, B., Mooney-Somers, J., Kerridge, I., 2014. Manifesto on Art, Design and Social Science - Method as Speculative Event. Leonardo. https://doi.org/10.1162/LEON_a_00928

Pritchard, H., 2017. Critter Compiler, in: Pritchard, H., Snodgrass, E., Tyżlik-Carver (Eds.), DATA Browser 06: Executing Practices. AUTONOMEDIA, New York, USA.

Raptis, D., Kjeldskov, J., Skov, M.B., Paay, J., 2014. What is a Digital Ecology?: Theoretical Foundations and a Unified Definition. Australian Journal of Intelligent Information Processing Systems 13.

Shaviro, S., 2014. The Universe of Things : On Speculative Realism, Posthumanities ; 30. University of Minnesota Press, Minneapolis.

The Dust Council, 2018. Microorganism from bog water at Sweetwater Wetlands, Tucson, Arizona - YouTube [WWW Document]. URL https://www.youtube.com/watch?v=QYwLmvRbfKU (accessed 3.10.18).

thesoundofscience, 2017. Phenotypic mixing in bacteria - YouTube [WWW Document]. URL https://www.youtube.com/watch?v=yYre4K_kJN0 (accessed 3.10.18).

World Community Grid, 2018. Microbiome Immunity Project [WWW Document]. URL https://www.worldcommunitygrid.org/research/mip1/overview.do (accessed 3.14.18).

Zylinska, J., 2014. Minimal Ethics for the Anthropocene. Open Humanities Press, Michigan.