On the development of slime mould morphological, intracellular and heterotic computing devices

The use of live biological substrates in the fabrication of unconventional computing (UC) devices is steadily transcending the barriers between science fiction and reality, but efforts in this direction are impeded by ethical considerations, the field’s restrictively broad multidisciplinarity and our incomplete knowledge of fundamental biological processes. As such, very few functional prototypes of biological UC devices have been produced to date. This thesis aims to demonstrate the computational polymorphism and polyfunctionality of a chosen biological substrate — slime mould Physarum polycephalum, an arguably ‘simple’ single-celled organism — and how these properties can be harnessed to create laboratory experimental prototypes of functionally-useful biological UC prototypes. Computing devices utilising live slime mould as their key constituent element can be developed into a) heterotic, or hybrid devices, which are based on electrical recognition of slime mould behaviour via machine-organism interfaces, b) whole-organism-scale morphological processors, whose output is the organism’s morphological adaptation to environmental stimuli (input) and c) intracellular processors wherein data are represented by energetic signalling events mediated by the cytoskeleton, a nano-scale protein network. It is demonstrated that each category of device is capable of implementing logic and furthermore, specific applications for each class may be engineered, such as image processing applications for morphological processors and biosensors in the case of heterotic devices. The results presented are supported by a range of computer modelling experiments using cellular automata and multi-agent modelling. We conclude that P. polycephalum is a polymorphic UC substrate insofar as it can process multimodal sensory input and polyfunctional in its demonstrable ability to undertake a variety of computing problems. Furthermore, our results are highly applicable to the study of other living UC substrates and will inform future work in UC, biosensing, and biomedicine

On Unconventional Computing for Sound and Music

Advances in technology have had a significant impact on the way in which we produce and consume music. The music industry is most likely to continue progressing in tandem with the evolution of electronics and computing technology. Despite the incredible power of today’s computers, it is commonly acknowledged that computing technology is bound to progress beyond today’s conventional models. Researchers working in the relatively new field of Unconventional Computing (UC) are investigating a number of alternative approaches to develop new types of computers, such as harnessing biological media to implement new kinds of processors. This chapter introduces the field of UC for sound and music, focusing on the work developed at Plymouth University’s Interdisciplinary Centre for Computer Music Research (ICCMR) in the UK. From musical experiments with Cellular Automata modelling and in vitro neural networks, to quantum computing and bioprocessing, this chapter introduces the substantial body of scientific and artistic work developed at ICCMR. Such work has paved the way for ongoing research towards the development of robust general-purpose bioprocessing components, referred to as biomemristors, and interactive musical biocomputers

Unconventional Computing and Music: An Investigation into Harnessing Physarum polycephalum

This thesis presents an investigation into developing musical systems with an Unconventional Computing substrate. Computer musicians have found it difficult to access the field of Unconventional Computing, which is likely due to its resource-intensive and complex nature. However, ongoing research is establishing the myxomycete Physarum polycephalum as a universally-accessible and versatile biological computing substrate. As such, the organism is a potential gateway for computer musicians to begin experimenting with aspects of Unconventional Computing. Physarum polycephalum, in its vegetative plasmodium form, is an amorphous unicellular organism that can respond with natural parallelism to the environmental conditions that surround it. This thesis explores the challenges and opportunities related to developing musical systems with Physarum polycephalum. As this area of inquiry is in its infancy, the research took inspiration from a common approach in Unconventional Computing: a journey of exploration and discovery. This journey consisted of a selection of waypoints that provided direction while allowing the research to explore applications of Physarum polycephalum in order to establish how it may be useful in Computer Music. These waypoints guided the research from adapting established prototypes for musical application to developing purpose-made musical demonstrators for use outside of the laboratory. Thus, the thesis reports on a series of Computer Music systems that explore one or more features of Physarum polycephalum's behaviour and physiology. First, the text presents an approach to algorithmic composition that exploits the organism's ability to form and reconfigure graph-like structures. Next, the thesis reports on systems that harness the plasmodium's electrical potential oscillations for sound synthesis and compositional tools. Finally, the thesis presents musical devices that encompass living plasmodium as electrical components. Where applicable, the thesis includes artefacts from demonstrations of these systems, some of which were developed in collaboration with a composer. The findings from this journey demonstrate that Physarum polycephalum is an appropriate substrate for computer musicians wanting to explore Unconventional Computing approaches creatively. Although Physarum polycephalum is relatively robust as a biological substrate, several obstacles arose during this project. This research addressed such obstacles by reviewing and selecting approaches that maintained the organism's accessibility to computer musicians. As a result, the work suggests methods for developing systems with the organism that are practical for the average music technologist and also beneficial to the wider group of scientists investigating Physarum polycephalum for other purposes.Plymouth University HumPA Studentshi

Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Toward a formal theory for computing machines made out of whatever physics offers: extended version

Approaching limitations of digital computing technologies have spurred research in neuromorphic and other unconventional approaches to computing. Here we argue that if we want to systematically engineer computing systems that are based on unconventional physical effects, we need guidance from a formal theory that is different from the symbolic-algorithmic theory of today's computer science textbooks. We propose a general strategy for developing such a theory, and within that general view, a specific approach that we call "fluent computing". In contrast to Turing, who modeled computing processes from a top-down perspective as symbolic reasoning, we adopt the scientific paradigm of physics and model physical computing systems bottom-up by formalizing what can ultimately be measured in any physical substrate. This leads to an understanding of computing as the structuring of processes, while classical models of computing systems describe the processing of structures.Comment: 76 pages. This is an extended version of a perspective article with the same title that will appear in Nature Communications soon after this manuscript goes public on arxi

Symmetry structure in discrete models of biochemical systems : natural subsystems and the weak control hierarchy in a new model of computation driven by interactions

© 2015 The Authors. Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.Interaction Computing (IC) is inspired by the observation that cell metabolic/regulatory systems construct order dynamically, through constrained interactions between their components and based on a wide range of possible inputs and environmental conditions. The goals of this work are (1) to identify and understand mathematically the natural subsystems and hierarchical relations in natural systems enabling this, and (2) to use the resulting insights to define a new model of computation based on interactions that is useful for both biology and computation. The dynamical characteristics of the cellular pathways studied in Systems Biology relate, mathematically, to the computational characteristics of automata derived from them, and their internal symmetry structures to computational power. Finite discrete automata models of biological systems such as the lac operon, Krebs cycle, and p53-mdm2 genetic regulation constructed from Systems Biology models have canonically associated algebraic structures { transformation semigroups. These contain permutation groups (local substructures exhibiting symmetry) that correspond to "pools of reversibility". These natural subsystems are related to one another in a hierarchical manner by the notion of "weak control ". We present natural subsystems arising from several biological examples and their weak control hierarchies in detail. Finite simple non-abelian groups (SNAGs) are found in biological examples and can be harnessed to realize nitary universal computation. This allows ensembles of cells to achieve any desired finitary computational transformation, depending on external inputs, via suitably constrained interactions. Based on this, interaction machines that grow and change their structure recursively are introduced and applied, providing a natural model of computation driven by interactions.Peer reviewe

Reaction–diffusion chemistry implementation of associative memory neural network

Unconventional computing paradigms are typically very difficult to program. By implementing efficient parallel control architectures such as artificial neural networks, we show that it is possible to program unconventional paradigms with relative ease. The work presented implements correlation matrix memories (a form of artificial neural network based on associative memory) in reaction–diffusion chemistry, and shows that implementations of such artificial neural networks can be trained and act in a similar way to conventional implementations

Natural Computing and Beyond

This book contains the joint proceedings of the Winter School of Hakodate (WSH) 2011 held in Hakodate, Japan, March 15–16, 2011, and the 6th International Workshop on Natural Computing (6th IWNC) held in Tokyo, Japan, March 28–30, 2012, organized by the Special Interest Group of Natural Computing (SIG-NAC), the Japanese Society for Artificial Intelligence (JSAI). This volume compiles refereed contributions to various aspects of natural computing, ranging from computing with slime mold, artificial chemistry, eco-physics, and synthetic biology, to computational aesthetics

Memristors for the Curious Outsiders

We present both an overview and a perspective of recent experimental advances and proposed new approaches to performing computation using memristors. A memristor is a 2-terminal passive component with a dynamic resistance depending on an internal parameter. We provide an brief historical introduction, as well as an overview over the physical mechanism that lead to memristive behavior. This review is meant to guide nonpractitioners in the field of memristive circuits and their connection to machine learning and neural computation.Comment: Perpective paper for MDPI Technologies; 43 page

Biohacking and code convergence : a transductive ethnography

Cette thèse se déploie dans un espace de discours et de pratiques revendicatrices, à l’inter- section des cultures amateures informatiques et biotechniques, euro-américaines contempo- raines. La problématique se dessinant dans ce croisement culturel examine des métaphores et analogies au coeur d’un traffic intense, au milieu de voies de commmunications imposantes, reliant les technologies informatiques et biotechniques comme lieux d’expression médiatique. L’examen retrace les lignes de force, les médiations expressives en ces lieux à travers leurs manifestations en tant que codes —à la fois informatiques et génétiques— et reconnaît les caractères analogiques d’expressivité des codes en tant que processus de convergence. Émergeant lentement, à partir des années 40 et 50, les visions convergentes des codes ont facilité l’entrée des ordinateurs personnels dans les marchés, ainsi que dans les garages de hackers, alors que des bricoleurs de l’informatique s’en réclamaient comme espace de liberté d’information —et surtout d’innovation. Plus de cinquante ans plus tard, l’analogie entre codes informatiques et génétiques sert de moteur aux revendications de liberté, informant cette fois les nouvelles applications de la biotechnologie de marché, ainsi que l’activité des biohackers, ces bricoleurs de garage en biologie synthétique. Les pratiques du biohacking sont ainsi comprises comme des individuations : des tentatives continues de résoudre des frictions, des tensions travaillant les revendications des cultures amateures informatiques et biotechniques. Une des manières de moduler ces tensions s’incarne dans un processus connu sous le nom de forking, entrevu ici comme l’expérience d’une bifurcation. Autrement dit, le forking est ici définit comme passage vers un seuil critique, déclinant la technologie et la biologie sur plusieurs modes. Le forking informe —c’est-à-dire permet et contraint— différentes vi- sions collectives de l’ouverture informationnelle. Le forking intervient aussi sur les plans des iii semio-matérialités et pouvoirs d’action investis dans les pratiques biotechniques et informa- tiques. Pris comme processus de co-constitution et de différentiation de l’action collective, les mouvements de bifurcation invitent les trois questions suivantes : 1) Comment le forking catalyse-t-il la solution des tensions participant aux revendications des pratiques du bioha- cking ? 2) Dans ce processus de solution, de quelles manières les revendications changent de phase, bifurquent et se transforment, parfois au point d’altérer radicalement ces pratiques ? 3) Quels nouveaux problèmes émergent de ces solutions ? L’effort de recherche a trouvé ces questions, ainsi que les plans correspondants d’action sémio-matérielle et collective, incarnées dans trois expériences ethnographiques réparties sur trois ans (2012-2015) : la première dans un laboratoire de biotechnologie communautaire new- yorkais, la seconde dans l’émergence d’un groupe de biotechnologie amateure à Montréal, et la troisième à Cork, en Irlande, au sein du premier accélérateur d’entreprises en biologie synthétique au monde. La logique de l’enquête n’est ni strictement inductive ou déductive, mais transductive. Elle emprunte à la philosophie de la communication et de l’information de Gilbert Simondon et découvre l’épistémologie en tant qu’acte de création opérant en milieux relationnels. L’heuristique transductive offre des rencontres inusitées entre les métaphores et les analogies des codes. Ces rencontres étonnantes ont aménagé l’expérience de la conver- gence des codes sous forme de jeux d’écritures. Elles se sont retrouvées dans la recherche ethnographique en tant que processus transductifs.This dissertation examines creative practices and discourses intersecting computer and biotech cultures. It queries influential metaphors and analogies on both sides of the inter- section, and their positioning of biotech and information technologies as expression media. It follows mediations across their incarnations as codes, both computational and biological, and situates their analogical expressivity and programmability as a process of code conver- gence. Converging visions of technological freedom facilitated the entrance of computers in 1960’s Western hobbyist hacker circles, as well as in consumer markets. Almost fifty years later, the analogy drives claims to freedom of information —and freedom of innovation— from biohacker hobbyist groups to new biotech consumer markets. Such biohacking practices are understood as individuations: as ongoing attempts to resolve frictions, tensions working through claims to freedom and openness animating software and biotech cultures. Tensions get modulated in many ways. One of them, otherwise known as “forking,” refers here to a critical bifurcation allowing for differing iterations of biotechnical and computa- tional configurations. Forking informs —that is, simultaneously affords and constrains— differing collective visions of openness. Forking also operates on the materiality and agency invested in biotechnical and computational practices. Taken as a significant process of co- constitution and differentiation in collective action, bifurcation invites the following three questions: 1) How does forking solve tensions working through claims to biotech freedom? 2) In this solving process, how can claims bifurcate and transform to the point of radically altering biotech practices? 3) what new problems do these solutions call into existence? This research found these questions, and both scales of material action and agency, in- carnated in three extensive ethnographical journeys spanning three years (2012-2015): the first in a Brooklyn-based biotech community laboratory, the second in the early days of a biotech community group in Montreal, and the third in the world’s first synthetic biology startup accelerator in Cork, Ireland. The inquiry’s guiding empirical logic is neither solely deductive or inductive, but transductive. It borrows from Gilbert Simondon’s philosophy of communication and information to experience epistemology as an act of analogical creation involving the radical, irreversible transformation of knower and known. Transductive heuris- tics offer unconvential encounters with practices, metaphors and analogies of code. In the end, transductive methods acknowledge code convergence as a metastable writing games, and ethnographical research itself as a transductive process