Investigating the properties of bio-chemical networks of artificial organisms with opposing behaviours

Organisms, be it singled-celled organisms or multi-cellular organisms, are constantly faced with opposing objectives requiring different sets of behaviours. These behaviours can be classified into two, predatory behaviours or anti-prey behaviours, with one set of behaviours causing an opposite effect to the other. A healthy organism aims to achieve its equilibrium state or to be in homeostasis. Homeostasis is achieved when a balance between the two opposing behaviours is created and maintained. This raises some questions: is there an innate mechanism that encodes for these categories of behaviours? Is there also an innate mechanism(s) that resolves conflicts and allows switching between these two opposing behaviours? If we consider artificial organisms as single-celled organisms, how do the organisms’ gene regulatory network, metabolic network and/or signalling network (their biochemical networks) maintain homeostasis of the organisms? This paper investigates the properties of the networks of best evolved artificial organisms, in order to help answer these questions, and guide the evolutionary development of controllers for artificial systems

Understanding the Regulation of Predatory and Anti-Prey Behaviours for an Artificial Organism

An organism’s behaviour can be categorised as being either predatory or anti-prey. Predatory behaviours are behaviours that try to improve the life of an organism. Anti-prey behaviours are those that attempt to prevent death. Regulation between these two opposing behaviours is necessary to ensure survivability—and gene regulatory networks and metabolic networks are the mechanisms that provide this regulation. We know that such regulatory behaviour is encoded in an organism’s genes. The question is, how is it encoded? The understanding of this encoding can help with the development of an artificial organism, for example an autonomous robotic system; whereby the robot will have the ability to autonomously regulate the switching between the opposing behaviours using this encoded mechanism, in order to ensure its sustainable and continuous system operations. This paper aims to look into the properties of an artificial bio-chemical network consisting of a genetic regulatory network and a metabolic network that can provide these capabilities

Computational aspects of cellular intelligence and their role in artificial intelligence.

The work presented in this thesis is concerned with an exploration of the computational aspects of the primitive intelligence associated with single-celled organisms. The main aim is to explore this Cellular Intelligence and its role within Artificial Intelligence. The findings of an extensive literature search into the biological characteristics, properties and mechanisms associated with Cellular Intelligence, its underlying machinery - Cell Signalling Networks and the existing computational methods used to capture it are reported. The results of this search are then used to fashion the development of a versatile new connectionist representation, termed the Artificial Reaction Network (ARN). The ARN belongs to the branch of Artificial Life known as Artificial Chemistry and has properties in common with both Artificial Intelligence and Systems Biology techniques, including: Artificial Neural Networks, Artificial Biochemical Networks, Gene Regulatory Networks, Random Boolean Networks, Petri Nets, and S-Systems. The thesis outlines the following original work: The ARN is used to model the chemotaxis pathway of Escherichia coli and is shown to capture emergent characteristics associated with this organism and Cellular Intelligence more generally. The computational properties of the ARN and its applications in robotic control are explored by combining functional motifs found in biochemical network to create temporal changing waveforms which control the gaits of limbed robots. This system is then extended into a complete control system by combining pattern recognition with limb control in a single ARN. The results show that the ARN can offer increased flexibility over existing methods. Multiple distributed cell-like ARN based agents termed Cytobots are created. These are first used to simulate aggregating cells based on the slime mould Dictyostelium discoideum. The Cytobots are shown to capture emergent behaviour arising from multiple stigmergic interactions. Applications of Cytobots within swarm robotics are investigated by applying them to benchmark search problems and to the task of cleaning up a simulated oil spill. The results are compared to those of established optimization algorithms using similar cell inspired strategies, and to other robotic agent strategies. Consideration is given to the advantages and disadvantages of the technique and suggestions are made for future work in the area. The report concludes that the Artificial Reaction Network is a versatile and powerful technique which has application in both simulation of chemical systems, and in robotic control, where it can offer a higher degree of flexibility and computational efficiency than benchmark alternatives. Furthermore, it provides a tool which may possibly throw further light on the origins and limitations of the primitive intelligence associated with cells

Composing with Matter: Interdisciplinary Explorations Between the Natural and the Artificial

This practice-based research, which includes a written thesis and a portfolio of creative practice, represents the interdisciplinary exploration of co-composition between natural and artificial matter as otherworldly phenomena. Accelerated by the application of recent technologies to control natural materials, matter has become merged between nature and artefacts, offering new potentials, where the boundaries are becoming increasingly blurred. This thesis presents a series of complementing sound art works, including transition [systemic], transition [characteristic], and moment, which were devised through co-composing towards a creative outcome that combines sonic and visual elements by integrating natural and artificial matter as co-authors and co-makers within the creative process to generate multiple perspectives. Raising questions of the boundary between nature and artificiality, it aims to consider a new methodology for sound art in the human-dominated, Anthropocene epoch. This research employs natural elements and processes to engage with sonic and visual anthropomorphism. It is focused on generative processes in the organisation of matter, here analysed and harnessed for sound expression, using acoustic phenomena including the inaudible range that can be perceived through matter. Through a laboratory-based study made in collaboration with scientists, three ‘life-like’ features of the generative processes of materials are discussed: 1) fusion and division, 2) network formation, and 3) pulse and rhythm. The practice explores these features to develop a new methodology of authorship and making, examining the following two questions. How can life-like behaviours of matter be portrayed through sonic and visual modes of expression? And in what ways might the expression of life-like behaviours be grasped by human perception? In conclusion, by integrating the agency of matter into the compositional processes, life-like features – as described by current theories in art, design, science, and philosophy – are made apparent

Designing stem cell niches for differentiation and self-renewal

Mesenchymal stem cells, characterized by their ability to differentiate into skeletal tissues and self-renew, hold great promise for both regenerative medicine and novel therapeutic discovery. However, their regenerative capacity is retained only when in contact with their specialized microenvironment, termed the stem cell niche. Niches provide structural and functional cues that are both biochemical and biophysical, stem cells integrate this complex array of signals with intrinsic regulatory networks to meet physiological demands. Although, some of these regulatory mechanisms remain poorly understood or difficult to harness with traditional culture systems. Biomaterial strategies are being developed that aim to recapitulate stem cell niches, by engineering microenvironments with physiological-like niche properties that aim to elucidate stem cell-regulatory mechanisms, and to harness their regenerative capacity in vitro. In the future, engineered niches will prove important tools for both regenerative medicine and therapeutic discoveries

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Stepping Beyond the Newtonian Paradigm in Biology. Towards an Integrable Model of Life: Accelerating Discovery in the Biological Foundations of Science

The INBIOSA project brings together a group of experts across many disciplines who believe that science requires a revolutionary transformative step in order to address many of the vexing challenges presented by the world. It is INBIOSA’s purpose to enable the focused collaboration of an interdisciplinary community of original thinkers. This paper sets out the case for support for this effort. The focus of the transformative research program proposal is biology-centric. We admit that biology to date has been more fact-oriented and less theoretical than physics. However, the key leverageable idea is that careful extension of the science of living systems can be more effectively applied to some of our most vexing modern problems than the prevailing scheme, derived from abstractions in physics. While these have some universal application and demonstrate computational advantages, they are not theoretically mandated for the living. A new set of mathematical abstractions derived from biology can now be similarly extended. This is made possible by leveraging new formal tools to understand abstraction and enable computability. [The latter has a much expanded meaning in our context from the one known and used in computer science and biology today, that is "by rote algorithmic means", since it is not known if a living system is computable in this sense (Mossio et al., 2009).] Two major challenges constitute the effort. The first challenge is to design an original general system of abstractions within the biological domain. The initial issue is descriptive leading to the explanatory. There has not yet been a serious formal examination of the abstractions of the biological domain. What is used today is an amalgam; much is inherited from physics (via the bridging abstractions of chemistry) and there are many new abstractions from advances in mathematics (incentivized by the need for more capable computational analyses). Interspersed are abstractions, concepts and underlying assumptions “native” to biology and distinct from the mechanical language of physics and computation as we know them. A pressing agenda should be to single out the most concrete and at the same time the most fundamental process-units in biology and to recruit them into the descriptive domain. Therefore, the first challenge is to build a coherent formal system of abstractions and operations that is truly native to living systems. Nothing will be thrown away, but many common methods will be philosophically recast, just as in physics relativity subsumed and reinterpreted Newtonian mechanics. This step is required because we need a comprehensible, formal system to apply in many domains. Emphasis should be placed on the distinction between multi-perspective analysis and synthesis and on what could be the basic terms or tools needed. The second challenge is relatively simple: the actual application of this set of biology-centric ways and means to cross-disciplinary problems. In its early stages, this will seem to be a “new science”. This White Paper sets out the case of continuing support of Information and Communication Technology (ICT) for transformative research in biology and information processing centered on paradigm changes in the epistemological, ontological, mathematical and computational bases of the science of living systems. Today, curiously, living systems cannot be said to be anything more than dissipative structures organized internally by genetic information. There is not anything substantially different from abiotic systems other than the empirical nature of their robustness. We believe that there are other new and unique properties and patterns comprehensible at this bio-logical level. The report lays out a fundamental set of approaches to articulate these properties and patterns, and is composed as follows. Sections 1 through 4 (preamble, introduction, motivation and major biomathematical problems) are incipient. Section 5 describes the issues affecting Integral Biomathics and Section 6 -- the aspects of the Grand Challenge we face with this project. Section 7 contemplates the effort to formalize a General Theory of Living Systems (GTLS) from what we have today. The goal is to have a formal system, equivalent to that which exists in the physics community. Here we define how to perceive the role of time in biology. Section 8 describes the initial efforts to apply this general theory of living systems in many domains, with special emphasis on crossdisciplinary problems and multiple domains spanning both “hard” and “soft” sciences. The expected result is a coherent collection of integrated mathematical techniques. Section 9 discusses the first two test cases, project proposals, of our approach. They are designed to demonstrate the ability of our approach to address “wicked problems” which span across physics, chemistry, biology, societies and societal dynamics. The solutions require integrated measurable results at multiple levels known as “grand challenges” to existing methods. Finally, Section 10 adheres to an appeal for action, advocating the necessity for further long-term support of the INBIOSA program. The report is concluded with preliminary non-exclusive list of challenging research themes to address, as well as required administrative actions. The efforts described in the ten sections of this White Paper will proceed concurrently. Collectively, they describe a program that can be managed and measured as it progresses

Modelling Early Transitions Toward Autonomous Protocells

This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the conceptual perspective developed. The central subject matter addressed is the emergence and maintenance of compartmentalised chemistries as precursors of more complex systems with a proper cellular organization. Whereas an evolutionary conception of life dominates prebiotic chemistry research and overflows into the protocells field, this thesis defends that the 'autonomous systems perspective' of living phenomena is a suitable - arguably the most suitable - conceptual framework to serve as a backdrop for protocell research. The autonomy approach allows a careful and thorough reformulation of the origins of cellular life problem as the problem of how integrated autopoietic chemical organisation, present in all full-fledged cells, originated and developed from more simple far-from-equilibrium chemical aggregate systems.Comment: 205 Pages, 27 Figures, PhD Thesis Defended Feb 201

Art and Technology: coherence, connectedness, and the integrative field

Merged with duplicate record 10026.1/690 on 03.04.2017 by CS (TIS)This thesis is a theoretical and practical intervention in the field of art and technology. It proceeds from the re-examination of four specific domains that in the past 40 years have considerably informed the invention of new aesthetic forms. They are: art, science, nature and technology. We have identified that each one of these domains and the way they inform one another reflects the influence of a Western analytical tradition based on fragmentation, dichotomies and dualities. In consequence of this, art of the last decades has suffered from a sort of mechanistic thought which results from a predominantly weary aesthetic model, founded in dualities such as: object/process, form/behaviour, meaning/information. The main question that the present study addresses is how to overcome this predominantly reductionist inheritance and to develop an aesthetic model able to interconnect in an integrative fashion those disparate domains, respective discourses and practices? The answer to this question, developed throughout this thesis, is an aesthetic principle built upon the notions of resonance, coherence and field models, rooted in an integrative view of living organisms based on the theory of biophotons. This constitutes the main contribution of the thesis to new knowledge. The theoretical approach of this thesis is developed upon the revision of the concept of form, supported by a Gestalt analysis as provided by Rudolf Arnheim, and has involved the consideration of the ideas of Gilbert Simondon (the concept of "concretisation") and Vilem Flusser (the concept of "apparatus"), in order to gain a deeper insight into the nature of technology. In conclusion, the practice-based methodology of this thesis has been to develop artworks based on the confluence of living organisms (plants) and artificial systems in order to permit empirical observation and reflection on the proposed theory. The major outcome of the practice is the artwork "Breathing", a hybrid creature made of a living organism (a plant) and an artificial system. The creature responds to its environment through movement, light and the noise of its mechanical parts and interacts with the observer through his/her act of breathing. This work is the result of an investigation into plants as sensitive agents for the creation of art. The intention was to explore new forms of artistic experience through the dialogue of natural and artificial processes