Adaptation from interactions between metabolism and behaviour: self-sensitive behaviour in protocells

This thesis considers the relationship between adaptive behaviour and metabolism, using theoretical arguments supported by computational models to demonstrate mechanisms of adaptation that are uniquely available to systems based upon the metabolic organisation of self-production. It is argued how, by being sensitive to their metabolic viability, an organism can respond to the quality of its environment with respect to its metabolic well-being. This makes possible simple but powerful ‘self-sensitive’ adaptive behaviours such as “If I am healthy now, keep doing the same as I have been doing – otherwise do something else.” This strategy provides several adaptive benefits, including the ability to respond appropriately to phenomena never previously experienced by the organism nor by any of its ancestors; the ability to integrate different environmental influences to produce an appropriate response; and sensitivity to the organism’s present context and history of experience. Computational models are used to demonstrate these capabilities, as well as the possibility that self-sensitive adaptive behaviour can facilitate the adaptive evolution of populations of self-sensitive organisms through (i) processes similar to the Baldwin effect, (ii) increasing the likelihood of speciation events, and (iii) automatic behavioural adaptation to changes in the organism itself (such as genetic changes). In addition to these theoretical contributions, a computational model of self-sensitive behaviour is presented that recreates chemotaxis patterns observed in bacteria such as Azospirillum brasilense and Campylobacter jejuni. The models also suggest new explanations for previously unexplained asymmetric distributions of bacteria performing aerotaxis. More broadly, the work advocates further research into the relationship between behaviour and the metabolic organisation of self-production, an organisational property shared by all life. It also acts as an example of how abstract models that target theoretical concepts rather than natural phenomena can play a valuable role in the scientific endeavour

Learning not to learn: Nature versus nurture in silico

Animals are equipped with a rich innate repertoire of sensory, behavioral and motor skills, which allows them to interact with the world immediately after birth. At the same time, many behaviors are highly adaptive and can be tailored to specific environments by means of learning. In this work, we use mathematical analysis and the framework of meta-learning (or 'learning to learn') to answer when it is beneficial to learn such an adaptive strategy and when to hard-code a heuristic behavior. We find that the interplay of ecological uncertainty, task complexity and the agents' lifetime has crucial effects on the meta-learned amortized Bayesian inference performed by an agent. There exist two regimes: One in which meta-learning yields a learning algorithm that implements task-dependent information-integration and a second regime in which meta-learning imprints a heuristic or 'hard-coded' behavior. Further analysis reveals that non-adaptive behaviors are not only optimal for aspects of the environment that are stable across individuals, but also in situations where an adaptation to the environment would in fact be highly beneficial, but could not be done quickly enough to be exploited within the remaining lifetime. Hard-coded behaviors should hence not only be those that always work, but also those that are too complex to be learned within a reasonable time frame

Bodies in place : enactive cognition as development of ecological norms

Les partisans de l’approche énactive soutiennent que la cognition se constitue à travers l’histoire des différentes formes d'interaction (biologique, sensorimotrice, intercorporelle, linguistique, etc.) entre un vivant et son environnement. Ces interactions ne sont pas aléatoires, mais des activités obéissant à certaines normes que les énactivistes appellent sense-making. La cognition est, de ce point de vue, une forme de sense-making. Malgré les avantages indéniables que confère une telle perspective pour étudier la cognition, la présente thèse développe un point de vue critique par rapport à l’approche énactive et soutient qu'il est nécessaire d'approfondir notre compréhension de la dimension écologique du sense-making. Le but principal de la thèse est en conséquence de montrer que l'environnement joue un rôle encore plus important que l’approche énactive ne lui attribue habituellement. En m'engageant de manière critique dans le répertoire conceptuel de la cognition énactive, de la phénoménologie et des approches écologiques de la cognition, l’objectif de cette thèse consiste à poser les bases conceptuelles d'une approche énactive-écologique de la cognition. Pour ce faire, la thèse s’attèle à mettre de l’avant trois idées principales. La première consiste à redéfinir le concept du sense-making : contrairement à la conception qui s’est traditionnellement imposée dans le mouvement énactif, nous allons démontrer qu’il s’agit d’un phénomène de développement (et non de création) de normes. La rencontre du corps et du monde est toujours ancrée dans un champ normatif prédéfini, de sorte que nous devons réévaluer le rôle que joue l'environnement dans les processus de sense-making. En effet, si les agents se retrouvent toujours-déjà plongés dans un champ normatif (et non dans un environnement purement causal et physique), il faut alors reconnaître que l'environnement joue un rôle actif dans la constitution et l'auto-transformation des normes de sense-making. La deuxième idée poursuit dans cette veine et porte sur cette nouvelle conception de l'environnement, qui est ici défini comme un champ normatif actif, incarnant une tension entre le passé habituel du système agent-environnement et les contingences incessantes des événements du monde qui poussent le système vers leur auto-transformation et développement. La troisième idée principale de cette thèse consiste en une description holistique du champ d'action des agents (un lieu énactif) et des normes édictées (enacted) par des processus de sense-making sur le terrain (normes de lieu). Une esquisse générale du lieu énactif montre que les activités de sense-making sont liées à des processus écologiques qui enchevêtrent de multiples agents et localités matérielles dans un réseau écologique local. Ces réseaux écologiques forment une unité systémique et résiliente qui se déploie dans le temps avec les habitants du lieu, et fonctionne comme un champ normatif qui contraint et motive l'auto-transformation de chaque système agent-environnementSupporters of autonomist enactivism or the enactive approach claim that cognition is a phenomenon constituted by the historical development of different forms of interaction (biological, sensorimotor, intercorporeal, and linguistic) between living bodies and their environments. For autonomist enactivists, the nature of these interactions is not entirely predetermined by general laws of causation but by norms enacted in the historical path of the agent-environment system, and thanks to processes of sense-making. Cognition is, from the enactivist standpoint, a form of sense-making. While there are multiple advantages in holding such perspective to study mind and cognition, this thesis develops a critical point of view and argues that it is necessary to deepen our understanding of the ecological dimension of sense-making. Specifically, the thesis aims to show that the environment plays a more critical role than autonomist enactivism usually attributes to it. By drawing on and critically engaging with the conceptual repertoire of enactive cognition, phenomenology, and ecological approaches to cognition, my objective is to set the conceptual foundations for an enactive-ecological approach to cognition. For this task, I propose three interrelated ideas. The first redefines sense-making as a phenomenon of norm development. The most common descriptions of sense-making involve the emergence of meaning from raw physical matter thanks to the activity of living organisms. As norm development, by contrast, sense-making refers to a constant enactment and re-enactment of norms of interaction from other pregiven norms, previously enacted in the past of the agent-environment system. I argue that the encounter of the body and the world is permanently embedded in a pregiven normative field and never in an abstract void where raw physical interactions occur. From this standpoint, we need, however, to re-evaluate the role that the environment plays in sense-making processes. If agents find themselves immersed in normative fields and not in raw physical landscapes, then the environment has a more active role for the constitution and self-transformation of sense-making norms than autonomist enactivists have acknowledged. In this vein, the second main idea of this thesis concerns the environment as an active normative field that incarnates a tension between the habitual past of the agent-environment system and the ongoing contingencies of worldly events that push the system to their self-transformation and development. The third main idea of this thesis consists of a holistic description of the field of action of agents (enactive place) and the norms enacted by processes of sense-making in the field (place-norms). A general sketch of enactive place shows that sense-making is tied to processes that entangle multiple agents and material localities into a local ecological web. An enactive place constitutes a systemic and resilient unity that unfolds in time altogether with its inhabitants, working as a normative field that constrains and motivates the self-transformation of each agent-environment system. Bodies are therefore part of wider unities of historical development: places

Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Manifesto of computational social science

The increasing integration of technology into our lives has created unprecedented volumes of data on society’s everyday behaviour. Such data opens up exciting new opportunities to work towards a quantitative understanding of our complex social systems, within the realms of a new discipline known as Computational Social Science. Against a background of financial crises, riots and international epidemics, the urgent need for a greater comprehension of the complexity of our interconnected global society and an ability to apply such insights in policy decisions is clear. This manifesto outlines the objectives of this new scientific direction, considering the challenges involved in it, and the extensive impact on science, technology and society that the success of this endeavour is likely to bring about

Adaptive dynamical networks

It is a fundamental challenge to understand how the function of a network is related to its structural organization. Adaptive dynamical networks represent a broad class of systems that can change their connectivity over time depending on their dynamical state. The most important feature of such systems is that their function depends on their structure and vice versa. While the properties of static networks have been extensively investigated in the past, the study of adaptive networks is much more challenging. Moreover, adaptive dynamical networks are of tremendous importance for various application fields, in particular, for the models for neuronal synaptic plasticity, adaptive networks in chemical, epidemic, biological, transport, and social systems, to name a few. In this review, we provide a detailed description of adaptive dynamical networks, show their applications in various areas of research, highlight their dynamical features and describe the arising dynamical phenomena, and give an overview of the available mathematical methods developed for understanding adaptive dynamical networks

Mental disorder as both natural and normative : developing the normative dimension of the 3e conceptual framework for psychopathology

Current arguments concerning the role of normativity within the concept of mental disorder are explored, and some requirements of a successful normative construal sketched out. We then shift to a discussion of "natural" normativity to lay the groundwork for our own understanding of what counts as a mental disorder. The view we present is grounded in an enactive, embodied, and embedded view of the mind (3e cognition). The position argued for is one where the labeling of a particular set of behaviors as disordered or dysfunctional is justified by the significant violation of norms, but where the norms in question are not socially imposed, rather they are the functional norms of the individual being diagnosed. The strengths and weaknesses of our position are discussed, and an addendum is proposed in response to a foreseeable counterargument. This construal provides a conceptual framework for thinking critically about normative issues in diagnosis, appreciates how central normativity is to the concept of mental disorder, and, finally (in being tied to the functionality of the individual), places the institutions of psychiatry and clinical psychology on good ethical ground and allows for consideration of cultural and individual variation during the diagnostic process

The primacy of Knowing-how : cognition, know-how and an enactive action first epistemology

The Enactive Approach (EA) is a project of naturalization of the mind. EA should be able to offer a naturalization of knowledge, such underlying naturalization is what is found in this dissertation. The result is an epistemology where the most basal aspect of knowledge is not to accurately represent. For an enactive epistemology, the primary relation is how knowers relate, contact or engage with what is known. I argue in the final chapter that knowing is a perspectival, affectively entangled, historically situated relation between knower and known. Knower, known and knowing are characterized in broad naturalistic terms. EA is first presented in the context of a larger trend of studying cognition in an ecological way. The understanding of mind in the context of the living leads me to argue that living systems and precarious autonomous systems in general are intrinsically teleological systems whose defining activity consists in being responsive to the viability boundaries or conditions of their own existence. Cognitive systems skillfully change in adaptive manners to not disintegrate, even if their changes are not optimal. The account provides a relational account of adaptive behavior as the basis for an account of know-how. The more general notion of know-how can be articulated from the notion of perception as mastery of sensorimotor contingencies. Know how in general is understood as the organization and reorganization of bodily processes and structures that enables reliable successful action. Know-how as the bodily sensitivities and capabilities relative to the cognitive domain that reliably result in the success of action is a feature of all forms of cognitive engagement. The cognition or knowing-how of languaging consists in acquiring, producing, interpreting and modifying the know-how shared within linguistic communities. Crucially, the influence of the interactive context in a participant’s sense-making varies in a continuum of participation. In one end of the spectrum one finds sense-making that remains largely (but not absolutely) individual and in the other end where what characterizes the activity is a joint process of sense-making. Knowing-how to language is knowing-how to be in dialogue with plural and idiosyncratic identities while being both yourself. A shared community of practices emerges as the basis of objectivity; knowing-how is a communal affair. If cognition is the skillful and not necessarily optimal adaptation of a precarious systemic identity to an always changing environment, all cognition rests on know how. Cognition rests on know-how in the sense that all cognition is understood in terms of skillful transition between states of a system struggling with possible disintegration. Intelligent behavior is not based on symbolic structures and context-free knowledge, it is based on richly detailed, context-specific know-how. The knowledgeable interaction with the world is the responsiveness to the now that incorporates the history leading up to it.A Abordagem Enativa (AE) é um projeto de naturalização da mente. AE deveria ser capaz de oferecer uma naturalização do conhecimento, tal naturalização subjacente é o que apresento ao leitor nesta tese. O resultado é uma epistemologia na qual o aspecto mais básico do conhecimento não é representar acuradamente. Para uma epistemologia enativa, a relação privilegiada é como conhecedores se relacionam, entram em contato ou engajam com o que é conhecido. Argumento no capítulo final que o conhecimento é uma relação perspectival, afectivamente emaranhada, historicamente situada entre conhecedor e conhecido. Conhecedor, conhecido e conhecer são caracterizados em termos liberalmente naturalistas. AE é primeiro apresentada no contexto de uma ampla tendência de estudar-se ecologicamente a cognição. O entendimento da vida no contexto do vivo me leva a argumentar que sistemas vivos e sistemas autônomos precários em geral são teleológicos e sua atividade definidora consiste em ser responsivo às fronteiras de viabilidade de sua própria existência. Sistemas cognitivos habilidosamente mudam de modos adaptativos evitando a desintegração, mesmo que as mudanças não sejam optimais. A abordagem provê uma visão relacional do comportamento adaptativo como base para o conhecimento prático [know-how]. A noção mais geral de conhecimento prático pode ser elaborada a partir da noção de percepção como maestria de contingências sensório-motoras. Conhecimento prático em geral é compreendido como a organização e reorganização de processos e estruturas corporais que possibilita de modo confiável a ação bem-sucedida. Conhecimento prático como as sensibilidades e capacidades corporais para o confiável sucesso da ação é uma característica de todas as formas de engajamento cognitivo. A cognição ou o sabendo-fazer do lingueajear consiste em adquirir, produzir, interpretar e modificar o conhecimento prático compartilhado entre comunidades linguísticas. Crucialmente, a influência do contexto interativo na produção de sentido de um participante de uma comunidade varia em um contínuo de participação. Num extremo encontra-se produção de sentido que permanece majoritariamente (mas não absolutamente individual, e no outro encontra-se atividades caracterizadas como processos conjuntos de produção de sentido. Sabendo-fazer linguagem é saber como estar em diálogo com identidades plurais e idiossincráticas enquanto se é uma você mesmo. Uma comunidade de práticas compartilhadas emerge como a base da objetividade, saber-como é um assunto comunal. Se a cognição é a adaptação habilidosa e não necessariamente optimal de uma identidade sistêmica precária em um ambiente constantemente mudando, toda cognição apoia se em conhecimento prático. Cognição apoia-se em conhecimento prático na medida que toda cognição é entendida em termos da transição habilidosa entre estados de um sistema sob a possibilidade de desintegração Comportamento inteligente não é baseado em estruturas simbólicas e conhecimento geral, baseia-se em conhecimento prático ricamente detalhado e relevante ao contexto específico. A interação com o mundo dotada de conhecimento é a responsividade para o agora que incorpora a história que nos levou até aqui

Adaptive value function approximation in reinforcement learning using wavelets

A thesis submitted to the Faculty of Science, School of Computational and Applied Mathematics University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, South Africa, July 2015.Reinforcement learning agents solve tasks by finding policies that maximise their reward over time. The policy can be found from the value function, which represents the value of each state-action pair. In continuous state spaces, the value function must be approximated. Often, this is done using a fixed linear combination of functions across all dimensions. We introduce and demonstrate the wavelet basis for reinforcement learning, a basis function scheme competitive against state of the art fixed bases. We extend two online adaptive tiling schemes to wavelet functions and show their performance improvement across standard domains. Finally we introduce the Multiscale Adaptive Wavelet Basis (MAWB), a wavelet-based adaptive basis scheme which is dimensionally scalable and insensitive to the initial level of detail. This scheme adaptively grows the basis function set by combining across dimensions, or splitting within a dimension those candidate functions which have a high estimated projection onto the Bellman error. A number of novel measures are used to find this estimate.