Causality, Information and Biological Computation: An algorithmic software approach to life, disease and the immune system

Biology has taken strong steps towards becoming a computer science aiming at reprogramming nature after the realisation that nature herself has reprogrammed organisms by harnessing the power of natural selection and the digital prescriptive nature of replicating DNA. Here we further unpack ideas related to computability, algorithmic information theory and software engineering, in the context of the extent to which biology can be (re)programmed, and with how we may go about doing so in a more systematic way with all the tools and concepts offered by theoretical computer science in a translation exercise from computing to molecular biology and back. These concepts provide a means to a hierarchical organization thereby blurring previously clear-cut lines between concepts like matter and life, or between tumour types that are otherwise taken as different and may not have however a different cause. This does not diminish the properties of life or make its components and functions less interesting. On the contrary, this approach makes for a more encompassing and integrated view of nature, one that subsumes observer and observed within the same system, and can generate new perspectives and tools with which to view complex diseases like cancer, approaching them afresh from a software-engineering viewpoint that casts evolution in the role of programmer, cells as computing machines, DNA and genes as instructions and computer programs, viruses as hacking devices, the immune system as a software debugging tool, and diseases as an information-theoretic battlefield where all these forces deploy. We show how information theory and algorithmic programming may explain fundamental mechanisms of life and death.Comment: 30 pages, 8 figures. Invited chapter contribution to Information and Causality: From Matter to Life. Sara I. Walker, Paul C.W. Davies and George Ellis (eds.), Cambridge University Pres

Part 1: a process view of nature. Multifunctional integration and the role of the construction agent

This is the first of two linked articles which draw s on emerging understanding in the field of biology and seeks to communicate it to those of construction, engineering and design. Its insight is that nature 'works' at the process level, where neither function nor form are distinctions, and materialisation is both the act of negotiating limited resource and encoding matter as 'memory', to sustain and integrate processes through time. It explores how biological agents derive work by creating 'interfaces' between adjacent locations as membranes, through feedback. Through the tension between simultaneous aggregation and disaggregation of matter by agents with opposing objectives, many functions are integrated into an interface as it unfolds. Significantly, biological agents induce flow and counterflow conditions within biological interfaces, by inducing phase transition responses in the matte r or energy passing through them, driving steep gradients from weak potentials (i.e. shorter distances and larger surfaces). As with biological agents, computing, programming and, increasingly digital sensor and effector technologies share the same 'agency' and are thus convergent

Checkpoint and run-time adaptation with pluggable parallelisation

Enabling applications for computational Grids requires new approaches to develop applications that can effectively cope with resource volatility. Applications must be resilient to resource faults, adapting the behaviour to available resources. This paper describes an approach to application-level adaptation that efficiently supports application-level checkpointing. The key of this work is the concept of pluggable parallelisation, which localises parallelisation issues into multiple modules that can be (un)plugged to match resource availability. This paper shows how pluggable parallelisation can be extended to effectively support checkpointing and run-time adaptation. We present the developed pluggable mechanism that helps the programmer to include checkpointing in the base (sequential). Based on these mechanisms and on previous work on pluggable parallelisation, our approach is able to automatically add support for checkpointing in parallel execution environments. Moreover, applications can adapt from a sequential execution to a multi-cluster configuration. Adaptation can be performed by checkpointing the application and restarting on a different mode or can be performed during run-time. Pluggable parallelisation intrinsically promotes the separation of software functionality from fault-tolerance and adaptation issues facilitating their analysis and evolution. The work presented in this paper reinforces this idea by showing the feasibility of the approach and performance benefits that can be achieved.(undefined

Online Personal Data Processing and EU Data Protection Reform. CEPS Task Force Report, April 2013

This report sheds light on the fundamental questions and underlying tensions between current policy objectives, compliance strategies and global trends in online personal data processing, assessing the existing and future framework in terms of effective regulation and public policy. Based on the discussions among the members of the CEPS Digital Forum and independent research carried out by the rapporteurs, policy conclusions are derived with the aim of making EU data protection policy more fit for purpose in today’s online technological context. This report constructively engages with the EU data protection framework, but does not provide a textual analysis of the EU data protection reform proposal as such

Mobile Business in the Vending Industry

The business of operating vending machines substantially changes by the use of telemetry via wireless technologies. This technology enables operators to change their business processes from a fixed periodical to a needs-based operating and maintenance, generating efficiency and effectiveness added values. In addition, significant advantages can be achieved by real-time error reports, by analyzing and optimizing the product range and the profitability. The paper provides a general introduction in the vending market and the operating process. Based on this, drawbacks and opportunities of the use of mobile communication techniques in vending machines for a business process reengineering are discussed and criteria for the choice of telemetry-equipped vending machines’ locations are developed. The feasibility of the proposed concepts is examined with regard to the current technical state-of-the-art. Finally, conclusions are drawn and an outlook on the future of mobile vending is given.mobile business; mobile business processes; mobile BPR; vending industry; telemetry

Subsistence agriculture in Central and Eastern Europe: how to break the vicious circle?

Subsistence agriculture is probably the least understood and the most neglected type of agriculture. In a globalised, market-driven world, it remains at the same time a myth and a marginal phenomenon. CONTENTS: Subsistence Agriculture in Development: Its Role in Processes of Structural Change; Franz Heidhues, Michael Brüntrup. Institutions and Technologies for Subsistence Agriculture: How to Increase Commercialization; Zvi Lerman. Policy Options to Overcome Subsistence Agriculture in the CEECs; Joachim von Braun, Daniela Lohlein. Decision Making Patterns of Subsistence Farmers in Bulgaria; Plamen Mishev, Philip Kostov. Commercialisation of Subsistence Agriculture in Transition Economies: On Imperfect Competition, Market Development and Support Policies; Ernst-August Nuppenau. Development Perspectives of Subsistence Farms in Southeastern Poland: Social Buffer Stock or Commercial Agriculture? Martin Petrick, Ewa Tyran. The Market Potential and Patterns of Contemporary Agriculture in Romania's Northwestern Plain; Csaba M. Kovács. Subsistence Farming in Bulgaria: Between Tradition and Market Requirements; Diana Kopeva, Nivelin Noev. The Significance of Subsistence Farming in Georgia as an Economic and Social Buffer; Hannah Kegel. Agrarian Reform and Subsistence Agriculture in Russia; Vladimir Yefimov. Economic Background and Development Opportunities of Individual Subsidiary Holdings in the Ukraine: Some Empirical Evidence; Andriy Nedoborovskyy. Modeling Subsistence Agriculture in Russia: Effects of Total Productivity Changes and Reduction of Marketing Margins; Peter Wehrheim, Peter Wobst --

Market Structure and Competition in Food Retail: Some Evidences from Brazil

The paper analyzes competition among supermarkets in Brazil. In contrast to part of the economic literature which suggests that the fast growth of big supermarket chains would destroy independent, medium and small supermarkets, the paper argues that big supermarket chains can coexist with different formats of independent food retailing. As a result, competition in food retail is complex and cannot be described as a simple Darwinian process of market concentration. The analysis is divided in two parts. In the first part, the competition between hypermarkets and supermarkets is examined. Evidences for the district of Sao Paulo, Brazil, suggest that these retailers form separate markets. The second part is focused on neighborhood supermarkets. The results differ from the general belief that independent supermarkets establish higher prices in comparison to big chain supermarkets. The analysis brings to light the heterogeneity of the competitive fringe in the oligopoly model of Brazilian retailing.Food retail, Supermarkets, Differentiation, Agribusiness, Industrial Organization,

Many is beautiful : commoditization as a source of disruptive innovation

Thesis (S.M.M.O.T.)--Massachusetts Institute of Technology, Sloan School of Management, Management of Technology Program, 2003.Includes bibliographical references (leaves 44-45).This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.The expression "disruptive technology" is now firmly embedded in the modern business lexicon. The mental model summarized by this concise phrase has great explanatory power for ex-post analysis of many revolutionary changes in business. Unfortunately, this paradigm can rarely be applied prescriptively. The classic formulation of a "disruptive technology" sheds little light on potential sources of innovation. This thesis seeks to extend this analysis by suggesting that many important disruptive technologies arise from commodities. The sudden availability of a high performance factor input at a low price often enables innovation in adjacent market segments. The thesis suggests main five reasons that commodities spur innovation: ** The emergence of a commodity collapses competition to the single dimension of price. Sudden changes in factor prices create new opportunities for supply driven innovation. Low prices enable innovators to substitute quantity for quality. ** The price / performance curve of a commodity creates an attractor that promotes demand aggregation. ** Commodities emerge after the establishment of a dominant design. Commodities have defined and stable interfaces. Well developed tool sets and experienced developer communities are available to work with commodities, decreasing the price of experimentation. ** Distributed architectures based on large number of simple, redundant components offer more predictable performance. Systems based on a small number of high performance components will have a higher standard deviation for uptime than high granularity systems based on large numbers of low power components. ** Distributed architectures are much more flexible than low granularity systems. Large integrated facilities often provide cost advantages when operating at the Minimum Efficient Scale of production. However, distributed architectures that can efficiently change production levels over time may be a superior solution based on the ability to adapt to changing market demand patterns. The evolution of third generation bus architectures in personal computers provides a comprehensive example of commodity based disruption, incorporating all five forces.by Richard Ellert Willey.S.M.M.O.T