Simulating self-replicating machines

A simulation framework is described in which sliding tiles moving in a discrete two-dimensional grid can be put together to build machines. The tiles can perform logical and mechanical functions, and can be connected to each other. A self-replicating machine has been designed in this environment and its operation is summarised. Observations are made about the usefulness and the limitations of the machine and its environment, and several ways in which the limitations could be addressed are described. A justification of the simulation approach for modelling self-replicating systems is given. © Springer Science+Business Media B.V. 2007

Ratcheting synthesis

Synthetic chemistry has traditionally relied on reactions between reactants of high chemical potential and transformations that proceed energetically downhill to either a global or local minimum (thermodynamic or kinetic control). Catalysts can be used to manipulate kinetic control, lowering activation energies to influence reaction outcomes. However, such chemistry is still constrained by the shape of one-dimensional reaction coordinates. Coupling synthesis to an orthogonal energy input can allow ratcheting of chemical reaction outcomes, reminiscent of the ways that molecular machines ratchet random thermal motion to bias conformational dynamics. This fundamentally distinct approach to synthesis allows multi-dimensional potential energy surfaces to be navigated, enabling reaction outcomes that cannot be achieved under conventional kinetic or thermodynamic control. In this Review, we discuss how ratcheted synthesis is ubiquitous throughout biology and consider how chemists might harness ratchet mechanisms to accelerate catalysis, drive chemical reactions uphill and programme complex reaction sequences.<br/

Frontiers of Adaptive Design, Synthetic Biology and Growing Skins for Ephemeral Hybrid Structures

The history of membranes is one of adaptation, from the development in living organisms to man-made versions, with a great variety of uses in temporary design: clothing, building, packaging, etc. Being versatile and simple to integrate, membranes have a strong sustainability potential, through an essential use of material resources and multifunctional design, representing one of the purest cases where “design follows function.” The introduction of new engineered materials and techniques, combined with a growing interest for Nature-inspired technologies are progressively merging man-made artifacts and biological processes with a high potential for innovation. This chapter introduces, through a number of examples, the broad variety of hybrid membranes in the contest of experimental Design, Art and Architecture, categorized following two different stages of biology-inspired approach with the aim of identifying potential developments. Biomimicry, is founded on the adoption of practices from nature in architecture though imitation: solutions are observed on a morphological, structural or procedural level and copied to design everything from nanoscale materials to building technologies. Synthetic biology relies on hybrid procedures mixing natural and synthetic materials and processes

First Steps Towards an Ethics of Robots and Artificial Intelligence

This article offers an overview of the main first-order ethical questions raised by robots and Artificial Intelligence (RAIs) under five broad rubrics: functionality, inherent significance, rights and responsibilities, side-effects, and threats. The first letter of each rubric taken together conveniently generates the acronym FIRST. Special attention is given to the rubrics of functionality and inherent significance given the centrality of the former and the tendency to neglect the latter in virtue of its somewhat nebulous and contested character. In addition to exploring some illustrative issues arising under each rubric, the article also emphasizes a number of more general themes. These include: the multiplicity of interacting levels on which ethical questions about RAIs arise, the need to recognise that RAIs potentially implicate the full gamut of human values (rather than exclusively or primarily some readily identifiable sub-set of ethical or legal principles), and the need for practically salient ethical reflection on RAIs to be informed by a realistic appreciation of their existing and foreseeable capacities

Towards a Model of Life and Cognition

What should be the ontology of the world such that life and cognition are possible? In this essay, I undertake to outline an alternative ontological foundation which makes biological and cognitive phenomena possible. The foundation is built by defining a model, which is presented in the form of a description of a hypothetical but a logically possible world with a defined ontological base. Biology rests today on quite a few not so well connected foundations: molecular biology based on the genetic dogma; evolutionary biology based on neo-Darwinian model; ecology based on systems view; developmental biology by morphogenetic models; connectionist models for neurophysiology and cognitive biology; pervasive teleonomic explanations for the goal-directed behavior across the discipline; etc. Can there be an underlying connecting theme or a model which could make these seemingly disparate domains interconnected? I shall atempt to answer this question. By following the semantic view of scientific theories, I tend to believe that the models employed by the present physical sciences are not rich enough to capture biological (and some of the non-biological) systems. A richer theory that could capture biological reality could also capture physical and chemical phenomena as limiting cases, but not vice versa

Nanotechnology and preventive arms control

"Nanotechnology (NT) is about analysis and engineering of structures with size between 0.1 and 100 nanometres (1 nm = 10 -9 m). At this scale, new effects occur and the boundaries between physics, chemistry and biology vanish. NT is predicted to lead to stronger but lighter materials, markedly smaller computers with immensely increased power, large and small autonomous robots, tools for manipulation of single molecules, targeted intervention within cells, connections between electronics and neurones, and more. In recent years military research and development (R&D) of NT has been expanded markedly, with the USA far in the lead. US work spans the full range from electronics via materials to biology. While much of this is still at the fundamental level, efforts are being made to bring applications to the armed forces soon. One quarter to one third of the Federal funding for NT goes to military R&D, and the USA outspends the rest of the world by a factor 4 to 10. NT applications will likely pervade all areas of the military. Very small electronics and computers will be used everywhere, e.g. in glasses, uniforms, munitions. Large-scale battle-management and strategy-planning systems will apply human-like reasoning at increasing levels of autonomy, integrating sensors, communication devices and displays into an ubiquitous network. Stronger but light-weight materials, more efficient energy storage and propulsion will allow faster and more agile vehicles in all media. NT-based materials and explosives can bring faster and more precise projectiles. Small arms, munitions and anti-personnel missiles without any metal can become possible. Systems worn by soldiers could monitor the body status and react to injury. Systems implanted into the body could monitor the biochemistry and release drugs, or make contacts to nerves and the brain to reduce the reaction time, later possibly to communicate complex information. Autonomous land vehicles, ships and aircraft would become possible mainly through strongly increased computing power. By using NT to miniaturise sensors, actuators and propulsion, autonomous systems (robots) could also become very small, principally down to below a millimetre - fully artificial or hybrid on the basis of e.g. insects or rats. Satellites and their launchers could become small and cheap, to be used in swarms for earth surveillance, or for anti-satellite attack. Whereas no marked change is expected concerning nuclear weapons, NT may lead to various new types of chemical and biological weapons that target specific organs or act selectively on a certain genetic or protein pattern. On the other hand, NT will allow cheap sensors for chemical or biological warfare agents as well as materials for decontamination. Most of these applications are ten or more years away. Using criteria of preventive arms control, potential military NT applications are evaluated. New conventional, chemical and biological weapons would jeopardise existing arms-control treaties. Armed autonomous systems would endanger the law of warfare. Military stability could decrease with small distributed battlefield sensors and in particular with armed autonomous systems. Arms racing and proliferation have to be feared with all applications. Strong dangers to humans would ensue from armed mini-/ micro-robots and new chemical/ biological weapons used by terrorists. Negative effects on human integrity and human rights could follow indirectly if body manipulation were applied in the military before a thorough societal debate on benefits, risks and regulation." (excerpt)"Die Nanotechnologie (NT) befasst sich mit der Untersuchung und Gestaltung von Strukturen, die sich in Größen zwischen 0,1 and 100 Nanometer (1 nm = 10 -9 m) bewegen. Bei dieser Größenordnung treten neue Effekte auf, und die Grenzen zwischen Physik, Chemie und Biologie verschwinden. Die Experten sagen voraus, dass NT festere und gleichzeitig leichtere Materialien, erheblich kleinere Computer mit unermesslich gesteigerter Leistung, große und kleine autonome Roboter, Werkzeuge für die Handhabung einzelner Moleküle, gezielte Eingriffe in Zellen, Verbindungen zwischen Elektronik und Neuronen und anderes mehr hervorbringen wird. In den letzten Jahren ist die militärische Forschung und Entwicklung (FuE) im Bereich der NT erheblich ausgeweitet worden. Im weltweiten Vergleich liegen die USA deutlich in Führung. Dort wird die gesamte Bandbreite von Elektronik über Materialien bis hin zur Biologie bearbeitet. Auch wenn vieles davon noch Grundlagenforschung ist, gibt es dort doch heute schon Vorbereitungen, den Streitkräften bald Anwendungsmöglichkeiten zur Verfügung zu stellen. Ein Viertel bis ein Drittel der Regierungsausgaben für NT auf Bundesebene steht für militärische FuE zur Verfügung, und die USA geben 4 bis 10 mal so viel dafür aus wie der Rest der Welt. NT-Anwendungen werden alle Bereiche des Militärs durchdringen. Hierzu zählt der umfassende Einsatz sehr kleiner Elektronik und Computer, z.B. in Brillen, Uniformen, Munition. Komplexe Schlachtführungs- und Strategieplanungssysteme werden zunehmend autonom funktionieren und menschenähnliche Überlegungen anstellen, wobei sie Sensoren, Kommunikationsgeräte und Anzeigeeinheiten zu einem allgegenwärtigen Netzwerk verbinden. Festere und dabei leichtere Materialien, effizientere Energiespeicher und Antriebe ermöglichen den Bau schnellerer und beweglicherer Land-, Wasser-, Luft- und Raumfahrzeuge. Des weiteren können NT-basierte Materialien und Sprengstoffe zur Herstellung schnellerer und genauerer Geschosse verwendet werden. Denkbar sind metallfreie Kleinwaffen, Munition und Antipersonen-Flugkörper. Zwar ist bei Kernwaffen keine große Veränderung zu erwarten, NT kann aber zu verschiedenen neuen Arten von chemischen und biologischen Waffen führen, die auf spezifische Organe zielen oder selektiv auf eine bestimmte Eiweißstruktur oder auf ein genetisches Muster hin aktiv werden. Andererseits wird NT billige Sensoren für chemische oder biologische Waffen sowie Materialien zur Entgiftung zur Verfügung stellen. Mit den meisten dieser Anwendungen ist erst in einem Zeitraum von zehn oder mehr Jahren zu rechnen. Mögliche militärische NT-Anwendungen müssen unter den Kriterien der Präventiven Rüstungskontrolle bewertet werden." (Textauszug

An Approach to the de Novo Synthesis of Life

[Image: see text] As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials

Biological machines and the mechanization of life

During its long history from antique hand-operated instruments to modern information processing automata the notion of the machine has several times received a shift in meaning. Today the concept of the machine has completely lost its attachment to any concrete material and is instead characterized by its functional behavior. Symbolic machines, i.e. the mathematical idea to mechanically operate with symbols, became a fundamental skill in many different scientific disciplines. In this paper we take a look on synthetic biology from the computational point of view and especially address the question whether it will once more challenge the notion of the machine. One obvious consequence of future biotechnologies is that we cannot any longer draw a strict line between technique and life. In the past machines did not assemble, maintain and reproduce themselves, they had to be fabricated by man and required human monitoring and directing. Through the technical use of biological processes this hallmark of the living becomes untenable. Self-strategies and especially self-referential functional descriptions like self-assembly, self-reproduction, and self-modification are at the center of the convergence of the natural and the artificial. Conversely the adoption of life-like qualities by technical artifacts will also challenge our image of life and organisms and our understanding of what aliveness could mean