Logic-Based Specification Languages for Intelligent Software Agents

The research field of Agent-Oriented Software Engineering (AOSE) aims to find abstractions, languages, methodologies and toolkits for modeling, verifying, validating and prototyping complex applications conceptualized as Multiagent Systems (MASs). A very lively research sub-field studies how formal methods can be used for AOSE. This paper presents a detailed survey of six logic-based executable agent specification languages that have been chosen for their potential to be integrated in our ARPEGGIO project, an open framework for specifying and prototyping a MAS. The six languages are ConGoLog, Agent-0, the IMPACT agent programming language, DyLog, Concurrent METATEM and Ehhf. For each executable language, the logic foundations are described and an example of use is shown. A comparison of the six languages and a survey of similar approaches complete the paper, together with considerations of the advantages of using logic-based languages in MAS modeling and prototyping.Comment: 67 pages, 1 table, 1 figure. Accepted for publication by the Journal "Theory and Practice of Logic Programming", volume 4, Maurice Bruynooghe Editor-in-Chie

Chemical communication between synthetic and natural cells: a possible experimental design

The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the synthesis of one or more functional proteins. Thanks to the in situ synthesized proteins, synthetic cells become able to perform several biomolecular functions, which can be exploited for a large variety of applications. This paves the way to several advanced uses of synthetic cells in basic science and biotechnology, thanks to their versatility, modularity, biocompatibility, and programmability. In the previous WIVACE (2012) we presented the state-of-the-art of semi-synthetic minimal cell (SSMC) technology and introduced, for the first time, the idea of chemical communication between synthetic cells and natural cells. The development of a proper synthetic communication protocol should be seen as a tool for the nascent field of bio/chemical-based Information and Communication Technologies (bio-chem-ICTs) and ultimately aimed at building soft-wet-micro-robots. In this contribution (WIVACE, 2013) we present a blueprint for realizing this project, and show some preliminary experimental results. We firstly discuss how our research goal (based on the natural capabilities of biological systems to manipulate chemical signals) finds a proper place in the current scientific and technological contexts. Then, we shortly comment on the experimental approaches from the viewpoints of (i) synthetic cell construction, and (ii) bioengineering of microorganisms, providing up-to-date results from our laboratory. Finally, we shortly discuss how autopoiesis can be used as a theoretical framework for defining synthetic minimal life, minimal cognition, and as bridge between synthetic biology and artificial intelligence.Comment: In Proceedings Wivace 2013, arXiv:1309.712

A dual role for prediction error in associative learning

Confronted with a rich sensory environment, the brain must learn statistical regularities across sensory domains to construct causal models of the world. Here, we used functional magnetic resonance imaging and dynamic causal modeling (DCM) to furnish neurophysiological evidence that statistical associations are learnt, even when task-irrelevant. Subjects performed an audio-visual target-detection task while being exposed to distractor stimuli. Unknown to them, auditory distractors predicted the presence or absence of subsequent visual distractors. We modeled incidental learning of these associations using a Rescorla--Wagner (RW) model. Activity in primary visual cortex and putamen reflected learning-dependent surprise: these areas responded progressively more to unpredicted, and progressively less to predicted visual stimuli. Critically, this prediction-error response was observed even when the absence of a visual stimulus was surprising. We investigated the underlying mechanism by embedding the RW model into a DCM to show that auditory to visual connectivity changed significantly over time as a function of prediction error. Thus, consistent with predictive coding models of perception, associative learning is mediated by prediction-error dependent changes in connectivity. These results posit a dual role for prediction-error in encoding surprise and driving associative plasticity

A simple model for the early events of quorum sensing in Pseudomonas aeruginosa: modeling bacterial swarming as the movement of an "activation zone"

<p>Abstract</p> <p>Background</p> <p>Quorum sensing (QS) is a form of gene regulation based on cell-density that depends on inter-cellular communication. While there are a variety of models for bacterial colony morphology, there is little work linking QS genes to movement in an open system.</p> <p>Results</p> <p>The onset of swarming in environmental <it>P. aeruginosa </it>PUPa3 was described with a simplified computational model in which cells in random motion communicate via a diffusible signal (representing <it>N</it>-acyl homoserine lactones, AHL) as well as diffusible, secreted factors (enzymes, biosurfactans, i.e. "public goods") that regulate the intensity of movement and metabolism in a threshold-dependent manner. As a result, an "activation zone" emerges in which nutrients and other public goods are present in sufficient quantities, and swarming is the spontaneous displacement of this high cell-density zone towards nutrients and/or exogenous signals. The model correctly predicts the behaviour of genomic knockout mutants in which the QS genes responsible either for the synthesis (<it>lasI, rhlI</it>) or the sensing (<it>lasR, rhlR</it>) of AHL signals were inactivated. For wild type cells the model predicts sustained colony growth that can however be collapsed by the overconsumption of nutrients.</p> <p>Conclusion</p> <p>While in more complex models include self-orienting abilities that allow cells to follow concentration gradients of nutrients and chemotactic agents, in this model, displacement towards nutrients or environmental signals is an emergent property of the community that results from the action of a few, well-defined QS genes and their products. Still the model qualitatively describes the salient properties of QS bacteria, i.e. the density-dependent onset of swarming as well as the response to exogenous signals or cues.</p> <p>Reviewers</p> <p>This paper was reviewed by Gáspár Jékely, L. Aravind, Eugene V. Koonin and Artem Novozhilov (nominated by Eugene V. Koonin).</p

A synthetic gene network architecture that propagates

Thesis (Ph.D.)--Boston UniversitySynthetic biology is a field that is tending towards maturity. Synthetic gene networks are becoming increasingly more complex, and are being engineered with functional outcomes as design goals rather than just logical demonstration. As complex as circuits become, it is still a difficult process to build a functional gene network. Much work has been done to reduce DNA assembly time, but none specifically addresses the complexity ofproducing functional networks. To this end, we present a synthetic gene network assembly strategy that emphasizes characterization-driven iteration. The Plug- and-Play methodology allows for post-construction modification to circuits, which enables the simple swapping of parts. This type of modification makes it possible to tune circuits for troubleshooting, or even to repurpose networks. We used a specified set of restriction enzymes, a library of optimized parts and a compatible backbone vector system to preserve uniqueness of cloning sites and allow maintained post-construction access to the network. To demonstrate the system, we rapidly constructed a bistable genetic toggle and subsequently transformed it into two functionally distinct networks, a 3 and 4-node feed-forward loop. We also designed a synthetic gene network that can propagate signals across a population ofisogenic bacteria. We used the Plug-and-Play methodology to quickly construct an excitable system that toggles between sending and receiving states. We developed a spatial assay platform that could accommodate long-term, large-scale plating experiments so as to visualize the propagation effect on the centimeter scale. We built several iterations ofthe propagating network, probed the regulatory dynamics ofthe various nodes and identified problematic nodes. We took steps to address these nodes with both orthogonal transcription machinery as well as multiple modes of genetic regulation. We integrated the propagating networks with a DNA-damage sensitive triggering module. This opened up the gene network to potentially complex applications such as antibiotic sensing, or longer-distance communication experiments

Free will, temptation, and self-control: We must believe in free will. We have no choice (Isaac B. Singer).

Baumeister, Sparks, Stillman, and Vohs (2007), sketch a theory of free will as the human ability to exert self-control. Self-control can produce goal-directed behavior, which free will conceptualized as random behavior cannot. We question whether consumer psychology can shed light on the ontological question of whether free will exists. We suggest that it is more fruitful for consumer psychology to examine consumer's belief in free will. Specifically, we propose that this belief arises from customers' phenomenological experience of exercising self-control in the face of moral or intertemporal conflicts of will. Based on extant literature in philosophy, psychology, and economics, we offer both a narrower conceptualization of the nature of self-control problems and a more general conceptualization of self-control strategies, involving not only willpower but also precommitment. We conclude with a discussion of the consequences of consumer's belief in free will.Research; Theory; Self-control; Behavior; IT; Experience; philosophy; Economics; Problems; Strategy;

Free will, temptation, and self-control: We must believe in free will, we have no choice (Isaac B. Singer).

Baumeister, Sparks, Stillman, and Vohs (2007) sketch a theory of free will as the humanability to exert self-control. Self-control can produce goal-directed behavior, which free will conceptualized as random behavior cannot. We question whether consumer psychology can shed light on the ontological question of whether free will exists. We suggest that it is more fruitful for consumer psychology to examine consumers' belief in freewill. Specifically, we propose that this belief arises from consumers' phenomenological experience of exercising self-control in the face of moral or intertemporal conflicts of will. Based on extant literature in philosophy, psychology, and economics, we offer both a narrower conceptualization of the nature of self-control problems and a more general conceptualization of self-control strategies, involving not only will power but also precommitment. We conclude with a discussion of the consequences of consumers' belief in free will.

Controlled ecological life support system - biological problems

The general processes and controls associated with two distinct experimental paradigms are examined. Specific areas for research related to biotic production (food production) and biotic decomposition (waste management) are explored. The workshop discussions were directed toward Elemental cycles and the biological factors that affect the transformations of nutrients into food, of food material into waste, and of waste into nutrients were discussed. To focus on biological issues, the discussion assumed that (1) food production would be by biological means (thus excluding chemical synthesis), (2) energy would not be a limiting factor, and (3) engineering capacity for composition and leak rate would be adequate