Open problems in artificial life

This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated

Varieties of Exploratory Experimentation in Nanotoxicology

There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and “high-throughput” instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order to distinguish these and other activities more effectively, the paper proposes a taxonomy that includes three dimensions along which types of EE vary: (1) the aim of the experimental activity, (2) the role of theory in the activity, and (3) the methods or strategies employed for varying experimental parameters

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

Challenges in experimental data integration within genome-scale metabolic models

A report of the meeting "Challenges in experimental data integration within genome-scale metabolic models", Institut Henri Poincar\'e, Paris, October 10-11 2009, organized by the CNRS-MPG joint program in Systems Biology.Comment: 5 page

Dynamical Hierarchies

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