30,468 research outputs found
Formal executable descriptions of biological systems
The similarities between systems of living entities and systems of concurrent processes may support biological experiments in silico. Process calculi offer a formal framework to describe biological systems, as well as to analyse their behaviour, both from a qualitative and a quantitative point of view. A couple of little examples help us in showing how this can be done. We mainly focus our attention on the qualitative and quantitative aspects of the considered biological systems, and briefly illustrate which kinds of analysis are possible. We use a known stochastic calculus for the first example. We then present some statistics collected by repeatedly running the specification, that turn out to agree with those obtained by experiments in vivo. Our second example motivates a richer calculus. Its stochastic extension requires a non trivial machinery to faithfully reflect the real dynamic behaviour of biological systems
Is defining life pointless? Operational definitions at the frontiers of Biology
Despite numerous and increasing attempts to define what life is, there is no consensus on necessary and sufficient conditions for life. Accordingly, some scholars have questioned the value of definitions of life and encouraged scientists and philosophers alike to discard the project. As an alternative to this pessimistic conclusion, we argue that critically rethinking the nature and uses of definitions can provide new insights into the epistemic roles of definitions of life for different research practices. This paper examines the possible contributions of definitions of life in scientific domains where such definitions are used most (e.g., Synthetic Biology, Origins of Life, Alife, and Astrobiology). Rather than as classificatory tools for demarcation of natural kinds, we highlight the pragmatic utility of what we call operational definitions that serve as theoretical and epistemic tools in scientific practice. In particular, we examine contexts where definitions integrate criteria for life into theoretical models that involve or enable observable operations. We show how these definitions of life play important roles in influencing research agendas and evaluating results, and we argue that to discard the project of defining life is neither sufficiently motivated, nor possible without dismissing important theoretical and practical research
On the emergence and evolution of artificial cell signaling networks
This PhD project is concerned with the evolution of Cell
Signaling Networks (CSNs) in silico. CSNs are complex biochemical networks responsible for the coordination of cellular activities. We are investigating the possibility to build an evolutionary simulation platform that would allow the spontaneous emergence and evolution of Artificial Cell Signaling Networks (ACSNs). From a practical point of view, realizing and evolving ACSNs may provide novel computational paradigms for a variety of application areas. This work may also contribute to the biological understanding of the origins and evolution of real CSNs
A review of wildland fire spread modelling, 1990-present 3: Mathematical analogues and simulation models
In recent years, advances in computational power and spatial data analysis
(GIS, remote sensing, etc) have led to an increase in attempts to model the
spread and behvaiour of wildland fires across the landscape. This series of
review papers endeavours to critically and comprehensively review all types of
surface fire spread models developed since 1990. This paper reviews models of a
simulation or mathematical analogue nature. Most simulation models are
implementations of existing empirical or quasi-empirical models and their
primary function is to convert these generally one dimensional models to two
dimensions and then propagate a fire perimeter across a modelled landscape.
Mathematical analogue models are those that are based on some mathematical
conceit (rather than a physical representation of fire spread) that
coincidentally simulates the spread of fire. Other papers in the series review
models of an physical or quasi-physical nature and empirical or quasi-empirical
nature. Many models are extensions or refinements of models developed before
1990. Where this is the case, these models are also discussed but much less
comprehensively.Comment: 20 pages + 9 pages references + 1 page figures. Submitted to the
International Journal of Wildland Fir
Artificial life meets computational creativity?
I review the history of work in Artificial Life on the problem of the open-ended evolutionary growth of complexity in computational worlds. This is then put into the context of evolutionary epistemology and human creativity
Enaction-Based Artificial Intelligence: Toward Coevolution with Humans in the Loop
This article deals with the links between the enaction paradigm and
artificial intelligence. Enaction is considered a metaphor for artificial
intelligence, as a number of the notions which it deals with are deemed
incompatible with the phenomenal field of the virtual. After explaining this
stance, we shall review previous works regarding this issue in terms of
artifical life and robotics. We shall focus on the lack of recognition of
co-evolution at the heart of these approaches. We propose to explicitly
integrate the evolution of the environment into our approach in order to refine
the ontogenesis of the artificial system, and to compare it with the enaction
paradigm. The growing complexity of the ontogenetic mechanisms to be activated
can therefore be compensated by an interactive guidance system emanating from
the environment. This proposition does not however resolve that of the
relevance of the meaning created by the machine (sense-making). Such
reflections lead us to integrate human interaction into this environment in
order to construct relevant meaning in terms of participative artificial
intelligence. This raises a number of questions with regards to setting up an
enactive interaction. The article concludes by exploring a number of issues,
thereby enabling us to associate current approaches with the principles of
morphogenesis, guidance, the phenomenology of interactions and the use of
minimal enactive interfaces in setting up experiments which will deal with the
problem of artificial intelligence in a variety of enaction-based ways
- …