The Machine Conception of the Organism in Development and Evolution: A Critical Analysis

This article critically examines one of the most prevalent metaphors in modern biology, namely the machine conception of the organism (MCO). Although the fundamental differences between organisms and machines make the MCO an inadequate metaphor for conceptualizing living systems, many biologists and philosophers continue to draw upon the MCO or tacitly accept it as the standard model of the organism. This paper analyses the specific difficulties that arise when the MCO is invoked in the study of development and evolution. In developmental biology the MCO underlies a logically incoherent model of ontogeny, the genetic program, which serves to legitimate three problematic theses about development: genetic animism, neo-preformationism, and developmental computability. In evolutionary biology the MCO is responsible for grounding unwarranted theoretical appeals to the concept of design as well as to the interpretation of natural selection as an engineer, which promote a distorted understanding of the process and products of evolutionary change. Overall, it is argued that, despite its heuristic value, the MCO today is impeding rather than enabling further progress in our comprehension of living systems

Modelling fungal colonies and communities:challenges and opportunities

This contribution, based on a Special Interest Group session held during IMC9, focuses on physiological based models of filamentous fungal colony growth and interactions. Fungi are known to be an important component of ecosystems, in terms of colony dynamics and interactions within and between trophic levels. We outline some of the essential components necessary to develop a fungal ecology: a mechanistic model of fungal colony growth and interactions, where observed behaviour can be linked to underlying function; a model of how fungi can cooperate at larger scales; and novel techniques for both exploring quantitatively the scales at which fungi operate; and addressing the computational challenges arising from this highly detailed quantification. We also propose a novel application area for fungi which may provide alternate routes for supporting scientific study of colony behaviour. This synthesis offers new potential to explore fungal community dynamics and the impact on ecosystem functioning

Theoretical ecology as etiological from the start

The world’s leading environmental advisory institutions look to ecological theory and research as an objective guide for policy and resource management decision-making. In addition to various theoretical merits of doing so, it is therefore crucially important to clear up confusions about ecology’s conceptual foundations and to make plain the basic workings of inferential methods used in the science. Through discussion of key moments in the genesis of the theoretical branch of ecology, this essay elucidates a general heuristic role of teleological metaphor in ecological research and defuses certain enduring confusions and misguided criticisms of current work in ecology

What is Computational Intelligence and where is it going?

What is Computational Intelligence (CI) and what are its relations with Artificial Intelligence (AI)? A brief survey of the scope of CI journals and books with ``computational intelligence'' in their title shows that at present it is an umbrella for three core technologies (neural, fuzzy and evolutionary), their applications, and selected fashionable pattern recognition methods. At present CI has no comprehensive foundations and is more a bag of tricks than a solid branch of science. The change of focus from methods to challenging problems is advocated, with CI defined as a part of computer and engineering sciences devoted to solution of non-algoritmizable problems. In this view AI is a part of CI focused on problems related to higher cognitive functions, while the rest of the CI community works on problems related to perception and control, or lower cognitive functions. Grand challenges on both sides of this spectrum are addressed

Niche Modeling: Ecological Metaphors for Sustainable Software in Science

This position paper is aimed at providing some history and provocations for the use of an ecological metaphor to describe software development environments. We do not claim that the ecological metaphor is the best or only way of looking at software - rather we want to ask if it can indeed be a productive and thought provoking one.Comment: Position paper submitted to: Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE) SC13, Sunday, 17 November 2013, Denver, CO, US

Selection, tinkering and emergence in complex networks: crossing the land of tinkering

Complex biological networks have very different origins than technologic ones. The latter involve extensive design and, as engineered structures, include a high level of optimization. The former involve (in principle) contingency and structural constraints, with new structures being incorporated through tinkering with previously evolved modules or units. However, the observation of the topological features of different biological nets suggests that nature can have a limited repertoire of ”attractors” that essentially optimize communication under some basic constraints of cost and architecture or that allow the biological nets to reach a high degree of homeostasis. Conversely, the topological features exhibited by some technology graphs indicate that tinkering and internal constraints play a key role, in spite of the ”designed” nature of these structures. Previous scenarios suggested to explain the overall trends of evolution are re-analyzed in light of topological patterns.Peer ReviewedPostprint (author's final draft

A metaphorical history of DNA patents

The aim of this paper is to retrace the history of genetic patents, analyzing the metaphors used in the public debate, in patent offices, and in courtrooms. I have identified three frames with corresponding metaphor clusters: the first is the industrial frame, built around the idea that DNA is a chemical; the second is the informational frame, assembled around the concept of genetic information; last is the soul frame, based on the idea that DNA is or contains the essence of the individual

An autonomous satellite architecture integrating deliberative reasoning and behavioural intelligence

This paper describes a method for the design of autonomous spacecraft, based upon behavioral approaches to intelligent robotics. First, a number of previous spacecraft automation projects are reviewed. A methodology for the design of autonomous spacecraft is then presented, drawing upon both the European Space Agency technological center (ESTEC) automation and robotics methodology and the subsumption architecture for autonomous robots. A layered competency model for autonomous orbital spacecraft is proposed. A simple example of low level competencies and their interaction is presented in order to illustrate the methodology. Finally, the general principles adopted for the control hardware design of the AUSTRALIS-1 spacecraft are described. This system will provide an orbital experimental platform for spacecraft autonomy studies, supporting the exploration of different logical control models, different computational metaphors within the behavioral control framework, and different mappings from the logical control model to its physical implementation