Explaining Engineered Computing Systems’ Behaviour: the Role of Abstraction and Idealization

This paper addresses the methodological problem of analysing what it is to explain observed behaviours of engineered computing systems (BECS), focusing on the crucial role that abstraction and idealization play in explanations of both correct and incorrect BECS. First, it is argued that an understanding of explanatory requests about observed miscomputations crucially involves reference to the rich background afforded by hierarchies of functional specifications. Second, many explanations concerning incorrect BECS are found to abstract away (and profitably so on account of both relevance and intelligibility of the explanans) from descriptions of physical components and processes of computing systems that one finds below the logic circuit and gate layer of functional specification hierarchies. Third, model-based explanations of both correct and incorrect BECS that are provided in the framework of formal verification methods often involve idealizations. Moreover, a distinction between restrictive and permissive idealizations is introduced and their roles in BECS explanations are analysed

Bacteria as computers making computers

Various efforts to integrate biological knowledge into networks of interactions have produced a lively microbial systems biology. Putting molecular biology and computer sciences in perspective, we review another trend in systems biology, in which recursivity and information replace the usual concepts of differential equations, feedback and feedforward loops and the like. Noting that the processes of gene expression separate the genome from the cell machinery, we analyse the role of the separation between machine and program in computers. However, computers do not make computers. For cells to make cells requires a specific organization of the genetic program, which we investigate using available knowledge. Microbial genomes are organized into a paleome (the name emphasizes the role of the corresponding functions from the time of the origin of life), comprising a constructor and a replicator, and a cenome (emphasizing community-relevant genes), made up of genes that permit life in a particular context. The cell duplication process supposes rejuvenation of the machine and replication of the program. The paleome also possesses genes that enable information to accumulate in a ratchet-like process down the generations. The systems biology must include the dynamics of information creation in its future developments

A note on discreteness and virtuality in analog computing

AbstractThe need for physically motivated discreteness and finiteness conditions emerges in models of both analog and digital computing that are genuinely concerned with physically realizable computational processes. This is brought out by a critical examination of notional analog superTuring devices which involve physically untenable idealizations about the perfect functioning of analog apparatuses and infinite precision of physical measurements. The capability for virtual behaviour, that is, the capability of interpreting, storing, transforming, creating the code, and thereby mimicking the behaviour of (Turing) machines, is used here to introduce a new dimension in the discussion of the analog–digital watershed. In the light of recent results on the analog simulation of digital computing, we examine the role of virtuality as a discriminating factor between these two species of computing, and immerse this problem in the context of natural computing. Is virtuality instantiated in parts of the natural world other than computer technology? This broad issue is examined in connection with the computational modelling of brain and mental information processing