André Stauffer

Embryonics: a new methodology for designing field-programmable gate arrays with self-repair and self-replicating properties

The growth and the operation of all living beings are directed through the interpretation, in each of their cells, of a chemical program, the DNA string or genome. This process is the source of inspiration for the Embryonics (embryonic electronics) project, whose final objective is the conception of very large scale integrated circuits endowed with properties usually associated with the living world: self-repair (cicatrization) and self-replication. We begin by showing that any logic system can be represented by an ordered binary decision diagram (OBDD), and then embedded into a fine-grained field-programmable gate array (FPGA) whose basic cell is a multiplexer with programmable connections. The cellular array thus obtained is perfectly homogeneous: the function of each cell is defined by a configuration (or gene) and all the genes in the array, each associated with a pair of coordinates, make up the blueprint (or genome) of the artificial organism. In the second part of the project, we add to the basic cell a memory and an interpreter to, respectively, store and decode the complete genome. The interpreter extracts from the genome the gene of a particular cell as a function of its position in the array (its coordinates) and thus determines the exact configuration of the relative multiplexer. The considerable redundancy introduced by the presence of a genome in each cell has significant advantages: self-replication (the automatic production of one or more copies of the original organism) and self-repair (the automatic repair of one or more faulty cells) become relatively simple operations. The multiplexer-based FPGA cell and the interpreter are finally embedded into an electronic module; an array of such modules make it possible to demonstrate self-repair and self-replication.

Static and dynamic configurable systems

Field-programmable gate arrays (FPGAs) are large, fast integrated circuits-that can be modified, or configured, almost at any point by the end user. Within the domain of configurable computing, we distinguish between two modes of configurability: static-where the configurable processors configuration string is loaded once at the outset, after which it does not change during execution of the task at hand, and dynamic-where the processors configuration may change at any moment. This paper describes four applications in the domain of configurable computing, considering both static and dynamic systems, including: SPYDER (a reconfigurable processor development system), RENCO (a reconfigurable network computer), Firefly (an evolving machine), and the BioWatch (a self-repairing watch). While static configurability mainly aims at attaining the classical computing goal of improving performance, dynamic configurability might bring about an entirely new breed of hardware devices-ones that are able to adapt within dynamic environments.

Phylogeny, Ontogeny, and Epigenesis: Three Sources of Biological Inspiration for Softening Hardware

Living beings are complex systems exhibiting a range of desirable qualifications that have eluded realization by traditional engineering methodologies. In recent years we are witness to a growing interest in Nature exhibited by engineers, wishing to imitate the observed processes, thereby creating powerful problem-solving methodologies. If one considers Life on earth since its very beginning, three levels of organization can be distinguished: the phylogenetic level concerns the temporal evolution of the genetic programs within individuals and species, the ontogenetic level concerns the developmental process of a single multicellular organism, and the epigenetic level concerns the learning processes during an individual organisms lifetime. In analogy to Nature, the space of bioinspired systems can be partitioned along these three axes, phylogeny, ontogeny, and epigenesis, giving rise to the POE model. This paper is an exposition and examination of bio-inspired systems within the POE framework. We first discuss each of the three axes separately, considering the systems created to date and plotting directions for continued progress along the axis in question. We end our exposition by a discussion of possible research directions, involving the construction of bio-inspired systems that are situated along two, and ultimately all three axes. This presents a vision for the future which will see the advent of novel systems, inspired by the powerful examples provided by Nature.

A robust multiplexer-based FPGA inspired by biological systems

Biological organisms are among the most robust systems known to man. Their robustness is based on a set of processes which cannot be adapted directly to the world of silicon but can provide an inspiration for the design of robust circuits. This paper introduces a multiplexer-based Field-Programmable Gate Array (FPGA) which we made capable of self-test and self-repair using an approach loosely based on biological mechanisms at the cellular level. The system is designed to provide on-line self-test and self-repair using a completely distributed system and a minimal amount of additional logic.

Self-replicating and self-repairing multicellular automata

Biological organisms are among the most intricate structures known to man, exhibiting highly complex behavior through the massively parallel cooperation of numerous relatively simple elements, the cells. As the development of computing systems approaches levels of complexity such that their synthesis begins to push the limits of human intelligence, engineers are starting to seek inspiration in nature for the design of computing systems, both at the software and at the hardware levels. We present one such endeavor, notably an attempt to draw inspiration from biology in the design of a novel digital circuit: a field-programmable gate array (FPGA). This reconfigurable logic circuit will be endowed with two features motivated and guided by the behavior of biological systems: self-replication and self-repair.

Von Neumann revisited : A Turing machine with self-repair and self-reproduction properties

Abstract The growth and the operation of all living beings are directed through the interpretation, in each of their cells, of a chemical program, the DNA. This program, called genome , is the blueprint of the organism and consists of a sequence of four discrete characters: A, C, G, and T. This process is the source of inspiration for the Embryonics (embryological electronics) project, whose final objective is the conception of very large scale integrated circuits endowed with properties usually associated with the living world: self-repair (cicatrization) and self-reproduction. Within this framework, we will present a new family of coarse-grained field-programmable gate arrays. Each cell is a binary decision machine whose microprogram represents the genome, and each part of the microprogram is a gene whose execution depends on the physical position of the cell in the array, i.e. on its coordinates. The considerable redundancy introduced by the presence of a genome in each cell has significant advantages: self-reproduction (the automatic production of one or more copies of the original organism) and self-repair (the automatic repair of one or more faulty cells) become relatively simple operations. Both self-reproduction and self-repair will be illustrated by a classical example of a special-purpose. Turing machine: a parenthesis checker. Even if the described system seems exceedingly complex, we believe that computer architectures inspired by molecular biology will allow the development of new FPGAs endowed with quasi-biological properties extremely useful in environments where human intervention is necessarily limited (nuclear plants, space applications, etc.)

Toward self-repairing and self-replicating hardware: the Embryonics approach

The growth and operation of all living beings are directed by the interpretation, in each of their cells, of a chemical program, the DNA string or genome. This process is the source of inspiration for the Embryonics (embryonic electronics) project, whose final objective is the design of highly robust integrated circuits, endowed with properties usually associated with the living world: self-repair (cicatrization) and self-replication. The Embryonics architecture is based on four hierarchical levels of organization: 1) The basic primitive of our system is the molecule, a multiplexer-based element of a novel programmable circuit. 2) A finite set of molecules makes up a cell, essentially a small processor with an associated memory. 3) A finite set of cells makes up an organism, an application-specific multiprocessor system. 4) The organism can itself replicate, giving rise to a population of identical organisms. In the conclusion, we describe our ongoing research efforts to meet three challenges: a scientific challenge, that of implementing the original specifications formulated by John von Neumann; a technical challenge, that of realizing very robust integrated circuits; and a biological challenge, that of attempting to show that the genomes of artificial and natural organisms share common properties.

A macroscopic view of self-replication

In 1953, Crick and Watson published their landmark paper revealing the detailed structure of the DNA double helix. Several years earlier, von Neumann embedded a very complex configuration, a universal interpreter-copier, into a cellular array. Astoundingly, the structure of this configuration, able to realize the self-replication of any computing machine, including a universal Turing machine, shares several common traits with the structure of living cells as defined by Crick and Watsons discovery. To commemorate the 100th anniversary of von Neumanns birth, this paper presents a macroscopic analysis of self-replication in computing machines using three examples. After describing self-replication in von Neumanns universal interpreter-copier, we will revisit the famous self-replicating loop designed by Langton in 1984. In order to overcome some of the major drawbacks of Langtons loop, namely, its lack of functionality and the fact that it is ill-adapted for a realization in electronic circuits, we present a novel self-replicating loop, the Tom Thumb loop. Endowed with the same capabilities as von Neumanns interpreter-copier, i.e., the possibility of replicating computing machines of any complexity, our loop is moreover specifically designed for the implementation of self-replicating structures in programmable digital logic.

Embryonics: The Birth of Synthetic Life

A novel architecture descending from the work of von Neumann, has been developed. This architecture borrows its main principles from living systems. Like living beings, the organisms considered here are able to autonomously develop, maintain their functionality and reproduce. These genomic architectures are developed on reprogrammable hardware. They are not restricted to a given class of functions but accept any combinational and sequential function to be downloaded. These architectures are fault tolerant by design, so they can adapt to failures affecting the silicon. They autonomously evolve so as to maintain their functionality and hence self-reconfigure when needed.

The data-and-signals cellular automaton and its application to growing structures

In a traditional cellular automaton (CA) a cell is implemented by a rule table defining its state at the next time step, given its present state and those of its neighbors. The cell thus deals only with states. We present a novel CA where the cell handles data and signals. The cell is designed as a digital system comprising a processing unit and a control unit. This allows the realization of various growing structures, including self-replicating loops and biomorphs. We also describe the hardware implementation of these structures within our electronic wall for bio-inspired applications, the BioWall.