Genomes

Genetic reproduction, in the abstract form originally proposed by von Neumann (1948), is illustrated in Figure 1. The Von Neumann reproducer is composed of three major subsystems: the tape is a more or less quiescent information carrier, subject to template style reproduction; the constructor is a machine capable both of copying a tape (to yield another with the same information content) and of ``decoding'' a tape (to yield more or less arbitrary machinery, as described by the information on the tape);² and finally the ancillary machinery is just a name for all additional machinery constituting the reproducer (i.e., with functionality not directly related to reproduction). In biological parlance, the tape can be regarded as the genome of the reproducing entity, while the constructor and ancillary machinery together constitute the phenotype. The reproductive cycle is driven by the constructor. The process is as follows:

The tape is copied.
A section of tape is decoded to yield a new constructor subsystem; a separate section of tape is decoded to yield new ancillary machinery. For simplicity, these are constrained to be initially quiescent.
The new tape, constructor and ancillary machinery are assembled together, and activated.

It is crucial to note that while the offspring tape is identical (in the informational sense) to the parental tape precisely because it is copied from it, the relationship between the parental and offspring phenotypes (constructor plus ancillary machinery) is not based on a copying process, and is in fact rather subtle. The offspring phenotype results from a decoding of the tape, mediated by the parental constructor. So the offspring phenotype will be similar or identical to the parental phenotype only if the parental tape ``happens'' to carry an accurate encoding of this parental phenotype.³ In practice, in order to design a reproducing machine with this architecture, von Neumann first designed the phenotype in detail, and then deliberately contrived a suitable tape by manually encoding that phenotype. With this is place, the whole system can then successfully reproduce.

In any case, having once devised such a reproducer, which ``breeds true'', it is clear that certain kinds of variants, or mutants, will also be capable of breeding true--i.e., that this architecture allows for a new form of unlimited, heritable, variation, at a level over and above that supported by the underlying template reproduction of the tapes. Indeed, achieving this was von Neumann's primary motivation (von Neumann, 1949, Fifth lecture, p. 86).

Specifically, such variants can arise through rather arbitrary perturbations of that part of the parental tape which encodes for the ancillary machinery. Provided that this happens before the reproductive cycle starts, the result will be an offspring with a variant genome with a matching variant phenotype, such that this combined variation will indeed recur, or breed true, in this new lineage.

The close parallels between this abstract model and our modern molecular level understanding of real biological reproduction, including the ``central dogma'' of one directional information flow from genome to phenotype, should be clear. This seems at least somewhat remarkable considering that von Neumann's model was first formulated in 1948, some five years before even the double helix structure of DNA was identified by Watson & Crick (1953).

Barry.McMullin@rince.ie