Nils Barricelli’s 5 Kilobyte Symbiogenesis simulations and ‘molecule shaped numbers’ – A precursor to DNA Computing
Wednesday, 6 June 2012
Processing simulation of Nils Barracelli’s Numerical Symbiorganism systems – Alex Galoway
‘We have created a class of numbers which are able to reproduce and undergo hereditary changes’ – Nils Barricelli. [circa 1952]
Described as balancing a thin line between truly original and a crank (an ultimate accolade) Nils Barricelli can claim rights to being a pioneer of computational biology and evolutionary algorithms – if not its originator. In the early 50’s he utilised the Institute of Advanced Study’s computer (one of the very first electronic computers) developed by John Von Neumann and his team for Hydrogen bomb simulations in Princeton, New Jersey. On night shifts Barricelli ran programs that mapped the foundations self-reproducing entities simulated entirely by numbers.
Barricelli’s computations were carried out to substantiate his alternative theories of evolution – one that argued for gene swapping in organisms or Symbiogenesis (the idea that complex organisms evolved from the symbiosis of simpler ones). A cycle of 512 generations of self-reproducing algorithmic organisms evolved in a numerical universe of 5 kilobytes. Representing genes as on/off states in pixels – his organisms appeared as self-organized textural patterns contained within autonomous shapes. He noted biophenomenon such as parasitic infiltration, natural disasters and stagnations. Barricelli’s algorithms were clearly the distant ancestors of Cellular Automata and well-known artificial-life simulations such as Conway’s Game of Life. In his most recent book ‘Turing’s Cathedral’ George Dyson hints that some of Barracelli’s work may well have been sublimated into Von Neumann’s posthumously published Theories of self-replicating Automata [PDF].
Output Card from Nils Barracelli’s Numerical Symbiorganism programs
As noted by Dyson there is some irony in the fact that the first computer in the human universe was by night seeding the first species of the digital Universe while at day it was solving problems of the most efficient way to destroy human life.
Alex Galloway has written an excellent essay for Cabinet magazine exploring the work of Barricelli which includes an in-depth appraisal of Barricelli’s strategies used in his bionumeric evolutionary systems. Even better, Alex has re-staged those original early 50’s experiments in Processing adding colour to the cellular values to increase clarity and enhance the visibility of individual organisms within this computational Universe.
Alex’s essay mentions a later paper by Barricelli, ‘ Numerical Testing of Evolution Theories’, in which a ‘chemo-analogical computer’ is proposed using DNA molecules, or ‘molecule shaped numbers’. Base-pair interactions of DNA nucleotides would be used to interpret commands, compute and run algorithms in their native wetware environments and then output to a more standard hardware environment.
The IAS Machine, circa 1952, Princeton, New Jersey
Now that lateral gene transfer has become more accepted, the theory of symbiogenetic organisms seem much less far-fetched – Barricelli was anything but a crank. His final (and intriguingly titled) paper ‘Suggestions for the Sharing of Numerical Evolutionary Processes intended to Evolve Symbiorganisms Capable of Developing a Language & Technology of their own’ was published in 1987.