Our “media friendly” summary is:
The ‘meaning’ of DNA lies in the act of translating a DNA sequence into a protein sequence. The mapping of DNA to proteins is identical in nearly all species, but some species have evolved alternative mappings. A new computer model uses an artificial chemistry to investigate evolutionary changes in these mappings, where the translating apparatus is encoded in the DNA and governs its own translation. As well as reproducing the known evolutionary mechanism of changing the meaning of DNA, the model predicts a novel mechanism for changing the mapping in biology that is not detectable by phylogenetic DNA sequence analysis.Our slightly less friendly paper abstract is:
Abstract: We present a novel stringmol-based artificial chemistry system modelled on the universal constructor architecture (UCA) first explored by von Neumann. In a UCA, machines interact with an abstract description of themselves to replicate by copying the abstract description and constructing the machines that the abstract description encodes. DNA-based replication follows this architecture, with DNA being the abstract description, the polymerase being the copier, and the ribosome being the principal machine in expressing what is encoded on the DNA. This architecture is semantically closed as the machine that defines what the abstract description means is itself encoded on that abstract description.We present a series of experiments with the stringmol UCA that show the evolution of the meaning of genomic material, allowing the concept of semantic closure and transitions between semantically closed states to be elucidated in the light of concrete examples. We present results where, for the first time in an in silico system, simultaneous evolution of the genomic material, copier and constructor of a UCA, giving rise to viable offspring.This is one of the key findings:
|Figure 6. Semantic change without mutation of the genome.|
The paper is open access and can be found at doi:10.1098/rsif.2016.1033.