New paper on iterated learning at the origins of life

Jorge, Nathaniel and I have published an extension of our iterated learning approach to the origins of the genetic code in the Proceedings of the Artificial Life Conference 2018. We unexpectedly found that the most likely sequences in which amino acids get incorporated into the emerging genetic codes in our simulation model exhibit a remarkable overlap with the sequence predicted in the literature based on empirical considerations.

We will present this work at the ALIFE conference in Tokyo as part of the special session on “Hybrid Life: Approaches to integrate biological, artificial and cognitive systems”.

An iterated learning approach to the origins of the standard genetic code can help to explain its sequence of amino acid assignments

Tom Froese, Jorge I. Campos, and Nathaniel Virgo

Artificial life has been developing a behavior-based perspective on the origins of life, which emphasizes the adaptive potential of agent-environment interaction even at that initial stage. So far this perspective has been closely aligned to metabolism-first theories, while most researchers who study life’s origins tend to assign an essential role to RNA. An outstanding challenge is to show that a behavior-based perspective can also address open questions related to the genetic system. Accordingly, we have recently applied this perspective to one of science’s most fascinating mysteries: the origins of the standard genetic code. We modeled horizontal transfer of cellular components in a population of protocells using an iterated learning approach and found that it can account for the emergence of several key properties of the standard code. Here we further investigated the diachronic emergence of artificial codes and discovered that the model’s most frequent sequence of amino acid assignments overlaps significantly with the predictions in the literature. Our explorations of the factors that favor early incorporation into an emerging artificial code revealed two aspects: an amino acid’s relative probability of horizontal transfer, and its relative ease of discriminability in chemical space.

Figure 2

Illustration of the architecture of the genetic system of one of our hypothetical protocells.


Explaining the origins of the genetic code without vertical descent

Here is the result of my two-month stay at the Earth-Life Science Institute (ELSI) of the Tokyo Institute of Technology, which was made possible by ELSI’s Origins Network. I quite like the implication that life could have been an inherently social phenomenon from its very origins!

Horizontal transfer of code fragments between protocells can explain the origins of the genetic code without vertical descent

Tom Froese, Jorge I. Campos, Kosuke Fujishima, Daisuke Kiga, and Nathaniel Virgo

Theories of the origin of the genetic code typically appeal to natural selection and/or mutation of hereditable traits to explain its regularities and error robustness, yet the present translation system presupposes high-fidelity replication. Woese’s solution to this bootstrapping problem was to assume that code optimization had played a key role in reducing the effect of errors caused by the early translation system. He further conjectured that initially evolution was dominated by horizontal exchange of cellular components among loosely organized protocells (“progenotes”), rather than by vertical transmission of genes. Here we simulated such communal evolution based on horizontal transfer of code fragments, possibly involving pairs of tRNAs and their cognate aminoacyl tRNA synthetases or a precursor tRNA ribozyme capable of catalysing its own aminoacylation, by using an iterated learning model. This is the first model to confirm Woese’s conjecture that regularity, optimality, and (near) universality could have emerged via horizontal interactions alone.