The standard genetic code can evolve from a two-letter GC code

The model of an iterated learning approach the origins of the genetic code inspired this related hypothesis about a simplified precursor to the standard four-letter genetic code, which will be released in Origins of Life and Evolution of Biospheres:

The standard genetic code can evolve from a two-letter GC code without information loss or costly reassignments

Alejandro Frank and Tom Froese

It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.

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Seminar on the origins of the genetic code

Next week Jorge and I will give a seminar to report on the work we did during our 2-month stay at the Earth-Life Science Institute:

An iterated learning model of the origin of the genetic code

Tom Froese (National Autonomous University of Mexico, UNAM)
Jorge Campos (National Autonomous University of Mexico, UNAM)

Date: July 25, 2017
Time: 14:00
Room: ELSI-2 Building – ELSI Lounge
Host: Nathaniel Virgo

Theories of the origin of the genetic code take translation for granted and assign an essential role to natural selection and/or mutation of hereditable traits to explain its non-randomness and error robustness. And yet the translation system depends on high fidelity replication. Woese proposed a solution to this fundamental bootstrapping problem by arguing that optimization of the code could have preceded and facilitated evolution of the translation system, and that its evolution was accelerated by communal innovation. He conjectured that early evolution was dominated by horizontal exchange of cellular components among loosely organized protocells rather than by vertical transmission of genetic material, and that lineages of individuals did not exist until after the emergence of the last universal common ancestor. Crucial outstanding problems are clarifying the agency of selection in communal evolution, and verifying whether it provides a rational basis for codon assignments. Here we demonstrate that horizontal transfer of code fragments can in principle give rise to key properties of the genetic code. In accordance with Woese’s claim that the dynamic of communal evolution is primarily determined by the organization of the recipient cell, and taking inspiration from comparisons between the advent of the genetic code and the emergence of human language, we created an iterated learning model of a group of protocells. Previous models of the origin of the genetic code have reproduced its regularity and optimality as well as its universality, but this is the first model to reproduce these features without vertical descent. This proof of concept suggests another modality of evolution: not only was Darwinian evolution (dominated by vertical transmission of genes) arguably preceded by Lamarckian evolution (vertical transmission with heredity of acquired traits), the latter was possibly preceded by Woesian evolution (dominated by horizontal acquisition).

Black box

European Conference on Artificial Life 2015

Next week the European Conference on Artificial Life 2015 will take place in York, England, July 20-24. I will be giving a poster presentation on the following topic:

Toward a behavior-based approach to the origins of life and the genetic system

Tom Froese

In the origin of life community there has been a dispute about whether metabolism or replication came first. Yet both of these approaches are in implicit agreement that the first forms of life were basically passive. That shared assumption has begun to be challenged by a new generation of metabolism-first approaches, emphasizing that movement and adaptive behavior could have played an important role right from the start. After introducing recent research on this behavior-based approach to the origin of life, I offer a preliminary assessment of what this new approach implies for the origins of the genetic system.

Click on the title to download the extended abstract.