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.


Special issue on ALIFE and society published

The organizers of 2016 edition of the International Conference on the Synthesis and Simulation of Living Systems (ALIFE VX) have edited a special issue of the journal Artificial Life by inviting extended versions of selected conference papers.

Emphasis was placed on papers related to the conference theme of “Artificial Life and Society”.

Here is a preprint of the editorial introduction:

ALife and Society: Editorial Introduction to the Artificial Life Conference 2016 Special Issue

Jesús M. Siqueiros-García, Tom Froese, Carlos Gershenson, Wendy Aguilar, Hiroki Sayama and Eduardo Izquierdo

Artificial life (ALife) research is not only about the production of knowledge, but is also a source of compelling and meaningful stories and narratives, especially now when they are needed most. Such power, so to speak, emerges from its own foundations as a discipline. It was Chris Langton in 1987 who said that “By extending the horizons of empirical research in biology beyond the territory currently circumscribed by life-as-we-know-it, the study of Artificial Life gives us access to the domain of life-as-it-could-be […]” [1]. The very notion of life-as-it-could-be opened up many possibilities to explore, and released the study of life from its material and our cognitive constraints. The study of life did not have to be limited to carbon-based entities, DNA or proteins. It could also be about general and universal processes that could be implemented and realized in multiple forms. Moreover, while ALife was about biology at the beginning, its rationale and methods are now shared by many other domains, including chemistry, engineering, and the social sciences. In other words, the power to envision and synthesize “what is possible” beyond “what is” has transcended disciplinary boundaries. It also produces the material for the exploration of narratives about how things can be in principle and not only about their current state of being.