An artificial life approach to the origins of the genetic code

I have been invited to give a talk at the “Special workshop: The Earth, Life and Artificial Life”, sponsored by ELSI, which will take place next Friday, July 27, as part of the International Conference on Artificial Life in Tokyo.

The title and abstract are as follows:

An artificial life approach to the origins of the genetic code

Tom Froese

A growing number of artificial life researchers propose that making progress on the problem of the origins of life requires taking seriously life’s embodiment: even very simple life-like systems that are spatially individuated can interact with their environment in an adaptive manner. This behavior-based approach has also opened up new perspectives on a related unsolved problem, namely the origin of the genetic code, which can now be seen as emerging out of iterated interactions in a community of individuals. Thus, artificial life demonstrates that the dominant scientific strategy of searching for the conditions of Darwinian evolution should be broadened to consider other possibilities of optimization.

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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.

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.

The 2nd Week on Complexity Sciences at C3-UNAM

The 2nd Week on Complexity Sciences will be held at the Center for Complexity Sciences (C3) at UNAM’s main campus from Jan. 31 to Feb 2. There will be many international invited speakers.

I will give a talk on the recent work I did with Prof. Alejandro Frank on the origins of the genetic code on Jan. 31 at 13:00. The title of our contribution is “A new approach to the origin of the genetic code”.

Collective origins of the genetic code

Later today I am giving the weekly colloquium at the Center for Complexity Sciences (C3) at our main campus of UNAM. The topic will be our ongoing work on a simulation model of the collective origins of the genetic code. Details of the colloquium below:

Cartel_Coloquio C3_07-1

EON Long-Term-Visitor Award

logoI have received an EON Long-Term-Visitor Award from the director of the Earth-Life Science Institute (ELSI) of the Tokyo Institute of Technology to work for two months (June and July 2017) with Dr. Virgo and his colleagues of the ELSI Origins Network (EON).

The aim is to create an agent-based model of the origins of the genetic code based on the mechanism of horizontal gene transmission. The model is inspired by the iterated learning model of the evolution of language.

New research project grant received

I am happy to report that my application for the 2017 call for research projects issued by UNAM’s “Programa de Apoyo a Proyectos de Investigación e Innovación Tecnológica” (PAPIIT) was successful.

The project is entitled “Explorando los alcances de la auto-organización social: desde la cultura hasta la célula” (IA104717). Its overarching aim is to support the activities of the 4E Cognition Group.