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.

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Emergence in Chemical Systems

On June 23-26 the University of Alaska, Anchorage, will host the international conference Emergence in Chemical Systems 4.0. I was invited to give a talk. My title and abstract are as follows:

Motility at the origin of life and the evolution of the genome

Tom Froese

Traditionally, there has been a dispute about whether metabolism or replication came first during the origin of life. 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 (1-3). I introduce this theory of a behavior-based origin of life and consider how it can help to inform our thinking about the origins of the genetic system.

References
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Talks at AISB 2015

I am giving two invited talks at this year’s meeting of the Society for the Study of Artificial Intelligence and Simulation of Behavior (AISB 2015), which is being held in Canterbury, April 20-22. Titles and short abstracts are as follows:

The enactive theory of social cognition: From theory to experiment

Tom Froese

For over a decade I have been working on applying an evolutionary robotics approach to gain a better understanding of the dynamics of social interaction. At the same time I have been developing the enactive theory of social cognition by drawing on the phenomenological philosophy of intersubjectivity. Recently I was able to test the predictions deriving from this research on the basis of a psychological experiment using a new variation of the perceptual crossing paradigm. The empirical results support a genuinely enactive conception of social cognition as primarily grounded in embodied intersubjectivity.

The behavior-based origin of life and the problem of genetic representation

Tom Froese

Traditionally, there has been a dispute about whether metabolism or replication came first during the origin of life. While the metabolism-first approach focuses on chemical self-constitution of an individual, the replicator-first approach focuses on generational self-replication of a population of informational molecules. Yet both implicitly agree that the first forms of life were isolated, passive, and static individuals. Both ignore the intermediate timescales of activity between chemical self-constitution and population evolution: no mention is made of behavior and development. These assumptions are challenged by a new generation of metabolism-first approaches, which emphasize that movement and adaptive behavior could have played an important role right from the start. I consider how this behavior-based approach to the origin of life can inform our thinking about a number of traditional problems.
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