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

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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

Research page updated

I finally found some time to update the research page of my website. Here is the opening paragraph:

I am a cognitive scientist interested in understanding the complexities of the human mind on the basis of embodied, embedded, extended, and enactive approaches to cognition (so called “4E cognition”). For me this means systematically investigating how our minds are shaped by being alive, by being sensorimotor animals, and by us leading socially, technologically, and culturally constituted ways of life (Froese and Di Paolo 2011; Torrance and Froese 2011). One of the most promising approaches to better appreciate the role these different facets can play is to try to understand their origins and the qualitative changes their appearance implies.

The rest can be found here on the research page.

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.

Talk on History and Philosophy of Origins Research

I have been invited to give a talk at the EON Workshop on History and Philosophy of Origins Research, which will be held August 24-26 at the Earth-Life Science Institute in Tokyo.

The title and abstract of my contribution are as follows:

The concept of the individual in cognitive science and origins of life

Tom Froese

The field of cognitive science was inaugurated on the basis of the computational theory of mind. The metaphor of the digital computer had several implications: it restricted the field to understanding all of cognition in terms of the manipulation of symbols; it focused research on passive information processing; and it limited the scope of inquiry to processes taking place within the physical boundaries of the system. This concept of an individual, as a system engaged in passive internal symbol manipulation, seems to be implicitly shared by theories of the origins of life that are focused on encapsulated processing of informational molecules. Yet in cognitive science this concept of the individual has been undergoing a series of deep revisions, such that it is now replaced by its exact opposite: an individual is seen as primarily a system that is embodied, extended, and as actively engaged in direct relations with the physical and social environment. I analyze what origins of life research could learn from this shift in the history of cognitive science.

Workshops at Artificial Life 2016

In addition to helping to organize this year’s International Conference on the Synthesis and Simulation of Living Systems (ALIFE 2016), I am contributing to the organization of two associated workshops. Here are the calls for abstracts.

The Biological Foundations of Enactivism

The workshop will bring together researchers in enactive cognition, computational modeling, biology, and philosophy, to discuss the biological foundations of enactivism. Of particular interest are issues related to the maintenance of autonomous systems, and the origins of autonomous systems.

Submissions to the workshop are extended abstracts (1 or 2 pages). Contributions may be original or previously published. Accepted abstracts will be put online. Authors of accepted submissions will present their project to the workshop in a 5-10 minute talk.

Submission deadline is May 13, 2016.

Multidisciplinary Applications of Evolutionary Game Theory

Evolutionary game theory is profoundly interdisciplinary and the flow of knowledge between different fields is of crucial importance for its future development and application. The goal of the workshop is to show the state-of-the-art of the field and connect researchers with different backgrounds, from physicists and computer scientists to economists and sociologists and invite them to share ideas and learn from each other.

We invite the submission of 1- to 4-page abstracts (Alife conference format). Contributions will be evaluated on their merit for presentation. After the workshop, the most relevant contributions will be invited to provide an extended manuscript for a special issue on evolutionary game theory in the Artificial Life journal (MIT Press).

The deadline for the submission of abstracts is April 17th, 2016.

Artificial Life XV in 2016, Cancun, Mexico

Next year’s International Conference on the Synthesis and Simulation of Living Systems (Artificial Life XV) will take place in beautiful Cancun, Mexico, July 4-8, 2016. I am part of the local organizing team, helping to make the first Alife conference in Latin America a memorable event.

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For more information see the conference website: http://xva.life

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.

Motility at the Origin of Life: Its Characterization and a Model

The conference paper I presented with Nathaniel Virgo and Takashi Ikegami at the 2011 European Conference on Artificial Life was selected for a special issue of the journal Artificial Life dedicated to showcasing the best work of that conference. Our expanded paper has finally become available.

Motility at the Origin of Life: Its Characterization and a Model

Tom Froese, Nathaniel Virgo and Takashi Ikegami

Due to recent advances in synthetic biology and artificial life, the origin of life is currently a hot topic of research. We review the literature and argue that the two traditionally competing replicator-first and metabolism-first approaches are merging into one integrated theory of individuation and evolution. We contribute to the maturation of this more inclusive approach by highlighting some problematic assumptions that still lead to an impoverished conception of the phenomenon of life. In particular, we argue that the new consensus has so far failed to consider the relevance of intermediate time scales. We propose that an adequate theory of life must account for the fact that all living beings are situated in at least four distinct time scales, which are typically associated with metabolism, motility, development, and evolution. In this view, self-movement, adaptive behavior, and morphological changes could have already been present at the origin of life. In order to illustrate this possibility, we analyze a minimal model of lifelike phenomena, namely, of precarious, individuated, dissipative structures that can be found in simple reaction-diffusion systems. Based on our analysis, we suggest that processes on intermediate time scales could have already been operative in prebiotic systems. They may have facilitated and constrained changes occurring in the faster- and slower-paced time scales of chemical self-individuation and evolution by natural selection, respectively.