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 Spanish translation: Donde hay vida, hay mente

I was invited to contribute a chapter to the book Biocomplejidad edited by Moisés Villegas, Lorena Caballero and Eduardo Vizcaya. The book will come out online in open access format later this year.

The contribution is a Spanish translation of an article written by Kirchhoff and Froese (2017). Here it is:

Donde hay vida, hay mente: en apoyo a una tesis fuerte de la continuidad vida-mente

Michael D. Kirchhoff and Tom Froese

El presente texto considera cuestiones en torno a la continuidad y la discontinuidad entre la vida y la mente. Inicia examinando dichas cuestiones desde la perspectiva del principio de energía libre (PEL). El PEL se ha vuelto considerablemente influyente tanto en la neurociencia como en la ciencia cognitiva. Postula que los organismos actúan para conservarse a sí mismos en sus estados biológicos y cognitivos esperados, y que lo logran al minimizar su energía libre, dado que el promedio de energía libre a largo plazo es entropía. El texto, por lo tanto, argumenta que no existe una sola interpretación del PEL para pensar la relación entre la vida y la mente. Algunas formulaciones del PEL dan cuenta de lo que llamamos una perspectiva de independencia entre la vida y la mente. Una perspectiva de independencia es la perspectiva cognitivista del PEL, misma que depende del procesamiento de información con contenido semántico, y por ende, restringe el rango de sistemas capaces de exhibir mentalidad. Otras perspectivas de independencia ejemplifican lo que llamamos la demasiado generosa perspectiva no-cognitivista del PEL, que parecen ir en dirección opuesta: sugieren que la mentalidad se encuentra casi en cualquier lugar. El texto continúa argumentando que el PEL no-cognitivista y sus implicaciones para pensar la relación entre la vida y la mente puede ser útilmente delimitado por las recientes aproximaciones enactivas a la ciencia cognitiva. Concluimos que la versión más contundente de la relación vida-mente las considera fuertemente continuas, y esta continuidad se basa en conceptos particulares de vida (autopoiesis y adaptabilidad) y mente (básica y no-semántica).

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

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.

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