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

Living systems: chaotic, stochastic, and/or indeterministic?

I was invited to lead the discussion in a session of the Seminar of Science and Society at the Centre for the Sciences of Complexity. I will focus on the relationship between autonomy and uncertainty. Details can be found in the flyer below:

C3 seminar

Cognitive science course next semester

Here is the information about the course I will teach at UNAM next semester.

The course will introduce ongoing debates in cognitive science about our changing understanding of the mind. Instead of being thought of as a digital computer inside the brain, mind is now widely considered to be an embodied, embedded and extended activity in the world. These ideas will be illustrated based on case studies of research in agent-based models, complex systems and human-computer interfaces, with special emphasis on demonstrating how social interactions and technologies shape our mind.

Students are not expected to program models nor to design interfaces, but to understand the implications of the new cognitive science and to apply them to their own research interests.

The course will be taught mainly in English to better prepare students for the special terms used by leading researchers in cognitive science.

For an introduction to this field, see this video:

Here is the official course information:

Posgrado en Ciencia e Ingeniería de la Computación (PCIC)

Plan: Maestría en Ciencia e Ingeniería de la Computación (Clave 80-4014)
Actividad académica: Temas Selectos de Inteligencia Artificial
Tema: Agentes autónomos y multiagentes (o: “Agentes Autónomos, Sistemas Sociales, y la Nueva Ciencia Cognitiva”)
Horarios: Lunes y Miércoles, 11:30 – 13:00
Profesor: Dr. Tom Froese

The course program can be downloaded here.

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.


For more information see the conference website:

Seminar: Mathematical approaches to exploring the social mind

Tomorrow I will give a presentation for the Mathematical Sociology group of UNAM. The title and abstract are as follows:

Mathematical approaches to exploring the social mind

Tom Froese

The sciences of man are sharply divided over the role played by sociality. On the one hand, cognitive science tries to reduce all explanations of behavior, including human social behavior, to a single person (and often even to nothing but a single organ: their brain). On the other hand, anthropology and sociology have long insisted that most (if not all) human behavior is an irreducible product of our shared socio-cultural environment. My research aims to build a bridge between these two viewpoints. In particular, I use mathematical models as formal proofs of concept for the possibility that the individual and the social co-determine each other. In order to illustrate this possibility I will present two case studies that are represent two different scales of sociality. First, I will briefly discuss a computer model of embodied agents in which a dyadic interaction process reconfigures the internal activity of each agent such that it exhibits mathematical properties that are in principle impossible for the agents in isolation. Second, I will present some results of a mathematical model that is loosely based on the social organization of the ancient Mexican city of Teotihuacan. The model demonstrates that local social interactions between agents who selfishly optimize their own utility can consistently give rise to globally optimal social configurations even without any a priori knowledge of the problem space.