Spontaneous emergence of a kind of digital life in a simulation

Saw this very interesting episode of Sean Carroll’s Mindscape podcast, where he interviews Blaise Agüera on the emergence of replication and computation:

The paper is here: https://arxiv.org/pdf/2406.19108

Much research on OoL and ALife focuses on the life period when self-replicators are already abundant. A central question during this period is: How do variation and complexity arise from simple self-replicators? Analyses often take the form of mathematical models and simulations [21]. In ALife, researchers often focus on selection for complex behaviors [22], which may include interactions with other agents [23]. Simulations may include tens of thousands of parameters and complex virtual ecosystems [24], but they can rarely modify the means of self-replication beyond adapting the mutation rate. The two most notable exceptions use assembly-like languages as computational substrate. In Tierra [18], simple assembly programs have no goals but are given time to execute their program and access and modify nearby memory. This causes them to self-replicate and manifest limited but interesting dynamics, including the rise of “parasites” that feed off other self-replicators. Avida [19] functions similarly: assembly-like programs are left running their code for a limited time. They can also self-replicate, this time by allocating new memory, writing their program in the new space, and then splitting. Avida adds a concept of fitness, since performing auxiliary computation increases a replicator’s allotted execution time. Notably, both Tierra and Avida are seeded with a hand-crafted self-replicator, called the “ancestor”. This puts them squarely into “life” dynamics, but still allows for modification of the self-replication mechanism.

But how does life begin? How do we get from a pre-life period devoid of self-replicators to one abundant with them?
(…)
In this paper we focus on computational substrates formed atop various programming languages. Here we highlight some of the most relevant previous investigations of the pre-life period on such substrates [29, 30, 31]. In all of these investigations, and in ours as well, there is no explicit fitness function that drives complexification or self-replicators to arise. Nevertheless, complex dynamics happen due to the implicit competition for scarce
resources (space, execution time, and sometimes energy).

Blaise explains in the podcast with Sean that intriguingly they find that replicators, despite being incredibly rare among possible programs (the vast majority of which do nothing at all), appear to be attractors in the space of all possible programs.

Despite there being no explicitly defined fitness function that favors any particular result, Darwinian evolution nevertheless unavoidably results from competition among replicators, and that replicators, at least initially, quickly grow more complex over time despite this also not being explicitly defined to be favorable (which shows how it being favored is a truly emergent byproduct of the competition among replicators).

There is also a video here depicting the graphical interface that shows when the replicators emerge:

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The podcast episode was intriguing and energizing; I’m looking forward to digging into the paper.

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I read the paper. I think the results are exciting. I was hoping for more details on one element from the podcast discussion: namely, that the path to self-reproduction had multiple stages, including something akin to autocatalytic sets. Maybe it was addressed more subtly and I missed it. Maybe there will be a follow-up paper or maybe that will be covered in the book which I believe was promised in the episode. I’m intrigued by how a self-reproducing entity might be built up from components with other functions.

Yeah I also got the impression that a lot of the things they spoke about in the podcast weren’t explicitly dealt with in the paper, so I gather it’s things they’ve observed in unpublished/ongoing work.

I’m very interested in seeing what they can do with this going forward. I definitely think they need to combine this sort of simulation with more physically relevant concepts such as material flows (fluid dynamics), energy consumption, degradation and so on.
To be really informative with respect to the origin of life the system needs to be able to test and reproduce effects often thought to be relevant to the origin of life, such as concentration-dependent reactions, the emergence of compartmentalization(however that could be implemented), and material transport.

I should preface this by saying that I have read the paper, Agüera y Arcas et al. [1], but have not yet listened to the podcast, so many of the observations and questions I have may be addressed in the podcast. I should also say that, though this work caught my eye, as far as I can tell, it has not been peer-reviewed yet.

This work is very interesting as a proof of concept, and helps answer key questions regarding some unpublished computational work a student of mine and I have been working on (and is related to work @sygarte has published [2,3]; it’s unlikely these replicating systems can be selected for on more than in individual level, given likely error thresholds for these systems). It was disappointing that the authors did not link their work to Eigen’s, and that is very fertile soil for those who can understand their paper, and Eigen’s monumental work (e.g. Eigen [4]).

I think this could provide a key to linking between function to self-replication and then from self-replication at low fidelity to self-replication at high fidelity.

The two big outstanding issues, or questions, in my mind are:

  1. How does this translate to a chemical system? Could it work for the Virtual Circular Genome, for instance [5]?
  2. How does this address the problem of the emergence of information? Manfred Eigen in his book “From Strange Simplicity to Complex Familiarity” [6] has done a good enough job explaining this problem that now even I can understand it, and I think there is a big open explanatory question of how to properly measure/quantify biologically relevant information and, on that measure (or measures), how does the information content of this system change over time? I would not be surprised if Delta Information = 0… This is presently (as far as I know) an unanswerable question, but a question where answers could be tested with a model like this one. Very exciting!

Maybe a promising, if small, step forward in explaining life’s origins. If it can be connected in a meaningful way to a real chemical system, that can be translated from geochemistry or near-geochemistry [7], to something a little closer to life [5].

(Agüera y Arcas et al. fail to cite some key literature to meaningfully ground their work, but they do cite Nowak and Ohtsuki [8], a brilliant paper that explains the problems that might turn out to be addressed by Agüera y Arcas et al. in a much more complete context.)

REFERENCES

[1] Agüera y Arcas, B., Alakuijala, J., Evans, J., Laurie, B., Mordvintsev, A., Niklasson, E., Randazzo, E. and Versari, L., 2024. Computational Life: How Well-formed, Self-replicating Programs Emerge from Simple Interaction. arXiv e-prints , arXiv-2406.

[2] Garte, S., 2021. Evidence for phase transitions in replication fidelity and survival probability at the origin of life. BioCosmos, 1(1), pp.2-10.

[3] Garte, S., 2024. Accurate phenotypic self-replication as a necessary cause for biological evolution. BioSystems , 237 , p.105154.

[4] Eigen, M., 1971. Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften, 58, pp.465-523.

[5] Zhou, L., Ding, D. and Szostak, J.W., 2021. The virtual circular genome model for primordial RNA replication. Rna , 27 (1), pp.1-11.

[6] Eigen, M., 2013. From strange simplicity to complex familiarity: a treatise on matter, information, life and thought. OUP Oxford.

[7] Baltussen, M.G., de Jong, T.J., Duez, Q., Robinson, W.E. and Huck, W.T., 2024. Chemical reservoir computation in a self-organizing reaction network. Nature, pp.1-7.

[8] Nowak, M.A. and Ohtsuki, H., 2008. Prevolutionary dynamics and the origin of evolution. Proceedings of the National Academy of Sciences , 105 (39), pp.14924-14927.

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Agreed, but I think that’s explained in the podcast. Agüera and his colleagues are computer programmers and admit to being total newbies in the origin of life field, coming at it from entirely different fields such as computer science, engineering, and physics, and having only been involved with it for about a year.

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MOD NOTE: I asked Andy to create this new topic, but didn’t see the other one he made. Folding this is here, but it may be redundant now.

I finally had the chance to read the preprint mentioned in this thread:

And wouldn’t you know it, they introduce a metric they call “high-order entropy” which is the difference of Shannon entropy and Kolmogorov complexity (as estimated via compression and normalized by string length). They demonstrate that this measure is useful for detecting phase transitions between populations with numerous unique and mostly random programs and populations that are dominated by many copies/variants of a self-replicating program.

(And while we’re at it, we can tie in another recent thread and note that this is a scenario Assembly Theory is intended to address/detect: when the copy number of an entity far exceeds what is expected from combinatorics and input abundance alone, suggesting reproduction and/or selection is involved.)

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