Focus III: The Emergence Chain from Proto-Matter to the First Cell

The Shared Scientific Mechanism Skeleton

Research on the origin of life understands the transition from nonliving chemistry to cellular life as a continuous process of organization and coupling:

1. non-equilibrium energy and material fluxes;
2. formation of organic molecules and reactive monomers;
3. polymers and catalytic or autocatalytic networks;
4. information replication and template inheritance;
5. compartmentalization, membranes, and protocells;
6. coupling of metabolism, replication, and compartments;
7. heritable variation and Darwinian selection;
8. stable cellular organization, genetic coding, and protein–nucleic-acid cooperation.

The RNA-world, metabolism-first, compartment-first, and co-evolution approaches are different routes along this research chain.

The Interface Between Rule 979 and the Scientific Emergence Chain

The Rule 979 simulator advances the PR–ER–LE architecture to the proto-matter level. Across all development, search, and validation runs, it executed approximately $4.435\times10^9$ LE updates. Among 32 perturbed initial ERs, persistent K5 was the leading candidate in 3/32, 21/32, 31/32, and 32/32 trajectories at $10^6$, $2\times10^6$, $5\times10^6$, and $10^7$ LE, respectively. Under the finite model's operational definition, this is positive evidence for persistent and reproducible proto-matter structure.

Rule 979 has not generated organic molecules, chemical reactions, or life. It supplies the lower interface preceding the scientific emergence chain. The next step is to obtain reproducible interactions, persistent compositional products, and selective transformations among proto-matter structures; only then can the model connect to the organic-molecule-and-above chain studied by prebiotic chemistry:

The two evidence levels must remain distinct. Rule 979 establishes the boxed proto-matter result. Modern origins-of-life research supplies experimentally tractable upper-level modules from organic building blocks through RNA template replication and lipid compartments to protocell selection. The model-to- chemistry correspondence between them remains a research bridge to be built.

The TGP Mapping in the Jia Baolong System

TGP gives a computational chain from topological generation to life-like organization:

This chain connects “persistent structure—binding—inheritance—selection” with the mainstream modules of origin-of-life research.

Proto-Matter in TGP

Proto-matter is a localized relational pattern in a changing background. It has:

• recognizable relational identity;
• the capacity to propagate and recur;
• reproducible interactions;
• metastability;
• effective types and quasi-conservation relations;
• structures that can be described by higher-level coarse-graining.

The paper represents particle types within the model by directed triangles and their mutual edge weights:

and obtains the mass spectrum:

From Proto-Matter to Proto-Chemistry

Repeatable collisions, binding, fusion, annihilation, and asymmetric disappearance form an algebra of interaction. Edge-sharing triangles form dimers with lifetimes:

The proto-chemical layer includes persistent identities, selective binding, composable structures, catalyst-like pathways, and a balance between stability and variation.

From Proto-Chemistry to Heredity

New triangles form in the neighborhood of existing triangles and inherit correlations in their weights, yielding template inheritance:

The hereditary stage in mainstream origin-of-life research likewise includes replicable information carriers, copying errors, heritable variation, and coupling among carriers, catalysis, and resource use.

From Heredity to Selection

At low LE decoherence parameters, different weight types show net fitness differences:

Darwinian selection consists of three conditions:

1. variation exists among individuals or compartments;
2. part of that variation is heritable;
3. different variations produce differential reproduction or differential persistence.

From Selection to the First Cell

The first cell is an evolvable unit in which replication, metabolism, and compartmentalization are coupled:

Further single-cellular organization includes:

• a semipermeable boundary and boundary regeneration;
• exchange of energy and matter;
• internal reaction networks;
• replication of genetic information;
• compartment growth and division;
• genotype–phenotype coupling;
• stable lineages and sustained Darwinian evolution.

Mainstream Mechanisms and the Original Mapping

The mainstream framework for the transition from nonliving systems to cellular life is the stepwise integration of non-equilibrium dynamics, persistent structure, catalysis / metabolism, information replication, compartmentalization, and Darwinian selection.

The original mapping of the Jia Baolong system connects the generative mechanism at the base to these functional modules through medium-free topological dynamics:

External Scholarly Anchors

• Patel and colleagues: a common prebiotically plausible reaction network can yield precursors of ribonucleotides, amino acids, and lipids. DOI
• Mansy and colleagues: template-directed synthesis of a genetic polymer within a fatty-acid model membrane. DOI
• Adamala and Szostak: an encapsulated catalyst can create differential fitness among model protocells. DOI
• Adamala, Engelhart, and Szostak: functional collaboration between primitive membranes and soluble catalysts. DOI
• Joyce and Szostak: protocells, RNA replication, and the joint replication of genetic material within compartments. DOI
• Otto and colleagues: replication, metabolism, compartmentalization, non-equilibrium maintenance, and open-ended Darwinian evolution.
• Koonin: co-evolution of cellular organization, membranes, energy conversion, and genetic systems.
• Pressman, Blanco, and Chen: the RNA world, ribozymes, and protocell compartments.
• Robertson and Joyce: heredity and catalysis in the RNA world.