This project explores the growth of stromatolites through a computational model that combines biological growth, sediment deposition and environmental processes.
The work began following a visit to the Oxford University Museum of Natural History and a renewed interest in some of Earth’s earliest evidence of life. Rather than viewing stromatolites simply as layered rock structures, the project asks a computational question:
Can recognisably stromatolite-like structures emerge from the interaction of a small number of simple biological and environmental processes?
The model treats stromatolite formation as a dynamic system in which microbial mat growth competes with sediment accumulation while responding to changing environmental conditions such as light availability, water depth, sediment supply and seasonal variation.
The project deliberately separates the biological model from its spatial representation. The same governing equations are first explored in a one-dimensional reference implementation before being extended to two-dimensional cross-sections, complete three-dimensional surfaces, circular stromatolite colonies and ultimately recognisable domed stromatolite morphologies.
This incremental approach allows increasing geometric realism to be introduced without changing the underlying biology.
The emphasis is not on reproducing any particular fossil exactly. Instead, the project investigates how increasingly realistic stromatolite morphology emerges as the same biological processes are represented within progressively richer spatial geometries. Each implementation therefore adds geometric realism while deliberately preserving the underlying biological model.
The project now demonstrates that a single, interpretable biological model can be carried unchanged from a one-dimensional growth column to a fully three-dimensional domed stromatolite through successive refinements of spatial geometry alone.
In this sense, the work represents an experiment in computational natural history. It sits somewhere between mathematical modelling, Earth system simulation and developmental biology, using code to explore how simple interactions between organisms and their environment can generate the layered structures preserved in the geological record.
Further documentation, including the mathematical model, implementation details, environmental processes, development notes and modelling observations, is available in the project Wiki.
The project currently includes:
- Biological growth modelling
- Sediment deposition and burial
- Layer-by-layer stromatolite development
- Environmental forcing
- Seasonal light variation
- Annual temperature cycles
- Variable sediment supply
- Stochastic burial events
- Water-depth-dependent light attenuation
- One-dimensional reference implementation
- Two-dimensional cross-sectional model
- Three-dimensional rectangular model
- Three-dimensional circular masked model
- Three-dimensional circular domed model
- Parameter-driven experimentation
This project is inspired by studies of stromatolites, microbial mats and early life on Earth, together with the broader traditions of computational modelling and theoretical morphology.
All code and implementations in this repository are original to this project.
To file issues or suggestions, please use the Issues page for this project on GitHub.
This project is licensed under the MIT License - see the LICENSE file for details