About[draft]
This website is my (ongoing) attempt to think through some puzzles about the evolution of multicellular complexity.
I’m not the only one puzzled. Despite enormous progress in biology, there are persistent debates about how best to think about the interplay of the various causes and processes in evolution.1 This is especially true when the organisms being studied are like us: beginning life as a single cell, yet developing into a complex form with limbs, organs, and attitude. Single-celled critters may still be the most common on our planet, but something special happens when nature starts putting a bunch of cells together.2
The particular puzzles I find most interesting, and the way I think about them, is driven by my background. I’m a software engineer and a philosopher of science.
As an engineer, what I find puzzling is how nature builds multicellular creatures. Embryogenesis is an alien technology3, a process utterly unlike the top-down way human engineers work, and yet still capable of reliably generating immensely complex structures. Not only that, but the process itself is malleable in a way that our own technology is not. So it’s not just how organisms are built, but how they can be modified, that makes their construction so fascinating.
As a philosopher, what interests me is the array of different explanations at play (in particular, the heated debates about what, or how much, genes explain). But also the concepts used in these explanations: a mix of often fuzzily-defined concepts such as evolvability, modularity, and robustness. FIXME: Adjudicating amongst explanations, and how do we nail down these concepts?
So how should we address these puzzles? A common approach is to study the real thing, and try to infer the causes and processes from empirical evidence.
The approach on this website is to use model-building as a thinking tool. First, to try and reproduce the puzzles by building simple worlds that exhibit at least some recognisable and relevant phenomena, but with far fewer moving parts than the real thing, along with the tools to display and examine them.
Then we can ask:
- Can we at least see how explanation works, or how concepts apply in, these simpler worlds?
- Does this provide any insight into the more complex biological ones?
Sometimes, I find just trying to build these worlds exposes some malformed or incomplete assumptions. Also, it is fun.
Acknowledgements
Many of these ideas, and the initial models, were developed during postdoctoral positions at the KLI in Vienna, with Paul Griffiths at the University of Sydney, in Joshua Epstein’s group at Johns Hopkins Centre for Emergency Medicine, and at the Centre for Biology and Society, ASU with Manfred Laubichler. I’m grateful to these people and institutions, and to many others who supported me during my embryonic stages in philosophy. I’m especially indebted to Kim Sterelny, who kick-started my interest in these ideas, and supported my early academic career.
Source Code
The code for these simulations is written with a combination of Rust, Python, and Javascript. Much of it relies on the fantastic existing contributions of many open source software developers. I do intend to open-source this code in the future. For now, however, please contact me if you are interested in using it.
Citing the Website
If you use or refer to material on this website, please cite it as:
Calcott, B. (2026). Minimal Epigenesis (Website version 2026.07.29). https://doi.org/10.5281/zenodo.21688378