lithoSpore — LTEE Targeted GuideStone

What This Is

🪨🌱 lithoSpore is the second 🪨✅ guideStone deployment artifact — and the first Targeted GuideStone. While hotSpring’s guideStone proves computational physics on consumer GPUs, lithoSpore proves evolutionary biology: 7 science modules reproducing LTEE papers from Barrick, Lenski, and collaborators across 75,000+ generations of continuous evolution.

The target audience is Barrick Lab, UT Austin — the continuation of Richard Lenski’s Long-Term Evolution Experiment. The artifact is designed to be handed to a researcher as a USB drive, plugged into any Linux machine, and validated with zero dependencies.

Anatomy of the Artifact

/media/lithoSpore/
├── .biomeos-spore                    # biomeOS detection marker
├── validate                          # symlink → bin/litho (argv[0] dispatch)
├── verify                            # symlink → bin/litho
├── refresh                           # symlink → bin/litho
├── spore                             # symlink → bin/litho (biomeOS entry)
├── liveSpore.json                    # Append-only provenance journal
├── GETTING_STARTED.md                # Human-readable guide
│
├── bin/
│   └── litho                         # Single musl-static binary (5.1 MB)
│
├── biomeOS/
│   ├── tower.toml                    # Tower config for spore composition
│   └── graphs/lithoSpore_validation.toml
│
├── artifact/
│   ├── data/                         # 7 LTEE data bundles (BLAKE3-anchored)
│   │   ├── wiser_2013/              # Module 1: power-law fitness
│   │   ├── barrick_2009/            # Module 2: mutation accumulation
│   │   ├── good_2017/               # Module 3: allele trajectories
│   │   ├── blount_2012/             # Module 4: citrate innovation
│   │   ├── biobricks_2024/          # Module 5: BioBrick burden
│   │   ├── tenaillon_2016/          # Module 6: 264 genomes
│   │   └── anderson_predictions/    # Module 7: disorder predictions
│   ├── data.toml                    # Data manifest (URIs + BLAKE3)
│   ├── scope.toml                   # Scope graph (birth certificate)
│   └── tolerances.toml              # Named tolerances with justification
│
├── validation/expected/              # Reference outputs (7 JSON files)
├── notebooks/                        # Python Tier 1 baselines
├── papers/                           # Registry (16 DOIs) + reading guide
└── figures/                          # Publication-quality SVG figures

The key difference from hotSpring’s artifact: a single binary replaces 7 separate module binaries. The litho binary detects its invocation name via argv[0] and dispatches accordingly — ./validate runs all 7 modules, ./verify checks BLAKE3 integrity, ./refresh fetches updated data.

The Seven Science Modules

75/75 checks passing at Tier 2 (Rust). Each module calls lib::run_validation() in-process — no subprocess spawning, no shell scripts.

Cross-Platform Validation

The musl-static binary has zero runtime dependencies — no libc, no Python, no containers. The Windows binary runs natively or through WSL2.

Three Operating Modes

The operating mode is detected automatically by probe_operating_mode() and recorded in liveSpore.json for provenance.

How to Verify

# From USB or tarball
cd /media/lithoSpore
./validate                    # Run all 7 modules (Tier 2)
./verify                      # BLAKE3 data integrity check
./validate --json             # Machine-readable output

# From source
cargo run --bin litho -- validate --json

# Self-test (artifact integrity)
bin/litho self-test

# Chaos testing (fault injection)
bin/litho chaos-test

The Hypogeal Cotyledon

lithoSpore is classified as a hypogeal cotyledon — a seed leaf that stays underground, nourishing the seedling until it can photosynthesize. The USB’s bundled data and runtime are the cotyledon: persistent, not consumed, providing sustenance until the spore connects to ⚛️🧬 NUCLEUS for full compute capability.

Get the Artifact

Repository: sporeGarden/lithoSpore

The artifact carries 16 DOIs, 7 data bundles, pre-rendered notebooks, and publication-quality SVG figures. See papers/READING_ORDER.md for the guided reading path through the LTEE literature.