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| 1 | +# Experiment: Cross-System Interaction |
| 2 | + |
| 3 | +**Date:** 2026-05-23 |
| 4 | +**Repo:** SuperInstance/flux-tensor-midi |
| 5 | +**File:** `experiments/experiment_cross_system.py` |
| 6 | + |
| 7 | +## Objective |
| 8 | + |
| 9 | +Wire multiple living systems (Ecosystem, GRN, MusicalCell, ProteinFolder) together and observe emergent behavior across system boundaries. |
| 10 | + |
| 11 | +--- |
| 12 | + |
| 13 | +## Experiment 1: Ecosystem Dynamics β Invasion & Extinction |
| 14 | + |
| 15 | +Set up a 5-species ecosystem (Jazz, Blues, Rock, Classical, HipHop) at Ξ΅=0.5, ran 50 ticks, then introduced an invasive species, triggered an extinction event, and observed recovery. |
| 16 | + |
| 17 | +### Results |
| 18 | + |
| 19 | +| Phase | Biodiversity | Living Species | |
| 20 | +|-------|-------------|----------------| |
| 21 | +| Before invasion | 0.9641 | HipHop + 1 immigrant | |
| 22 | +| After invasion | 1.5064 | Techno + 2 immigrants | |
| 23 | +| After extinction | 1.8821 | Pop + 3 immigrants | |
| 24 | +| After recovery | 1.9552 | Pop, Rock, Punk + 1 immigrant | |
| 25 | + |
| 26 | +### Key Observations |
| 27 | + |
| 28 | +- **Original species displaced**: None of the original 5 survived to the end β all were outcompeted by emergent immigrant species. This is classic ecological succession. |
| 29 | +- **Invasion increases diversity**: Biodiversity rose from 0.96 β 1.51 after invasion, showing the ecosystem absorbed the perturbation productively. |
| 30 | +- **Extinction event was surprisingly constructive**: The extinction event (threshold=0.5) actually *increased* diversity to 1.88 by clearing niches for new species. |
| 31 | +- **Immigration-driven speciation**: The ecosystem auto-generated 23 extinct species over 180 ticks, demonstrating continuous creative destruction. |
| 32 | + |
| 33 | +--- |
| 34 | + |
| 35 | +## Experiment 2: Gene Regulatory Network β Cell |
| 36 | + |
| 37 | +A GRN with 20 gene nodes (TONIC, DOMINANT, REST, SYNCOPATION, etc.) was wired into a MusicalCell. The GRN's gene expression levels became transcription factor signals for the cell. |
| 38 | + |
| 39 | +### Results |
| 40 | + |
| 41 | +- Cell energy **converged** from ~0.74 β 0.50 over 20 ticks (damped oscillation toward equilibrium) |
| 42 | +- All 20 GRN genes remained active (expression > 0.5) throughout β the GRN was in a stable attractor state |
| 43 | +- Cell produced 1-2 MIDI events per tick consistently |
| 44 | + |
| 45 | +### Key Observations |
| 46 | + |
| 47 | +- **Homeostatic convergence**: The cell-GRN system naturally seeks an energy equilibrium near 0.5, analogous to biological homeostasis. |
| 48 | +- **GRN acts as a stable controller**: The regulatory network, once settled, provides consistent transcription factor signals β a biological "steady state." |
| 49 | +- **Minimal variation**: With all genes active and energy converged, the system reached a fixed point rather than exhibiting chaotic dynamics. |
| 50 | + |
| 51 | +--- |
| 52 | + |
| 53 | +## Experiment 3: Protein Folding Energy Landscape |
| 54 | + |
| 55 | +5 random amino acid sequences (10-21 residues) were folded using the lattice folding algorithm. |
| 56 | + |
| 57 | +### Results |
| 58 | + |
| 59 | +| Sequence | Length | Energy | Radius of Gyration | Folded | |
| 60 | +|----------|--------|--------|--------------------|----| |
| 61 | +| VYWYMLIGVCG | 11 | 27.28 | 0.88 | β
| |
| 62 | +| PQSADYYFKK | 10 | 39.95 | 0.63 | β
| |
| 63 | +| IHLDCWAKWVTMIDAGDQMQC | 21 | 24.59 | 0.89 | β
| |
| 64 | +| GDEDVYWMYQAQVMRPRSN | 19 | 73.74 | 1.00 | β
| |
| 65 | +| MYVEWDLGEQQDL | 13 | 48.31 | 0.71 | β
| |
| 66 | + |
| 67 | +- **Energy funnel** from origin to folded endpoint: (-2.27, -0.68), confirming the downhill energy landscape expected from a foldable protein. |
| 68 | + |
| 69 | +### Key Observations |
| 70 | + |
| 71 | +- **All sequences folded successfully** regardless of length or composition β the lattice model is permissive. |
| 72 | +- **Energy varies widely** (24.6 β 73.7) across sequences, reflecting different amino acid interaction strengths. |
| 73 | +- **Compactness varies inversely with length**: shorter sequences achieve lower radius of gyration (0.63 for 10aa vs 1.00 for 19aa). |
| 74 | +- The energy funnel confirms the system has a proper thermodynamic gradient driving folding. |
| 75 | + |
| 76 | +--- |
| 77 | + |
| 78 | +## Experiment 4: Cross-System β GRN β Cell β Ecosystem |
| 79 | + |
| 80 | +Three MusicalCells were driven by a shared GRN. The cells' average energy was tracked alongside an ecosystem of 3 species (Alpha, Beta, Gamma) running in parallel. |
| 81 | + |
| 82 | +### Results |
| 83 | + |
| 84 | +| Tick | Biodiversity | Avg Cell Energy | Living Species | |
| 85 | +|------|-------------|-----------------|----------------| |
| 86 | +| 0 | 1.5849 | 0.502 | Alpha, Beta, Gamma | |
| 87 | +| 20 | 2.5307 | 0.501 | Alpha + 4 immigrants, Classical | |
| 88 | +| 40 | 2.2413 | 0.500 | 2 immigrants, Reggae, Techno | |
| 89 | +| 60 | 2.2186 | 0.500 | 5 immigrants | |
| 90 | +| 80 | 0.0000 | 0.500 | 1 immigrant (bottleneck!) | |
| 91 | +| 100 | 2.4472 | 0.500 | 5 immigrants + Folk | |
| 92 | + |
| 93 | +### Key Observations |
| 94 | + |
| 95 | +- **Cell energy was decoupled from ecosystem dynamics**: Cells settled at energy=0.50 and stayed there regardless of ecosystem upheaval. The GRN provided stable regulation. |
| 96 | +- **Ecosystem went through dramatic turnover**: Original species (Alpha, Beta, Gamma) were replaced by immigrant species within 20 ticks. |
| 97 | +- **Biodiversity bottleneck at tick 80**: Diversity crashed to 0 briefly (only 1 species), then recovered to 2.45 by tick 100. This is a classic ecological boom-bust cycle. |
| 98 | +- **Cross-system emergence**: The GRN's stability + ecosystem's volatility created an interesting contrast β biological regulation (cells) vs ecological dynamics (species). |
| 99 | + |
| 100 | +--- |
| 101 | + |
| 102 | +## Overall Conclusions |
| 103 | + |
| 104 | +1. **Systems have distinct timescales**: GRN settles in ~10 ticks, cells in ~20, ecosystems take 100+ ticks to reach quasi-equilibrium. |
| 105 | +2. **Immigration is the dominant force**: In all ecosystem runs, immigrant species (auto-generated) outcompeted seeded species, suggesting the immigration/speciation model is very active. |
| 106 | +3. **Homeostasis emerges naturally**: Both the cell-GRN system and the protein folding system converge to stable states without external intervention. |
| 107 | +4. **Cross-system wiring works but shows limited coupling**: The GRN β Cell pipeline was effective, but the Cell β Ecosystem coupling was indirect (cells ran alongside, not feeding into, the ecosystem). True feedback loops would require additional wiring. |
| 108 | +5. **Creative destruction is constant**: The ecosystem generates 20-30 species over 100-180 ticks, with most going extinct β a healthy evolutionary churn rate. |
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