Tier 0 · open
phenol destruction (coking/refinery effluent)
SUPER-ADDITIVE CONSORTIUM (reducible)
corpus v0.3.0 · hash 3574ed92836e…
Model licensing
This run includes model(s) we cannot re-serve. They are named and cited so you can obtain them directly from the source. Naming a model in a result is not redistribution.
- link-only: Unconfirmed (repo MIT; vmh.life data license not confirmed, preprint noted CC-BY-NC 4.0) -- obtain a license from the source before reuse; source: https://vmh.life/files/reconstructions/AGORA2/version2.01/
The remaining models are openly redistributable (CC-BY).
Provenanced sample report (Syntropa discovery, role-aware Stage-1). Corpus v0.3.0 (15717 models, fingerprint 3574ed92836e) · tools v0.1.0 (git 38fbc04, code 7965284a0cdb) · env py3.13.13 win32 swiglpk5.0.13+osqp1.1.3+highspy1.15.1+pyscipopt6.2.1+optlang1.9.1 (deps fec80ac6eed5). Feed={'phenol': 5} target=phenol mode=destroy. Report id 2fa697ba5c20 (content-addressed to config + EXACT corpus + EXACT tools -> reproducible/auditable). Honest-by-construction: read the caveats.
Verdict: SUPER-ADDITIVE CONSORTIUM (reducible)
the consortium produces FAR more than any single member (super-additive), but a feasible SUBSET already produces the target, so the full set is NOT irreducibly required. Honest framing.
Super-additivity + honest scope
- Best SINGLE organism reaches 0.511; best CONSORTIUM reaches 5.000 (~9.8x) -- a real multi-member effect.
- The 23210 feedstock-dependent candidates are COMBINATIONS over a diverse front-end core and largely SHARE the finisher(s) ['cme_gcf000010085', 'cme_gcf001443605', 'cme_gcf002355415'] -- they are variations on a small number of core relays, NOT 23210 independent discoveries. The biological finding is the finisher + its best partners, not the raw count.
Ranked feedstock-dependent candidates (top 10 of 23210)
| rank | n | production | emergence | members |
|---|---|---|---|---|
| 1 | 3 | 5.000 | super-additive/reducible | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000010085 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + embl_legionella_maceachernii_atcc_35300 (embl_gems (CarveMe RefSeq, Machado 2018)/draft) |
| 2 | 3 | 5.000 | super-additive/reducible | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000025505 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf003610635 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 3 | 3 | 5.000 | super-additive/reducible | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000010085 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + embl_thermomicrobium_roseum_dsm_5159 (embl_gems (CarveMe RefSeq, Machado 2018)/draft) |
| 4 | 3 | 5.000 | super-additive/reducible | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000010085 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf009708955 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 5 | 3 | 5.000 | super-additive/reducible | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000025505 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf010131535 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 6 | 3 | 5.000 | additive | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000317795 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf036251705 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 7 | 3 | 5.000 | additive | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf000025505 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf036251705 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 8 | 3 | 5.000 | additive | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf001443605 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf036251705 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 9 | 3 | 5.000 | additive | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf002151505 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf010131535 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
| 10 | 3 | 5.000 | additive | agora2_desulfovibrio_legalliikhc7 (AGORA2 v2.01 (Heinken 2023)/semi-curated) + cme_gcf002151505 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) + cme_gcf002355415 (CarveMe 1.6.6 reconstruction from NCBI RefSeq proteome/draft) |
Attribution
Every model above is credited by id + source. Model authors: your reconstruction appears in this result. (Impact-ledger stamping = flywheel, pending.)
Caveats (disclosed up front)
- FBA proves a route is stoichiometrically POSSIBLE, not that a living cell will do it.
- Every consortium here is a HYPOTHESIS until cultured; nothing is wet-lab validated.
- Feedstock-dependence is the anti-medium-artifact control: withdraw the feed and the product must collapse (a NOT-feedstock-dependent result is flagged SUSPECT, not a discovery).
- The ranking score is a documented heuristic for human review, not a truth or biology claim.
- Stage-1 selects finisher x diverse front-ends; multi-finisher relays are out of scope. Stage-2 expansion of winners is pending -- these are PRELIMINARY until it runs.