Resolve R1-R8 data concerns for desert_farm_leverage_points.csv#25
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Resolve R1-R8 data concerns for desert_farm_leverage_points.csv#25madsCodeBuddy wants to merge 3 commits into
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R1: CO2 fixation Time_min 7.69E-03 → 6.67E-02 (Bar-On natural kcat ceiling)
R2: Replace Moore et al. 2013 mis-citations on Nutrient transport, Biochemical
synthesis, and Cell growth (formerly Growth) with Milo & Phillips (2015)
Cell Biology by the Numbers
R3: Rename Growth → Cell growth; tighten bounds to single algal cell
(Time 1e3-1e5 s, Space 1e-18 to 1e-14 m³). Population scale stays in
Community Ecology row.
R4: MD Space_max 1e-27 → 1e-22 m³ (genuine modern atomistic-MD reach)
R5: Community Metabolic Models Time_min 99 → 1.00E+02 (formatting consistency)
R6: Fill empty Reference cells:
- Molecular Dynamics Models: Karplus & McCammon (2002) Nat Struct Biol 9:646
- Community Metabolic Models: Zakem et al. (2020) ISME J 14:288
- Biogeochemical Circulation Models: Levine et al. (2025) Annu Rev
Earth Planet Sci 53:595
R7: Rename Extraction → Fossil-fuel formation; Time bounds 3.16E+13 to
3.16E+15 s reflect formation duration (kerogen maturation + coalification)
rather than deposit age
R8: Extend CO2 fixation Reference text to justify both time (Bar-On kcat) and
space (RuBisCO L8S8 enzyme volume) bounds. Drop Igamberdiev CA mechanism
reference; no longer needed once Time_min reflects intrinsic RuBisCO kcat.
25 entries justifying time/space bounds for Cell growth (8), Biochemical synthesis (8), and Nutrient transport (9) rows. Each entry includes bion_id, value, units, organism, and direct URL to the BioNumbers page. Phototroph-specific where available; generic-organism proxies used where phototroph data was unavailable in BioNumbers.
Schema, curation criteria, known gaps (including the Cell growth Time_min mismatch flagged by the BioNumbers data), update procedure, and BioNumbers attribution per Milo et al. (2010) Nucleic Acids Res 38:D750.
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Superseded by a fresh-from-main port — branch fell behind main during the BioNumbers subset addition. New PR uses branch |
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Resolves R1–R8 data concerns from desert_farm_dataset_issues working list.
Changes
Time_min7.69e-3 → 6.67e-2 (Bar-On natural RuBisCO kcat ceiling, 15/s)Community EcologyrowSpace_max1e-27 → 1e-22 m³ (modern atomistic MD reaches 100-nm boxes)Time_min99→1.00E+02(formatting consistency)New references
Rename impact check
Searched repo for
GrowthandExtractionstring usage. No external code/docs reference these specific row labels in the desert farm context (other CSVs use them in unrelated rows likeGrass blade growth,Coral reef growth,Oil reservoir extraction— all distinct).Risks / open items
Community Ecologyrow was too large to justifydata/references/and link from Reference cells when readyTime_minreflects intrinsic RuBisCO kcat rather than CA-enhanced apparent rate; revert if you want to keep the mechanistic note