Resolve R1-R8 desert_farm_leverage_points + add BioNumbers subset

data/datasets/desert_farm_leverage_points.csv

@@ -1,13 +1,13 @@
 Prefix,ShortName,Time_min,Time_max,Space_min,Space_max,Color,Reference
-model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-27,#013333,
-process,CO2 fixation,7.69E-03,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat dependent on HCO3- pool via carbonic anhydrase (Igamberdiev 2015)
-process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Moore et al. (2013) Nature Geosci 6:701
-process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Moore et al. (2013) Nature Geosci 6:701
-process,Growth,1.00E+05,1.00E+06,1.00E-20,1.00E-10,#006666,Moore et al. (2013) Nature Geosci 6:701
-model,Community Metabolic Models,99,1.00E+07,1.00E-18,1.00E-03,#013333,
+model,Molecular Dynamics Models,1.00E-15,1.00E-09,1.00E-30,1.00E-22,#013333,Karplus & McCammon (2002) Nat Struct Biol 9:646
+process,CO2 fixation,6.67E-02,2.38E-01,5.79E-26,1.19E-24,#006666,Bar-On et al. (2019) PNAS 116:4738 — kcat = 3-15/s natural RuBisCO; space = 0.1×–1.7× RuBisCO L8S8 enzyme volume (~7e-25 m³)
+process,Nutrient transport,1.00E-02,1.00E+00,1.00E-22,1.00E-20,#006666,Milo & Phillips (2015) Cell Biology by the Numbers
+process,Biochemical synthesis,1.00E+00,1.00E+01,1.00E-21,1.00E-19,#006666,Milo & Phillips (2015) Cell Biology by the Numbers
+process,Photoautotroph cell growth,7.56E+03,1.00E+05,1.00E-18,1.00E-14,#006666,Milo & Phillips (2015) Cell Biology by the Numbers; Yu et al. (2015) Sci Rep 5:8132 (UTEX 2973 fastest)
+model,Community Metabolic Models,1.00E+02,1.00E+07,1.00E-18,1.00E-03,#013333,Zakem et al. (2020) ISME J 14:288
 leverage point,Community Ecology,1.00E+06,1.00E+08,1.00E-09,1.00E+00,#FF9900,Moore et al. (2013) Nature Geosci 6:701
 leverage point,Flocculation,1.00E+03,86400,1.00E-15,1.00E-09,#FF9900,Salim et al. (2011) J Appl Phycol; Vandamme et al. (2013) Biotechnol Adv 31:1680
 leverage point,Ponds,86400,3.15E+07,2000,2.00E+04,#FF9900,Design basis: 10x100x3m deep ponds (3000 m3); depth for photoinhibition protection and floc settling
-model,Biogeochemical Circulation Models,1.00E+05,1.00E+10,1.00E+09,1.00E+16,#013333,
+model,Biogeochemical Circulation Models,1.00E+05,1.00E+10,1.00E+09,1.00E+16,#013333,Levine et al. (2025) Annu Rev Earth Planet Sci 53:595
 leverage point,Sequestration,3.15E+08,1.00E+11,3.12E+09,2.91E+10,#FF9900,40 GtCO2/yr: Space_min=C as diamond (3.5 t/m3) Space_max=biomass+salt+sand (rho~1.5 t/m3) per year
-process,Extraction,3.16E+14,6.31E+15,2.03E+12,2.05E+14,#006666,Carboniferous coal (~300 Mya) + Mesozoic petroleum (~252-66 Mya); Tissot & Welte (1984)
+process,Fossil-fuel formation,3.16E+13,3.16E+15,2.03E+12,2.05E+14,#006666,Kerogen→petroleum maturation (~1-10 My) + coalification (~10-100 My); Tissot & Welte (1984)

data/references/README.md

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+# References
+
+Standalone reference data — not coupled to any specific dataset in this repo.
+
+## Files
+
+- `bionumbers_subset.csv` — curated phototroph-relevant entries from the [BioNumbers database](https://bionumbers.hms.harvard.edu/) (Milo & Phillips, *Cell Biology by the Numbers*) with stable `bion_id` identifiers and direct URLs.
+
+## `bionumbers_subset.csv` schema
+
+| Column | Description |
+|---|---|
+| `bion_id` | BioNumbers entry ID (stable identifier) |
+| `Properties` | Description of the measured quantity |
+| `Organism` | Organism the measurement is from |
+| `Value` | Reported value |
+| `Range` | Reported range (often empty) |
+| `Units` | Units of `Value` |
+| `URL` | Direct link to the BioNumbers entry |
+
+## Scope
+
+Curated to phototroph-relevant entries (cyanobacteria, green algae, diatoms) across three categories: cell generation/doubling times, biochemical synthesis rates (transcription/translation elongation), and nutrient transport (small-molecule diffusion, transporter kinetics). Where phototroph-specific entries were unavailable, generic or model-organism data (e.g., E. coli, Xenopus) was kept as a proxy and noted in `Organism`.
+
+The full BioNumbers database has ~14,300 entries (~27 MB HTML export); this is a focused subset kept as a resource for future work.
+
+## Attribution
+
+BioNumbers is a project of the Milo Lab (Weizmann Institute) and Harvard Medical School. Cite as: Milo R, Jorgensen P, Moran U, Weber G, Springer M (2010). *BioNumbers — the database of key numbers in molecular and cell biology*. Nucleic Acids Res. 38:D750–D753. DOI: [10.1093/nar/gkp889](https://doi.org/10.1093/nar/gkp889).
+
+For the broader synthesis: Milo R, Phillips R (2015). *Cell Biology by the Numbers*. Garland Science.

data/references/bionumbers_subset.csv

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+bion_id,Properties,Organism,Value,Range,Units,URL
+100289,Generation time,Cyanobacteria Synechocystis PCC 6803,6.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100289
+102211,Mean generation time (on acetate),Green algae chlorella,20.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102211
+102212,mean generation time (photoautotrophic growth),Green algae chlorella,11.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102212
+104195,Generation time,Diatom Phaeodactylum tricornutum,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104195
+104196,Generation time,Green algae Dunaliella tertiolecta,15.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104196
+105638,Generation time at 30°C,Green algae Dunaliella salina,20.0,,Hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105638
+111252,Doubling time,Cyanobacteria Synechocystis PCC 6803,12.0,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111252
+111335,Fastest generation time,Cyanobacteria Synechocystis PCC 6803,5.13,,hours,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=111335
+100233,Translation rate of beta-galactosidase in E. coli,Bacteria Escherichia coli,14.5,'13-16,aa/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100233
+105067,Translation rate for short peptides,Bacteria Escherichia coli,22.0,'Table link - http://bionumbers.hms.harvard.edu/files/Maximal%20translation%20rate.pdf,1/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=105067
+104300,Translation rate on culture of nitrogen bases and glucose,Budding yeast Saccharomyces cerevisiae,9.3,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104300
+104598,Translation rate,Human Homo sapiens,5.0,,aa/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104598
+100060,RNA polymerase transcription rate of stable RNA,Bacteria Escherichia coli,85.0,'Table link - http://bionumbers.hms.harvard.edu/files/Parameters%20pertaining%20to%20the%20macromolecular%20synthesis%20rates%20in%20exponentially%20growing%20E.%20coli%20Br%20as%20a%20function%20of%20growth%20rate%20at%2037%20degrees%20celsius.pdf,nt/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100060
+101904,Transcription elongation rate of rRNA operons,Bacteria Escherichia coli,42.0,'±2,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=101904
+100664,Single molecule RNA polymerase II transcription rates,Bacteria Escherichia coli,12.8,'±4.9,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100664
+100662,Maximum RNA polymerase II transcription elongation rate,Mammalian tissue culture cell,71.6,,nucleotides/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=100662
+104089,Diffusion coefficient of glucose in water,Generic,600.0,'Table link - http://bionumbers.hms.harvard.edu/files/Diffusion%20coefficients%20of%20various%20substances%20in%20Water.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104089
+104437,Diffusion coefficient of ammonium in water,Generic,1860.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104437
+104439,Diffusion coefficient of nitrate in water,Generic,1700.0,'Table link - http://bionumbers.hms.harvard.edu/files/Biofilm%20model%20parameters.pdf,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=104439
+109504,Diffusion coefficient glucose in water at 25°C,Generic,673.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109504
+110618,Diffusion coefficient of CO2 in red blood cell,Human Homo sapiens,650.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=110618
+117305,Diffusion coefficient of CO2 in air,air,1.4e-05,,m2/s,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=117305
+102428,Intracellular diffusion coefficient for glucose transporter,African clawed frog Xenopus laevis,100.0,,µm^2/sec,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=102428
+109673,Highest glucose uptake rate that still allows the maximal NADH formation rate,Bacteria Escherichia coli,2.4,,mmol/(gCDW·…h),https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109673
+109686,Glucose uptake rate of strain C-3000 in minimal M9 media,Bacteria Escherichia coli,12.0,'±0.5,mmol/gDW/h,https://bionumbers.hms.harvard.edu/bionumber.aspx?id=109686