HOMEOFRAMEE.COLIYEASTC.ELEGANSREF STACKMATHORGANISMS
REFERENCE STACKTIER S+A+B+CALLOMETRYCOMPARATIVEγ₁=14.134725141734693
OFRAME REFERENCE STACK
7 ORGANISMS · 5 DIMENSIONS · ALLOMETRY · EOSE LABS DAY 97
From E. coli (4.6 Mb) to H. sapiens (3.2 Gb) · Tier S/A/B/C classification · All major model organisms
Allometric scaling laws · Generation time · Neuron counts · Coding density
γ₁ = 14.134725141734693 — the invariant across all scales of life
Five Dimensions · All Tier-S/A Organisms
Every living system can be characterized across five fundamental dimensions. These are not arbitrary — they emerge from SET theory applied to biology. Each dimension is a necessary condition for life as we know it.
ORGANISMBOUNDARYMETABOLISMINFORMATIONREPLICATIONRESPONSE
E. coli K-12Phospholipid bilayer + peptidoglycan300+ pathways, 20 min doubling4.6 Mb DNA, 300 TFs, 600 operonsBinary fission, oriCChemotaxis, quorum sensing
S. cerevisiaeCell wall (chitin/glucan) + membraneCrabtree effect, fermentation/respiration12.1 Mb, 16 chr, epigenomeBudding or mating/meiosisPheromone, stress HOG pathway
C. elegansCuticle + hypodermis + body wallPharynx-driven, ~3d generation100 Mb, 302-neuron brain, connectomeSelf-fertilization or matingChemotaxis, thermotaxis, learning
D. melanogasterExoskeleton + epitheliumInsect metabolism, 10d generation140 Mb, ~14,000 genes, complex brainSexual, complex meiosisVision, olfaction, courtship
A. thalianaCell wall + cuticle + epidermisPhotosynthesis + respiration, 6wk135 Mb, ~27,000 genes, circadianFlowers (sexual), seeds (dormant)Light, gravity, water, temperature
M. musculusSkin, immune system, organ barriersMammalian endothermy, 10wk generation2.7 Gb, ~23,000 genes, 70M neuronsPlacental viviparityComplex behavior, learning, immune
H. sapiensSkin + immune + cultural boundaries2,000 kcal/day, 25yr generation3.2 Gb, ~21,000 genes, 86B neuronsPlacental viviparity, cultureLanguage, tools, civilization
Genome Size · Visual Scale
Genome size does not correlate with organismal complexity (the C-value paradox). Onions have larger genomes than humans. Coding density decreases as organisms become more complex.
E. coli K-12
4.6 Mb
88% coding
S. cerevisiae
12.1 Mb
70% coding
C. elegans
100 Mb
25% coding
D. melanogaster
140 Mb
20% coding
A. thaliana
135 Mb
25% coding
M. musculus
2.7 Gb
3% coding
H. sapiens
3.2 Gb
1.5% coding
C-value paradox: genome size ≠ complexity. Non-coding = regulatory infrastructure.
Allometric Scaling Laws · Kleiber's Law
Metabolic rate scales as mass to the 3/4 power across 27 orders of magnitude of body size. This is one of the most universal laws in biology. γ₁ = 14.134725141734693 appears as the energy quantum in the derivation of the 3/4 exponent.
SCALING EQUATIONS
Metabolic rate ∝ M3/4
Lifespan ∝ M0.25
Heart rate ∝ M-0.25
~1.5 billion heartbeats per mammalian lifetime
This number is conserved: mouse (2yr) to elephant (70yr)
γ₁ appears in the 3/4 exponent derivation: fractal network optimization
GENERATION TIME SCALING
ORGANISMGENERATION TIME
E. coli20 min
S. cerevisiae90 min
C. elegans3 days
D. melanogaster10 days
A. thaliana6 weeks
M. musculus10 weeks
H. sapiens25 years
Neuron Scaling · Log Scale
Neuron counts span 11 orders of magnitude from C. elegans (302) to estimates of neural complexity in large networks. The scaling is roughly linear on log scale. C. elegans proves that cognition (learning, memory, behavior) emerges from very few neurons.
C. elegans
302
D. melanogaster
140K
M. musculus
70M
H. sapiens
86B
Log scale. 302 → 140K → 70M → 86B. C. elegans: proof that complex behavior emerges from minimal neurons.
Coding Density · Regulatory Infrastructure
As organisms increase in complexity, coding density drops. The non-coding DNA is not “junk” — it is the regulatory layer: enhancers, silencers, insulator elements, non-coding RNAs, repetitive elements that provide organizational structure. More complexity = more regulation needed.
E. coli K-12
88%
S. cerevisiae
70%
C. elegans
25%
D. melanogaster
20%
A. thaliana
25%
M. musculus
3%
H. sapiens
1.5%
Database Stack · Primary References
ORGANISMPRIMARY DBGENOME DBPATHWAY DBEXPRESSION DB
E. coli K-12EcoCycNCBI RefSeqBiGG/KEGGGEO
S. cerevisiaeSGDNCBI RefSeqKEGG/ReactomeGEO/SRA
C. elegansWormBaseWormBaseWormBaseWormBase
D. melanogasterFlyBaseFlyBaseKEGGmodENCODE
A. thalianaTAIRTAIRAraCycGEO
M. musculusMGIEnsembl/NCBIReactomeAllen Brain
H. sapiensHGNC/UniProtGRCh38ReactomeGTEx/ENCODE
Tier B/C Extended List
TIERORGANISMGENOMEPRIMARY USE
BD. rerio (zebrafish)1.7 GbVertebrate development, live imaging
BX. laevis (frog)3.1 GbCell biology, oocyte systems
BG. gallus (chicken)1.0 GbDevelopmental biology, amniote reference
CN. crassa (bread mold)41 MbCircadian clock, epigenetics
CT. brucei (trypanosome)35 MbKinetoplast biology, disease
CP. falciparum (malaria)23 MbParasite biology, drug targets
CH. vulgaris (hydra)1.0 GbRegeneration, stem cells
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