A field-notebook for the living world. Cell, organism, ecosystem, biosphere — each level emerges from the one below. Equations are scarce here; pattern is everything.
Biology is a science of nested levels. A self-replicating chemistry inside a membrane gives a cell. Cells, by collaboration or differentiation, become an organism. Many organisms together form an ecosystem; all of them, our biosphere.
~10⁻⁵ m
~1 m (a vertebrate)
~km
~10⁷ m
All known life is cellular. Two great divisions: prokaryotes (no membrane-bound nucleus — bacteria, archaea) and eukaryotes (organelles inside, including the nucleus).
The eukaryotic cell is itself a community. Mitochondria — once free-living α-proteobacteria — were engulfed about 2 billion years ago. Chloroplasts came from cyanobacteria. Endosymbiosis, in Lynn Margulis's word.
A schematic eukaryote, 14× life size
Crick's "central dogma" (1958): genetic information flows from DNA to RNA by transcription, and from RNA to protein by translation. The flow is mostly one-way; reverse-transcription (retroviruses) is the exception.
Double helix. 4 bases A, T, G, C. ~3 × 10⁹ base pairs in human genome. ~2 m of it per cell, packed into a 6 μm nucleus.
Single strand. mRNA carries code; tRNA carries amino acids; rRNA is structural in the ribosome. Some RNAs catalyze (ribozymes).
20 amino acids form polypeptides that fold into 3D shapes. Catalysis (enzymes), structure (collagen), signaling (hormones), defense (antibodies).
6 CO2 + 6 H2O + light → C6H12O6 + 6 O2
Light reactions in thylakoids split water, pump H⁺, make ATP and NADPH. Calvin cycle (RuBisCO) fixes CO₂ into 3-carbon sugars in the stroma.
Earth's atmospheric O₂ is the cumulative byproduct of ~3 billion years of photosynthesis.
C6H12O6 + 6 O2 → 6 CO2 + 6 H2O + ~30 ATP
Glycolysis (cytoplasm) → pyruvate → mitochondrial Krebs cycle → electron transport chain. Each glucose yields up to 30–32 ATP.
Anaerobic versions: lactic acid fermentation (muscles), ethanol fermentation (yeast).
Carl Woese, 1977: ribosomal RNA sequences split prokaryotes into two anciently divergent domains. Today: Bacteria, Archaea, Eukarya. Eukaryotes nest inside the Archaea — we are an Asgard archaean lineage that swallowed a proteobacterium.
An animal body is roughly 11 organ systems: integumentary, skeletal, muscular, nervous, endocrine, cardiovascular, lymphatic, respiratory, digestive, urinary, reproductive. Plants run on three tissue systems (dermal, ground, vascular) and four organs (root, stem, leaf, flower).
Homeostasis is the central physiological idea (Claude Bernard, 1865; Walter Cannon coined the word, 1926): self-regulation around set-points — pH 7.4, T 37 °C, blood Na⁺ 142 mM.
Temperate canopy, Pacific Northwest. ~30 m above the forest floor; light intensity ~5 % of incident.
Producers (autotrophs) capture sunlight at ~1 % efficiency. Herbivores eat them at ~10 % transfer; carnivores ~10 % again. Hence the 4–5-link cap on most food chains.
Matter — C, N, P, S, H₂O — cycles between abiotic reservoirs and biotic compartments. Biogeochemistry. Ecology in the Vernadsky / Lindeman / Odum tradition reads the planet as a metabolism.
1707–78. Binomial nomenclature. Systema Naturae, 1735.
1809–82. Natural selection; HMS Beagle; Origin of Species, 1859.
1822–84. Particulate inheritance, peas in Brno.
1822–95. Germ theory; vaccination; pasteurization.
1799–1847. Lyme Regis fossils; ichthyosaur, plesiosaur.
1928–2012. rRNA tree; Archaea as third domain.
1938–2011. Endosymbiotic theory; Gaia.
1902–92. Transposable elements; Nobel 1983.
Earliest chemical evidence of life — graphite inclusions in Greenland.
Great Oxygenation Event. Cyanobacteria poison the early atmosphere with O₂.
Eukaryotic radiation; first reliable fossil eukaryotes.
Multicellular animals (Ediacaran biota); Cambrian explosion at 540 Mya.
Francesco Redi's flies-in-jars: spontaneous generation in doubt.
Schleiden & Schwann's cell theory.
Darwin's Origin of Species.
Watson, Crick, Wilkins — DNA double helix; Franklin's Photo 51.
Dolly the sheep, somatic-cell nuclear transfer.
Human Genome Project: 92 % complete; T2T finished it 2022.
Doudna & Charpentier — CRISPR-Cas9 as gene-editing tool.
AlphaFold 3 predicts complexes; ~ 2 × 10⁸ protein structures public.
Catalogue of Life, 2024 update. Mostly insects, plants, fungi.
Mora et al. 2011, eukaryotes only. Most still unknown.
Bacteria, archaea, fungi, viruses largely uncharacterized.
Distribution is wildly uneven: ~25 hotspots (Conservation International) hold ~50 % of plant species and 42 % of land vertebrates on 2.5 % of land. The IUCN Red List, 2024: 46,000+ species threatened with extinction.
"There is grandeur in this view of life..."— Charles Darwin, 1859
The biosphere is ~20 km thick: from deep-sea trenches to the upper troposphere where some bacteria still drift. Vladimir Vernadsky in 1926 described it as a geological force; James Lovelock and Lynn Margulis later proposed Gaia, in which life maintains conditions for life.
Atmospheric composition by volume: 78 % N₂, 21 % O₂, 0.93 % Ar, 0.043 % CO₂. The non-equilibrium of O₂ and CH₄ together is itself a biosignature.
JCVI-syn3A — minimal genome, 473 genes, replicates. Bottom-up cell construction proceeding by modules.
Atlases of human cell types (HCA: ~10⁸ cells profiled); spatial transcriptomics maps cells in tissue.
Brain, intestine, kidney, retina — self-organizing 3D mini-organs from stem cells.
Live biotherapeutic products approved by FDA. C. diff recurrence prevention.
Self-propagating CRISPR cassettes in mosquitoes — could eliminate malaria. Trials underway.
Colossal Bio is working toward thylacine, mammoth, dodo proxies. Ethics, ecology fiercely debated.
Plus PBS Eons for deep time, and Crash Course Biology with Hank Green.
Field notes are a draft of the world. They are always being revised.