# Biology

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Category: Science
Slides: 17
Updated: 2026-05-17T20:51:12.928Z
Tags: science, biology

## Summary

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. Key sections include: Biology The four nested scales; Cell · organism · ecosystem · biosphere.; The smallest thing that lives.; DNA → RNA → protein.; How life eats sunlight.; Three domains , many kingdoms.; Tissues to physiology.; Energy flows; matter cycles.; Whose hands opened biology.; Of life and the science of it..

## Slide Outline

1. Biology The four nested scales
2. Cell · organism · ecosystem · biosphere.
3. The smallest thing that lives.
4. DNA → RNA → protein.
5. How life eats sunlight.
6. Three domains , many kingdoms.
7. Tissues to physiology.
8. Energy flows; matter cycles.
9. Whose hands opened biology.
10. Of life and the science of it.
11. How many species?
12. One thin green-blue film.
13. What's new in 2026.
14. Things we still don't understand.
15. Watch & read.

## Slide Transcript

### Slide 1: Cell · organism · ecosystem · biosphere.

- P. 01 — the four scales
- 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.
- Cell
- ~10⁻⁵ m
- Organism
- ~1 m (a vertebrate)
- Ecosystem
- ~km
- Biosphere
- ~10⁷ m

### Slide 2: The smallest thing that lives.

- P. 02 — the cell, unpacked
- 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.
- Plasma membrane — phospholipid bilayer, ~5 nm
- Nucleus — chromatin, nucleolus, pores
- Mitochondria — Krebs cycle, ATP synthesis
- Endoplasmic reticulum — protein/lipid synthesis
- Golgi apparatus — packaging, sorting
- Lysosomes — pH 4.5 garbage disposals
- Cytoskeleton — actin, microtubules, intermediate filaments
- A schematic eukaryote, 14× life size

### Slide 3: DNA → RNA → protein.

- P. 03 — the central dogma
- 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.
- DNA
- 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.
- RNA
- Single strand. mRNA carries code; tRNA carries amino acids; rRNA is structural in the ribosome. Some RNAs catalyze (ribozymes).
- Protein
- 20 amino acids form polypeptides that fold into 3D shapes. Catalysis (enzymes), structure (collagen), signaling (hormones), defense (antibodies).

### Slide 4: How life eats sunlight.

- P. 04 — energy in & out
- Photosynthesis
- 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.
- Respiration
- 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).

### Slide 5: Three domains, many kingdoms.

- P. 05 — the tree
- 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.
- Bacteria — E. coli, Streptomyces, cyanobacteria
- Archaea — methanogens, halophiles, thermophiles, Asgard
- Eukarya — animals, plants, fungi, protists

### Slide 6: Tissues to physiology.

- P. 06 — the organism
- 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.
- Negative-feedback loop

### Slide 7: Plate I

- Temperate canopy, Pacific Northwest. ~30 m above the forest floor; light intensity ~5 % of incident.

### Slide 8: Energy flows; matter cycles.

- P. 08 — the ecosystem
- 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.
- Net primary productivity, terrestrial: ~56 PgC/yr
- Marine NPP: ~48 PgC/yr
- Standing biomass, all life: ~550 GtC
- Plants: ~450 GtC · animals: ~2 GtC · humans: 0.06 GtC

### Slide 9: Whose hands opened biology.

- P. 09 — naturalists, microbiologists, ecologists
- Linnaeus
- 1707–78. Binomial nomenclature. Systema Naturae, 1735.
- Darwin
- 1809–82. Natural selection; HMS Beagle; Origin of Species, 1859.
- Mendel
- 1822–84. Particulate inheritance, peas in Brno.
- Pasteur
- 1822–95. Germ theory; vaccination; pasteurization.
- Mary Anning
- 1799–1847. Lyme Regis fossils; ichthyosaur, plesiosaur.
- Carl Woese
- 1928–2012. rRNA tree; Archaea as third domain.
- Lynn Margulis
- 1938–2011. Endosymbiotic theory; Gaia.
- Barbara McClintock
- 1902–92. Transposable elements; Nobel 1983.

### Slide 10: Of life and the science of it.

- P. 10 — a timeline
- ~3.8 GyaEarliest chemical evidence of life — graphite inclusions in Greenland.
- ~2.4 GyaGreat Oxygenation Event. Cyanobacteria poison the early atmosphere with O₂.
- ~1.6 GyaEukaryotic radiation; first reliable fossil eukaryotes.
- ~600 MyaMulticellular animals (Ediacaran biota); Cambrian explosion at 540 Mya.
- 1668Francesco Redi's flies-in-jars: spontaneous generation in doubt.
- 1838Schleiden & Schwann's cell theory.
- 1859Darwin's Origin of Species.
- 1953Watson, Crick, Wilkins — DNA double helix; Franklin's Photo 51.
- 1996Dolly the sheep, somatic-cell nuclear transfer.
- 2003Human Genome Project: 92 % complete; T2T finished it 2022.
- 2012Doudna & Charpentier — CRISPR-Cas9 as gene-editing tool.
- 2024AlphaFold 3 predicts complexes; ~ 2 × 10⁸ protein structures public.

### Slide 11: How many species?

- P. 11 — biodiversity
- ~ 2.16 M described
- Catalogue of Life, 2024 update. Mostly insects, plants, fungi.
- ~ 8.7 M estimated
- Mora et al. 2011, eukaryotes only. Most still unknown.
- ~ 10⁹ – 10¹² microbes?
- 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.

### Slide 12: Slide 12

- P. 12 — pull quote
- "There is grandeur in this view of life..."— Charles Darwin, 1859

### Slide 13: One thin green-blue film.

- P. 13 — the biosphere
- 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.
- Carbon cycle, simplified

### Slide 14: What's new in 2026.

- P. 14 — frontier
- Synthetic cells
- JCVI-syn3A — minimal genome, 473 genes, replicates. Bottom-up cell construction proceeding by modules.
- Single-cell omics
- Atlases of human cell types (HCA: ~10⁸ cells profiled); spatial transcriptomics maps cells in tissue.
- Organoids
- Brain, intestine, kidney, retina — self-organizing 3D mini-organs from stem cells.
- Microbiome therapeutics
- Live biotherapeutic products approved by FDA. C. diff recurrence prevention.
- Gene drives
- Self-propagating CRISPR cassettes in mosquitoes — could eliminate malaria. Trials underway.
- De-extinction
- Colossal Bio is working toward thylacine, mammoth, dodo proxies. Ethics, ecology fiercely debated.

### Slide 15: Things we still don't understand.

- P. 15 — open questions
- How did life begin? RNA world? Iron-sulfur world? Off-world panspermia?
- What is the upper bound on cellular complexity?
- Are there forms of life with chemistry unlike ours (alternative biochemistry)?
- How does an embryo turn a single cell into a butterfly with ~5 × 10⁹ cells, in the right places?
- Why do most species go extinct within ~1–10 Myr of arising?
- How much of the microbial dark matter — uncultured archaea, bacteriophages, giant viruses — remains undescribed?
- Is aging a single mechanism or many tangled ones? Is it tunable?

### Slide 16: Watch & read.

- P. 16 — go deeper
- Kurzgesagt — Cells and Microbes Series
- Plus PBS Eons for deep time, and Crash Course Biology with Hank Green.
- Watch ↗
- References
- Alberts et al. — Molecular Biology of the Cell (7th ed.)
- Campbell — Biology (12th ed.)
- Begon, Townsend, Harper — Ecology
- Margulis & Sagan — Microcosmos (1986)
- Wilson — The Diversity of Life (1992)
- Lane — The Vital Question (2015)

### Slide 17: Slide 17

- — end of notebook —
- Field notes are a draft of the world. They are always being revised.


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