Foundations

The science everything leans on · Cambridge IGCSE Biology 0610, topics 2–5

by Dr Daniel Mompel Riera · NLCS Jeju

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What this is

One shelf of the Biology Hub, for the four topics every other topic leans on. The other shelves move across something (a body, a plant, a tree of life); this one moves down into one: a zoom ladder from a whole human to the molecules of one of her cells. The map teaches Topic 2 by being it, and each topic sits at the level it is about:

Level	What you see	Topics here
Organism	a real woman's body, from a medical atlas	2
Organ system	her reproductive system	2
Organ	the uterus and its cervix, cut open: muscle tissue, connective tissue and a lining	2
Tissue	a model of the lining of the cervix, cut like a slide and traced from the real micrograph beside it	2
Cell	the middle of one real HeLa cell, imaged in 3D by an electron microscope (the block's cut edges are marked); Eric Betzig (Nobel Prize in Chemistry 2014) says why the pictures in biology books are wrong	2 · 3
Organelles	inside that cell, beside the nucleus, every part at its measured size and place: 553,130 ribosomes in one small box, and a real electron micrograph of the same cell beside it	2 · 3
Molecules	a model, labelled as one: real protein shapes in the numbers a HeLa cell holds, and a kinesin walking a microtubule through the crowd	4 · 5, the Protein & Enzyme Sim

One zoom, no jumps. Scroll (or pinch) to move in and out through all seven levels: the camera flies on, the organ is cut open, the tissue grows out of the cut face, one lining cell becomes the HeLa cell, and the way into the organelles is one straight line from the cell's view, through the cell membrane into the cytoplasm. Where two levels meet, each is drawn whole and the two pictures are blended, so the screen never goes dark. Names appear on the parts as they come into reach, and on whatever the pointer is on; a colour means the same thing at every level.

A size ruler runs from 1 m to 10 nm, with each topic bracketed beside its levels; the caption gives each level's definition in the words the exam uses, and how many times bigger the next step makes things. Tap any part to see its name, what it does, and whether the syllabus names it.

The labs behind it. Each topic's door shows in the caption of the levels it belongs to. Topic 2's opens the Cells Lab, open since 8 October 2026. The labs for topics 3, 4 and 5 are being built; until then the Protein & Enzyme Sim covers topics 4 and 5.

Adding a lab

The tools/ named here stay on Daniel's computer: they are not in this repository (since 18 Oct 2026).

Edit js/topics.js: give the topic its url and set status: 'live'. Then, outside this repository: its row in labs-shared/labs.json, the front door's js/shelves.js open list, the labs script's LABS, and the sitemap. Run node tools/stamp.mjs here before pushing, so browsers fetch the new files.

• The body and her organs: the HuBMAP Human Reference Atlas, United Female v1.10, made from the Visible Human Female of the US National Library of Medicine (CC BY 4.0). Only the parts used were read from the atlas's 375 MB file.
• The organ cut open: the Atlas's own outline of the uterus and cervix, sliced through the canal; the layers inside the wall drawn at the widths histology describes, in the colours of a stained slide.
• The tissue: a model whose cut face is traced from a micrograph of the endocervix by Mikael Häggström, M.D. (CC0), shown beside it with a closer one; one lining cell then rises out and spreads flat, as such cells do in a dish, and becomes the HeLa cell.
• The electron micrograph: one raw slice of the same HeLa cell, with the parts the computer found outlined.
• The cell and its organelles: Janelia Research Campus, OpenOrganelle jrc_hela-2 (CC BY 4.0): a HeLa cell frozen under high pressure, set in resin and imaged by focused-ion-beam scanning electron microscopy, about 6,400 slices 5 nm apart (Xu et al. 2021), its organelles found by machine learning (Heinrich et al. 2021). The camera flies in through a real gap in the data, 64 nm at its narrowest.
• The molecules: a model. Protein Data Bank shapes; protein numbers measured in HeLa cells (Mueller et al. 2020); 3 million protein molecules per cubic micrometre (Milo 2013). Kinesin takes 8 nm steps; here it takes one a second instead of about a hundred.
• The picture is drawn with three.js (vendored, no CDN), with ambient occlusion, outlines and haze added in one pass, the style of crowded-cell paintings.

assets/CREDITS.md lists every source and every change; tools/model-build/ holds the scripts that made the files (their downloaded data are not kept here).

Licence

The software is AGPL-3.0 (LICENSE); the teaching material is CC BY-NC-SA 4.0 (LICENSE-CONTENT). Third-party data, pictures and the film keep their own terms: see NOTICE.

Something wrong, or a suggestion? Please contact me: [email protected]