Developmental Biology

How a single egg builds a patterned, growing body

About this course

How embryos develop — gastrulation and axes, morphogen gradients and Turing patterns, segmentation and Hox genes, signalling and stem cells — then morphogenesis, growth and scaling, regeneration and evo-devo.

What you will be able to do

  • Explain how gastrulation establishes the body axes
  • Model pattern formation with morphogen gradients and Turing mechanisms
  • Describe how segmentation and Hox genes lay out the body plan
  • Explain how signalling drives cell-fate decisions and stem-cell differentiation
  • Relate the mechanics of morphogenesis, growth control and regeneration to tissue form

What this course covers

  • Mosaic vs. regulative development (Roux and Driesch)
  • Cleavage: division without growth
  • The egg: size and stored contents
  • The midblastula transition as a titration
  • Fed vs. stocked embryo strategies
  • The doubling ledger: mass and cell number to birth
  • Pregnancy on a log axis: the Fermi of doublings
  • The segmentation cascade: four tiers, twenty-eight genes
  • The syncytium and why the fly was the key animal
  • The Nüsslein-Volhard/Wieschaus screen and Poisson saturation
  • The stripe as a logic gate on four gradients
  • Measured inputs versus fitted parameters in the stripe model
  • Border sharpness and the sharpening cascade
  • Worked evaluation of the stripe gate at two egg positions
  • Lateral inhibition: patterning without a gradient
  • The hidden switch: population averages vs. single-cell responses
  • Gradient and lateral inhibition combined
  • Bistability: positive feedback, threshold, and memory
  • Experimental tests distinguishing bistability from steep graded response
  • Ligand range: the square root of D·τ
  • Eighth clause: a decision is a bistable switch
  • Morphogen gradient: synthesis, diffusion, degradation
  • French flag model: thresholds and boundary shifts
  • Positional information as a coordinate; historical landmarks
  • Precision of positional reading: the counting limit
  • Exponential gradient in real tissues: effective diffusion with membranes
  • Fermi estimate: same law in a wing; failure to scale
  • Fitting a gradient: log-linear transform and parameter recovery
  • Differential adhesion and tissue sorting
  • Cortical tension versus cadherin adhesion
  • Apical constriction and sheet folding
  • Tissue viscoelasticity and jamming
  • Laplace pressure and lumen formation
  • Genome writes the map; physics draws the shape
  • Branching morphogenesis and lung surface area
  • Stem cell definition and spleen-colony assay
  • The stem cell tree: 23 doublings and 36 root divisions per day
  • Waddington landscape as a mathematical potential
  • Stem cell niche and asymmetric division
  • Reprogramming: four factors, one in a thousand, and a Poisson
  • Telomere counter: fifty doublings and the body's division budget
  • Worked example: reconstructing the full blood-cell tree
  • Gompertz Growth Curve and Fetal Growth
  • Why the Growth Rate Falls: Three Causes
  • Allometry and Power Laws
  • Gradient Scaling and the Expander Mechanism
  • The ¾ Law as Mechanism, Not Just Fit
  • Size as a Stop: Liver Set Point and Species Doublings
  • Worked Example: Reading the Gompertz at Three Ages
  • Gastrulation: three germ layers from a hollow ball
  • Convergent extension and intercalation geometry
  • Forces of morphogenesis and tissue viscous flow
  • Tissue surface tension and shape stability
  • BMP gradient, decay length, and the organizer
  • Left–right symmetry breaking by nodal flow
  • Worked example: exponential intercalation over time
  • Turing instability: core idea and motivation
  • Activator-inhibitor pair: Jacobian and stability
  • Dispersion relation and the band of unstable wavelengths
  • How cells achieve the required diffusion ratio
  • Pattern growth from noise
  • Turing vs. French-flag: tests and biological examples
  • Threshold diffusion ratio: analytic derivation
  • The Hox Code as a Positional Address
  • Deep Homology and the Homeobox
  • Collinearity: One Order in Three Places
  • Why Mammals Are Fixed at Seven Cervical Vertebrae
  • The Vertebral Formula as Hox Boundaries
  • Hox Cluster Duplication and the Vertebrate Tree
  • Worked Example: Vertebral Formula Arithmetic
  • Regeneration as development re-run from positional memory
  • Poisson limit on planarian fragment size
  • Wnt gradient and wound polarity in planarians
  • Liver regeneration: doublings, cell divisions, and the logistic race
  • When tissues use stem cells versus working-cell division
  • Blastema doublings and the polar-coordinate positional memory
  • The gut ledger, the scar, and why the heart cannot wait
  • Somitogenesis: axis as count times period
  • Cooke and Zeeman clock-and-wavefront model
  • Delayed negative-feedback gene as a clock
  • Notch coupling keeps noisy clocks in phase
  • Wavefront boundary positions: x = VkT
  • Experimental falsification of the delay-feedback clock
  • Species tempo: human clock two and a half times slower
  • Arithmetic of human–chimpanzee genome differences
  • Deep homology and the developmental toolkit
  • Switch evolvability: enhancers vs. protein-coding sequence
  • When protein-coding sequence can evolve
  • Heterochrony: timing changes build new body plans
  • The beak as a dial: BMP4, calmodulin, and measurable selection
  • Central thesis: evolution edits switches, not parts
  • Human developmental doublings: thirty then eleven
  • The placenta: second organ and supply limit
  • The organogenesis window and teratogen sensitivity
  • Human versus animal data: what is seen, inferred, or different
  • Aneuploidy risk versus maternal age: exponential curve and its cause
  • The status of developmental laws: fitted constants, not derived
  • IVF arithmetic: the funnel and cumulative cycle probability

Syllabus

  1. Early Embryo

    1. L1 · The Egg and the Embryo
    2. L2 · Gastrulation and Axes

  2. Pattern Formation

    1. L3 · Morphogens and the French Flag
    2. L4 · Turing Patterns

  3. Segments and the Body Plan

    1. L5 · The Fly's Segments
    2. L6 · Hox Genes and the Body Plan
    3. L7 · The Segmentation Clock

  4. Cell Fate

    1. L8 · Signalling and Decisions
    2. L9 · Stem Cells and Differentiation

  5. Form, Growth and Evolution

    1. L10 · Morphogenesis and Mechanics
    2. L11 · Growth, Size and Scaling
    3. L12 · Regeneration and Repair
    4. L13 · Evo-Devo
    5. L14 · The Human, and the Close