Lec 12 Full Delivery Script - Color Patterns I
2026-05-05 11:27:55 • 19:02
Lecture 12, Color Patterns I.
EB 187, Ecology and Evolution of Color Week 6 Professor Michael Alfaro May 7th, 2026
Source Deck.
LEC 12, Slides.QMD, 23 Content Slides Plus 1 Title, Q Conventions.
For Fragment Reveals, For Think Pair Share, Stage Directions in.
Title Slide.
Good Morning.
Lecture 12, Color Patterns.
On Tuesday, we ended with the mixing continuum, the synthesis of the entire color mechanism
unit.
Today we leave mechanism behind and ask the next question.
Once a mechanism is in place, how does the body decide where to put it?
Slide 1, Tuesday recap.
Six Photographs.
Six positions on the continuum.
Quick pass.
Position 1, Turrico.
Pure pigment.
Turrico-Verdin in the Feather Barbe.
Bleach the Feather, color is gone.
Grind the Feather, color survives.
Position 2, Tannager.
Karatanoid in the Cortex Plus, an ordered keratin layer beneath.
The reflective backing double saturation.
Position 3, Papilio.
Yellow pigment plus a concave multi-layer adding blue iridescence.
I mixes them to emerald.
Position 4, Green Parrot.
Spungy beta keratin makes the blue.
Cidico-Folven filters at yellow.
Subtractive mixing in tissue gives green.
Position 5, Peacock.
Melanon rods packed in a 2D photonic lattice.
The pigment is the building block of the structure.
Position 6, Morpho.
Christmas tree ridges of clear chiton.
No pigment in the blue.
Bleach does nothing.
Grind destroys it.
Mechanism is set.
Today, how does it get arranged in space and stripes, bars and spots?
Slide 2, Cuddlefish camouflage.
Last week, we talked about chromatophores as units of color.
Here is what they look like in action.
Sephalopod chromatophores expand and contract in milliseconds.
Same machinery as the Salopris and Tree Frog from Tuesday, just on a faster clock.
Slide 3, Camelian iridophores.
The video opens with a Morpho butterfly intro, a LEC-11 callback.
The structural color framework.
Then it cuts to the Camelian.
Watch the iridophore lattice spacing change.
Cells expand.
Latis spacing increases.
Reflected wavelength shifts red.
That is structural color modulated by cell biology, pure LEC-9-10 physics, with LEC-11
cellular control.
Slide 4, Bird of Paradise.
The superb bird of paradise.
Watch the courtship display.
This bird is using mechanism, structural color in the throat shield, super black background
feathers from LEC-11 and a precisely arranged spatial pattern.
The pattern is the signal.
Three questions latent in this video.
First, how does the male assemble those colors?
LEC-8-11.
We did that.
Second, how does the body know to put those patches where they are?
Today's lecture.
Third, why does the female care?
LEC-14-16.
Coming up.
Today's pivot is from mechanism to arrangement.
Slide 5, three questions.
The agenda for today.
One, what patterns exist?
Stripes, bars, spots, a cell-eye, reticulations.
Two, where do the cells come from?
Neural crust for chromata-4 lineages.
Three, how do cells self-organize?
Short-range repulsion.
Long-range help.
Turing dynamics.
The arc note at the bottom.
Mechanism.
LEC-8-11.
Arrangement today.
In LEC-14-16, we are in the middle of a four-week structural arc.
Slide 6, pattern diversity.
Eight photographs.
I'm not going to lecture.
I'm going to point.
Tiger.
Zebra.
Leopard.
Giraffe.
Cuddlefish.
Dark frog.
Bicyclus eye spots.
Peacock eye spots.
Every one of these started as an un-patterned embryo.
What rules could possibly produce all of this?
A single developmental program would be impossible.
But a small toolkit of patterning rules applied to different cells with different parameters
in different body regions can produce everything you see here.
That is the through line for both days.
Slide 7, naming patterns.
A taxonomy of pattern elements.
Stripe.
Bar.
Spot.
Ocelas.
Reticulation.
Vermiculation.
Don't memorize this.
Use it as a reference.
Two terminology warnings.
Ictheologists call horizontal bands stripes.
Some herpetologists call vertical bands stripes.
The Nymphilid ground plan is the lepidoptuist system.
Cross-taxon comparisons need explicit definitions.
The important pedagogical move is here.
Endler 1978 pattern is measurable.
Spot size, spacing, contrast, orientation.
Modern tools, microtoolbox, patTR3D do the same job
in software.
For the project, you should think about pattern in measurable terms, not just verbal categories.
A pattern is only a pattern if a viewer can resolve it.
LEC's six spatial acuity sets the pattern's effective grain.
Slide 8, cell palette.
The chromato-4 lineages.
We met these in LEC-11 at the molecular level.
Today we treat them as spatial agents, units that get placed somewhere in the skin.
Melanophor, melanin, black and brown.
LEC-8, Santa IV, Teradins and Caratenoids Yellow.
LEC-8, Erithro IV, Keto Caratenoids Red.
LEC-8, Iridiphor, Guanine platelets, Blue and Silver.
LEC-9 and 10.
Mammals and birds have only melanocytes.
Pattern complexity reflects palette size.
Fish and herps with the full four cell palette get an order of magnitude larger pattern phenotypes
face.
That asymmetry is going to come back when we hit Murray's Scaling role later.
Slide 9, TPS, Cell Stack.
Three organisms.
Emperor Angelfish.
Lepard.
Dark frog.
Pairs for each identify which chromato-4 types are involved and what stacking order.
90 seconds.
Talk to your neighbor.
The expected answers.
Emperor Angelfish.
Full palette.
Iridiphor, Guanine layer giving the blue.
Melanophor's stripe pattern on top.
Santa IV over yellow regions.
Stacking matters for the green where Santa IV and Iridiphor overlap.
Lepard.
Melanocytes only.
The spotted appearance comes entirely from spatial regulation of one cell type.
You melanin clumps in spot regions.
Dark frog.
Three layer chromato-4 unit from LEC-11.
The four on top.
Iridiphor middle.
Melanophor deep.
Here is the reveal.
The dark frog and the Emperor Angelfish use the same chromato-4 stack.
The leopard uses one cell type.
The cell palette doesn't predict the pattern.
The rules of cell placement do.
That is where Turing comes in.
Slide 10, two ways.
This is the conceptual heart of the lecture.
Two genuinely different developmental logics.
Both real.
Both operating in nature.
Three pattern.
Wulpert 1969.
The French flag model.
A morphogen is set up across a tissue.
Bicoid in flyambrias.
BMP in vertebrae limbs.
Cells read concentration like reading a thermometer and decide identity from where they sit.
Identity is positional.
Body coordinates map to color.
Examples.
Butterfly eye spots.
Fly bristles.
Vertebrae limb digits.
Cell organization.
During 1952, reaction diffusion.
Two diffusible signals couple.
Activator promotes itself plus the inhibitor.
Inhibitor diffuses faster.
Periodic instability emerges spontaneously.
There is no pre-existing map.
The pattern is the dynamics.
Examples.
Zebrafish stripes.
Jaguar rosettes.
Cichlid bars.
Real animals do both.
Different body regions can use different logic and the same animal.
A leopard's body is a touring canvas.
A leopard's face is positional information.
Today we tour the evidence for each.
Slide 11 condo angel fish.
This is the single most persuasive slide in the developmental biology side of the course.
Pomechanthus imparata.
The emperor angel fish.
As the fish grows, the number of stripes increases.
If stripes were a fixed pre-pattern, they would just spread apart as the body lengthens.
Instead, new stripes appear by branching.
Exactly what a touring simulation predicts.
Condo and Ause wrote down the equations and matched the stripes-facing dynamics quantitatively.
This is the proof that touring operates in a real animal.
Forty-three years after touring's 1952 paper proposed reaction diffusion.
The biology lagged the math by half a century.
Then the biology arrived.
Slide 12 cheetah cubs.
Cone is not a fixed image.
It is a developmental trajectory.
Cheetah cubs are born with a long-silvery dorsal mantle that obscures their spots.
The mantle fades over the first three months.
The adult phenotype emerges.
Same point applies to taper babies, lion cubs, wild boar piglets.
Stripes that fade with age.
A simple touring parameter set is unlikely to explain this.
There must be temporal modulation of the patterning machinery.
The bridge to the previous slide is intentional.
Condo just showed us pattern rearranging on a growing fish.
Cheetah cubs show pattern fading on a growing mammal.
Pattern is dynamic across the lifespan.
Slide 13.
Turing math.
Minute Earth.
The equations on screen are exactly Turing's 1952 reaction diffusion equations.
The cartoon explainer just walked us through the math.
Now let's see how those equations get extracted from real cells.
Number 14.
Cell rules.
Nakamasu at all 2009 used cell ablation in zebrafish to extract the actual cell interaction
rules.
Remove melanophores and defined regions.
Watch what happens to surrounding zanthophores.
Two rules.
Rule 1.
Short range.
Melanaphore and zanthophore repel each other.
Rule 2.
Long range.
Melanaphore promotes zanthophore survival via gap junctions.
Watanabe and Condo 2015 showed the long range channel is gap junction mediated.
The fronthofer 2013 zebrafish mutant figure.
Wild type at panel A full stripes.
Panel C through F. Iridiform mutants RSE and Shud.
Stripes break up into spots.
Same Turing system.
One gene perturbed.
Spots not stripes.
The leopard zebrafish story.
Watanabe 2006 is the same logic with a different gene.
The next in 41.8.
The pedagogical point is not the math.
It is this.
Cells follow simple local rules.
A single gene change alters the rules.
The global pattern reorganizes.
That is Turing flavor evo-devo in one slide.
Slide 15.
Cell migration video.
Watch the cells move.
Black cells are melanophores, moving by a me-boyd motility.
Yellow cells are zanthophores, filling the spaces.
They repel each other on contact.
They sustain each other at distance through gap junctions.
After hundreds of cell cell interactions, stripes emerge.
There is no master plan.
No coordinate system.
Just thousands of cells executing two interaction rules.
The pattern is what emerges when the rules run to equilibrium.
LEC 11 callback.
Last week we met chromatophores as the units of color.
Today we are seeing them as the units of pattern.
Cells 2 functional roles.
Slide 16.
Labyrinth intuition.
Why a labyrinth?
Every white wiggle is a high activator pocket.
A region of cells locked into one state.
Around each wiggle, a faster spreading inhibitor keeps neighbors at bay.
Three local rules produce the labyrinth.
One.
Activator self promotes.
Wiggle tips can extend.
Two.
Inhibitor diffuses faster.
Wiggles can't merge.
Three.
Tips bend away from other tips.
Wiggles snake and branch instead of straightening and stripes.
The parameter knob.
Tweak the diffusion ratio.
Ratio up stripes.
Middle labyrinth.
Ratio down spots.
Same equations.
Three different patterns.
No map.
No designer.
Just chemistry.
This exact labyrinth zone is where every spotted by inverse spotted, salmoned hybrid
lands.
Once a parent at one end of parameter space with a parent at the other end.
The F1 sits in the labyrinth zone in between.
We will see it Tuesday.
Slide 17.
Murray scaling.
A teaser.
Tuesday we go deeper.
Today the punchline.
Mouse uniform.
Body too small for one wavelength.
Cheetah spots.
Lepard rosettes.
Tiger stripes.
Elephant uniform.
Too large.
Body damps.
Same touring equation.
Body size is the boundary condition.
James Murray showed this with a single equation in 1981.
The bonus fact.
Spotted cuts can have striped tails.
But striped cuts never have spotted tails.
Cheetahs have stripes on the tail tip.
Tigers don't have spots.
The model predicts this.
At the small diameter of a tail, the same activator inhibitor dynamics produce stripes
by default.
LEC 11 callback.
This is mostly a mammal story because mammals have only one chromatofore type.
The same scaling rule applied to fish or herp would be cleaner if the cell palette weren't
already adding pattern dimensions.
Slide 18.
I spots.
The alternative logic to touring.
Bicyclus and inana.
Wing I spots.
The focal cell.
A small group of cells in the late wing disc.
Secreta morphogen.
Surrounding cells read the gradient and decide their identity from where they sit.
Concentric pigment rings.
That is positional information in the strict sense.
The experimental punchline is striking.
Breakfield, Carol.
Bell-Dade transplant experiments.
Take a fragment of larval wing disc containing the focal cells.
Graphed it to a new location on another wing.
An ectopic eye spot appears centered on the graft.
The eye spot is positionally specified by the focal cells.
The connection to mechanism layers is nontrivial.
The rings of an eye spot are not monochromatic.
The inner black ring is melanin LEC 8.
The outer rings often involve structural color, LEC 9 and 10.
So an eye spot is positional information saying where to put rings, plus mechanism saying
how each ring colors itself.
Both lecture stack.
Same animal class as zebrafish.
Completely different developmental logic.
Slide 19, Mimulus.
Plant petal patterns are nearly always walt-pert.
Plants don't have migrating cells.
Anthosine and biosynthesis is decided locally, positioned by position, based on transcription
factor gradients of MYB, BCHLH and WD40 proteins.
Animals migrate cells so they can self-organize.
Plants don't migrate cells so they can't.
The Mimulus Luicyye, the bumblebee pollinated monkey flower.
The bullseye.
In VUV vision, LEC 6 callback, the center is darker.
UV absorbing anthosine.
The periphery is brighter.
The bullseye is invisible to humans, but obvious to a foraging bee.
Pollinator vision sets the receiver context for plant pattern.
Pattern plus receiver equals signal.
That is next week.
Slide 20 synthesis.
!
Turing.
Local rules.
Periodic output.
Zebrafish, Sicklid, Jaguar, C-shell.
Pre-pattern on the right.
Walt-pert.
Gradient.
Positional readout.
Butterfly icepot.
Feather barbule.
Vertibrate digit.
Most real animals use both in different body regions.
The same animal can be touring on the body and Walt-pert on the face.
Slide 21.
Project TPS.
Pull up the fish photo you've chosen for the project.
Three minutes with your neighbor.
Three questions.
One cell palette.
Which chromatophore types are present?
Eradessent blue means iridipore.
Matt-black means melanophore dominant.
Saturated red means erytherphore.
Two, Patterning Rule.
Does the pattern look more positional with specific markings that specific locations
or self-organized with periodic stripes or spots?
Three, one testable prediction.
If you knocked out melanophore's anthropore communication, what would change?
The project framing is now structured.
Three questions.
Every fish.
Every time.
Bring your answers to Lab Wednesday.
They will seed the project right up.
Slide 22.
Looking ahead.
Tuesday.
Five threats.
Pattern blending.
Mia's always hybrid salmonates.
Murray's Scaling Rule.
Full version.
With the Cheetah Tail prediction.
Evodivo, Heliconius, Master Regulators, W and T.A. Optics, Double Sex.
Single gene flips.
Aguda, Leopard, ALX3.
Bridge to function.
Same patterns.
Three different jobs.
Entrance ticket Tuesday.
Predict the F1 hybrid pattern from two salmated parents.
Bring your intuition.
We will test it.
Slide 23.
Exit ticket.
Three options.
Pick one.
Could a butterfly icepot form by a turn dynamics?
Why or why not?
The could a zebrafish stripe form by a positional information?
Why or why not?
See Pick One organism from today and identify its cell palette and likely patterning rule.
Submit on Bruin Learn before midnight.
The framework you used in the project TPS is the framework you will use for the rest
of the unit.
Today we made the move from mechanism to arrangement.
Tuesday we go from arrangement to evolution.
See you Tuesday.