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Secrets of life text organization (in flux)
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I. |
Introduction: Why understanding biology matters to you
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A) |
Modern medicine
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1] |
What is disease
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Genetic
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Invaders
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2] |
What are drugs and where do they come from
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3] |
What are the consequences of releasing drugs into the environment
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4] |
What are ‘stem cells’ and what hopes and risks do they present?
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B) |
We know the code; we have the power to design
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1] |
GMO
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2] |
Causing & reversing extinctions
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3] |
Modifying humans
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C) |
Decisions about resources and the environment
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1] |
pesticides, glyphosate
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2] |
GMOs: frankenstein’s monster or corn?
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3] |
hormones in rivers
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4] |
Our influence on the climate
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the Anthropocene
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5] |
Our influence on ecosystems
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II. |
Ways of knowing: the scientific approach (introduce periodic table?)
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A) |
From patterns to predictions
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1] |
How we know: origins & meaning of the periodic table
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Author guidance
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2] |
Interesting tidbit: a language that acknowledges certainty grammatically
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“Grammatical evidentiality may be expressed in different forms (depending on the language), such as through affixes, clitics, or particles. For example, Eastern Pomo has four evidential suffixes that are added to verbs, -ink’e (nonvisual sensory), -ine (inferential), -·le (hearsay), -ya (direct knowledge). Evidentials in Eastern Pomo Evidential type Example verb Gloss nonvisual sensory pʰa·békʰ-ink’e "burned" [speaker felt the sensation] inferential pʰa·bék-ine "must have burned" [speaker saw circumstantial evidence] hearsay (reportative) pʰa·békʰ-·le "burned, they say" [speaker is reporting what was told] direct knowledge pʰa·bék-a "burned" [speaker has direct evidence, probably visual] (McLendon 2003)”
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3] |
Tidbit: Feynman speech (cited on Wikipedia)
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In the South Seas there is a cargo cult of people. During the war they saw airplanes land with lots of good materials, and they want the same thing to happen now. So they've arranged to imitate things like runways, to put fires along the sides of the runways, to make a wooden hut for a man to sit in, with two wooden pieces on his head like headphones and bars of bamboo sticking out like antennas—he's the controller—and they wait for the airplanes to land. They're doing everything right. The form is perfect. It looks exactly the way it looked before. But it doesn't work. No airplanes land. So I call these things cargo cult science, because they follow all the apparent precepts and forms of scientific investigation, but they're missing something essential, because the planes don't land.
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B) |
Scurvy and vitamin C
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C) |
John Snow and the pump handle
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D) |
Biology’s guiding hand: evolution
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1] |
“Nothing in biology makes sense except in the light of evolution”—Theodosius Dobzhansky
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2] |
Mayr’s summary of Darwin
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3] |
Does the theory of evolution make predictions?
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Where the theory comes from
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Written in your DNA
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JBS Haldane: Rabbits in the precambrian
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E) |
Comings and goings of red-green vision? (alt: put in evolution)
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F) |
The price of ignoring it
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III. |
Life in the Molecular World
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A) |
Building blocks: atoms & the Periodic Table
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1] |
Discovery, predictions, tests (History of table if not in II)
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2] |
Electrons in shells
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3] |
bonds as e- sharing: equal and unequal
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B) |
Putting atoms together: molecules
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C) |
Figuring out surfaces
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1] |
BaseChar (example of interactive; simpler version using simpler molecules will be used here)
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D) |
Water, water everywhere
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1] |
Tidbit (Bee in a Cathedral): if water did not hydrogen bond, it would boil @ -90˚C
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2] |
Tidbit: Average speed of water molecule @ room temp: 650m/s
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3] |
Try it yourself
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stale bread, wet bread
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floating a staple
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pepper & detergent
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4] |
Video demo:
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E) |
Oil: the anti-water
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1] |
Uses: fencing in cells with membranes
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???? Does this go here??? two kinds of cells: prokaryotes and eukaryotes
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Endosymbiosis: don’t steal FROM your neighbor; kidnap your neighbor
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Author guidance (it’s a subheading)
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IV. |
Proteins: Life’s Machines
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A) |
Parts list: the amino acids
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1] |
Image (I created with Frieda Reichsmann)
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2] |
Special properties of different pieces
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Author guide
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Gly, Pro, hydrophobes, charges, His, Cys
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Try it yourself: pH sensing histidine (miraculin, lemons)
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3] |
Stringing together: protein
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4] |
A string of beads in water: folding
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5] |
Movie: folding simulation
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6] |
Exercise: 2D folding
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B) |
INTERACTIVE: Hemoglobin a carrying machine that is a string of amino acids
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1] |
Introduction
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hydrophobic inside
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Amino acids ‘talking’ to each other
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2] |
How machines move & change
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complementary sidechains
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two shapes with different connections
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3] |
Nuts and bolts: Hemoglobin & pH in lungs vs tissues
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Histidine revisited: a very special amino acid
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V. |
Inside a working machine: ATPase
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A) |
Author guide & resources
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B) |
How the cell pays for things: ATP
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1] |
Where’s the ‘energy’ in ATP?
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Big idea: negative charges held together
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C) |
Why doesn’t ATP explode instantly all the time??
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1] |
the ins and outs of a chemical reaction
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2] |
Barriers 1: the unlikely approach of water
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3] |
Barriers 2: the discomfort of planar oxygens
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examples: you make YOUR fingers planar (video)
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D) |
Enzymes makes it easy
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1] |
If anything gets easier… you’re an enzyme
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E) |
Case study: power through understanding a machine => Gleevec
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VI. |
DNA and RNA: Life’s Instructions
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A) |
Learning goals
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1] |
Concepts
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Each of four units chemically ‘sticks’ to one other
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No machine or intelligence is required to make/detect the match
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2] |
Consequences
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A sequence of nucleotides creates a unique chemical surface… matched by the surface of a string of partners
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By ‘viewing’ a number of variant sequences, we can quickly determine exactly which human being’s DNA we have
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Everyone is a ‘living fossil’: a collection of ‘edits’ to instructions that have been handed down since life began
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3] |
Applications
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Nature (and now we) can build machines that target specific genes and even specific gene variants
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Analyze crime scene DNA find out who was there
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Determine paternity
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Trace the origin of populations, genes and even organelles (mitochondria are captured bacteria)
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B) |
Core values: doing, copying
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1] |
Action, organization, reproduction
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C) |
How can molecules ‘mean’ something?
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1] |
embedded video: operating the BasePairer tool
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2] |
(embedded task: ‘decorating’ the pairs)
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E) |
DNA from RNA: a fossil in your cells
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1] |
Two changes; two improvements
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Author guidance; resources
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2] |
Set up for Origins of Life
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F) |
End chapter questions
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1] |
parts of a base
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2] |
Chapter review interactive:
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3] |
complementary structure
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4] |
complementary sequence
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VII. |
Making machines from instructions
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A) |
Author guide
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B) |
Changing languages: translating nucleotides to amino acids
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1] |
Interactive exercise: building a shape from coded pieces (needs programming; functional, complete example exists)
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C) |
The code comes in pieces: synthetases
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REMAKE to more clearly indicate specificity at the basepairing end; show TWO to indicate the aa matching; de-emphasize ATP
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D) |
Interactive: translating (evolve from existing Info_Flow)
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E) |
Change the instructions, change the machine
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1] |
If meaning is partnering, changing partners changes meaning
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embedded task: comparing tautomers
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embedded questions: would X pair like Y?
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2] |
Sickle cell anemia: a genetic disease
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One nucleotide => one amino acid (we’ll see how in next chapter)
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Change a property, change function
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VIII. |
(Tools of the trade: molecular biology & research)
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A) |
PCR as DNA replication
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B) |
Cloning: co-opting bacterial self-defense
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C) |
(CRISPR-Cas9 currently in DNA chapter)
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D) |
Antibodies: matching DNA is easy; matching proteins is a crapshoot (literally)
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IX. |
Your ancestors live on
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A) |
You are the instructions that made your parents… and their parents… and
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B) |
Mutations accumulate over time (silent, good, and ill)
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Just as you are ‘more related’ to your immediate family, so also to your ‘branch’ on the Tree of Life
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C) |
# mutations ~= amount of time
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D) |
# differences ~= degree of relatedness
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E) |
Examples: surprises, findings
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Tidbit: phylogenetic analysis has been used to reconstruct Chaucer
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2] |
elephant shrew is an elephant
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whales are hippo cousins
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4] |
Tree of brewing yeasts
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X. |
Genes: instructions + control
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A) |
Author guidance; materials
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B) |
‘Reading’ basepairs
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1] |
major groove
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2] |
exposed information and proteins that read it
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C) |
(A simple example: E. coli decides to eat lactose)
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D) |
One pathway to rule them all: mammalian coloration
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1] |
Lava and sand: colored rats
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E) |
Where human traits come from: our (recent) evolutionary history
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1] |
Evolution happens to us
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2] |
Blue eyes
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Don’t it make your brown eyes blue
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One pathway, many outcomes (hair, skin, eyes)
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Genes: instructions, controls
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Blue eyes are broken brown eyes
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Foreshadowing: dominance
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How do we know what happened? DNA sequencing
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Origins
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Deduction: all the same
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3] |
Drinking milk
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Origins
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It didn’t used to be that way (lactose unique to infant/milk diet)
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Domestication: cows & camels convert grass to never-spoiling milk & meat
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Multiple origins: the sequence changes
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Resources: HHMI
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4] |
Hemoglobin again: Baby-as-parasite: taking oxygen from mom
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BPG: another story (molecule interactions re-visited)
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Where new things come from: copy and change
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Control: a progression of Hemoglobinopathies
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XI. |
Footprints in the sand: what does life today tell us about life’s beginnings?
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A) |
chicken-and-egg
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a way out: today’s intermediate is yesterday’s entire story
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B) |
biochemical fossils: biosynthetic pathways, cofactors, ATP
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C) |
Review: from RNA, DNA
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D) |
experiments demonstrate we’re hot on (a) trail
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XII. |
Modifying life I: We Made This (human selection)
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A) |
What Darwin law
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B) |
Brassicaceaae
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1] |
cabbage-cauliflower-brussels sprouts-broccoli-kohlrabi-kale
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C) |
Corn
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1] |
From small things baby, big things one day come
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D) |
dogs/pigeons?
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1] |
Darwin was a pigeon fancier before he (failed to) notice the finches
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E) |
The Galapagos turtles
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F) |
A pictorial tour of what we have wrought
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1] |
flowers, fruits, vegetables, grains, dogs, cats, horses, cattle (any of the options above)
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G) |
Beyond the tip of the iceberg: short-legged dogs—different branches on the same tree?!?
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1] |
Author resources
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XIII. |
Modifying life II: Evolution
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A) |
Principle: Blind Watchmaker (Dawkins book) version of Info_Flow (interactive animation I created for translation that could combine powerfully to demo evolution of ‘proteins’)
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B) |
limbs (divergent evolution)
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1] |
Wings: bird-bat-pteranadon
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2] |
Bat vs. mouse
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Public domain 
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C) |
eyes I: how hard to make them?
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1] |
multiple origins (60+?)
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D) |
eyes II: (divergent evolution) all manner of eyes
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we still see ‘primitive’ forms; these indicate a plausible path, but are NOT a path
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2] |
primitive form may be well-suited; not ‘becoming’ (sharks, Nautilus)
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E) |
eyes III: (convergent evolution): human & squid eye
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F) |
eyes IV: the comings & goings of color vision
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XIV. |
Modifying life III: Designer genes, designer organisms
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A) |
What we know: sequencing whole genomes
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B) |
(What we know: model organisms & their importance?)
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C) |
The toolkit: sneaking into mother nature's toolshed biological processes
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1] |
scissors and glue: restriction enzymes (Bacterial self-defense) & ligase
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2] |
xeroxing: PCR (basepairing and machines re-visited)
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3] |
getting fancy, getting newsworthy: CRISPR-Cas9
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D) |
Ian: “Your scientists were so preoccupied with whether or not they could, they didn’t stop to think if they should.” —Jurassic park
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1] |
implications, history of eugenics
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2] |
some promising approaches, successes vs. genetic disease
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3] |
approaches to malaria
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4] |
ivermectin: miracle… with a price
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E) |
Decisions: Taking pregnancies to term
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F) |
Decisions: Knowledge of diseases we cannot treat
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XV. |
The Big Picture: Cells
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A) |
Compartments: a place for everything and everything in its place
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1] |
The other guys: prokaryotes—special skills for special lifestyles
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B) |
Deductions and history: symbiosis and mitochondria (chloroplasts?)
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C) |
How cells eat: the lysosome
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1] |
Inside vs. outside: cells have stomachs too
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Compartmentalization re-visited: a bathroom is a good thing
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2] |
Trojan horse: How the flu gets into you (pH re-visited; protein machine function re-visited)
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Author guidance & resources
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XVI. |
Making & sharing copies: the essence of life
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A) |
Copying the instructions
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1] |
The importance of “copyability”
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2] |
basepairing re-visited
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B) |
A copy for everyone (Mitosis)
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C) |
Coping the organism (Meiosis)
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1] |
Why does sex exist?
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2] |
How we know: Mendel, biological scientist
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3] |
Interactive exercise: From phenotype, genotype
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4] |
Interactive exercise: deductions from pedigrees
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XVII. |
Organizing & Diversifying: Development
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A) |
Principles: blueprints, instructions, recipes
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1] |
Dawkins: recipe is better, because the ticker tape of DNA bears no direct to outcome
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The role of genes is often more subtle and more distributed than a part
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A change in recipe can have broad and non-obvious consequences
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B) |
Bodyplan for a fly what happens; how we know
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C) |
Great experiments
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1] |
Author guide
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XVIII. |
Energy from sugar; energy from the sun
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A) |
Taking on fuel (sugar)
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1] |
Author guide: TCA cycle
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B) |
Resources
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C) |
Energetic electrons: electron transport in photosynthesis and respiration
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1] |
Energizing electrons with sunlight
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2] |
harvesting “already peppy” electrons from glucose
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3] |
PARALLELS: in photosynthesis & respiration, electrons pump protons
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4] |
Protons flow back through a wonderful millwheel, slamming ATP back together again
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XIX. |
(The human condition: diseases from within & without) should this be distributed or collected?
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A) |
(Hemoglobin: distribute to proteins)
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B) |
(Flu: distribute to pH/organelles/protein structure-function)
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C) |
(Gleevec: distribute to protein structure-function? Or here under modern-molecular medicine?
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D) |
River blindness/ivermectin: here, or under ecology?
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1] |
Great benefit; unknown cost
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E) |
Malaria: with hemoglobin & with genetic engineering
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1] |
Natures answers: sickle cell anemia (5x or more), Duffy
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2] |
Our answers: sterile males; CRISPR adjustments
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F) |
Pesticides & bee hive deaths
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XX. |
The biggest picture: Ecosystems & Climate
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A) |
Comings & goings: mass extinctions and their causes
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1] |
Pieces of the puzzle: how we assemble & interpret the evidence
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B) |
What is diversity and why does it matter?
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C) |
Balances and cycles: webs of interaction
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1] |
Imbalance and consequence: red tides, algal blooms, rabbits in Australia, kudzu
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2] |
The list: invasive species
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Rats and pigs everywhere
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Mussels in the Great Lakes
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Asian carp
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Kudzu
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XXI. |
Other lifestyles & dependencies: relationships
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A) |
Parasites
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1] |
fascinating interactions: parasite-driven behavioral modifications
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2] |
Muliple forms (parallels to insects, amphibians that have distinctly different lifestyle choices @ different stages)
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B) |
Friends
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1] |
nitrogen fixing bacteria
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2] |
lichens
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Recent breakthrough: there’s a yeast too!
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3] |
endosymbiosis (revisited?)
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XXII. |
Drugs: first from nature; now from design
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A) |
Willow bark is aspirin
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B) |
Animals taking ‘drugs’
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1] |
flamingo coloration
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2] |
caterpillar chemical defenses (monarch)
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XXIII. |
Here and now: what’s happening to earth’s climate
|
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|
A) |
Pieces of the puzzle: how we assemble & interpret the evidence
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B) |
It’s happened before: The Great Dying
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XXIV. |
Footprints: humans were here (Pick best examples)
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|
A) |
Extinctions of dodo
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|
B) |
Ivory & elephants
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|
C) |
North American megafauna?
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D) |
Unspoiled places
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E) |
The giant Pacific garbage patch
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F) |
pollutants in (Antarctica?)
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G) |
Space junk
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XXV. |
***Appendix The “WetList”: suggested experiments for lab or home interactions
|
|
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|
A) |
miraculin tablets
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|
1] |
|
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|
C) |
isopropanol
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D) |
Beet powder
|
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E) |
PTC test strip
|
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|
|
2] |
DNA test reagents (PCR machine required)
|
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|
F) |
Pedigree pagesfor common family traits—PTC, earlobe, eye color (some research needed to verify these)
|
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XXVI. |
Other: The Long View: Nth generation targets for the eBook
|
|
|
|
A) |
If javascript + jsMol, we’re ready for all the 3D functionality Gen. 1
|
|
|
|
B) |
Creation of programmatically simple, lightweight interactive exercises
|
|
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|
1] |
pedigree solver
|
|
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|
2] |
Gamete-maker
|
|
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|
3] |
meiosis deducer
|
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|
4] |
translation interactive
|
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|
5] |
Flower evolver
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|
6] |
Principles of evolution
|
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|
7] |
Aligning sequences & deducing
|
|
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|
C) |
Incorporate widgets a laBookry.com? At their heart, these are
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D) |
Random questions drawn from a subset?
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|
1] |
Related: each user gets account and code. Problems are sent to top hat servers, then to an app that generates a problem with answer secretly matched to top hat code
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