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L03 — The Code Breakers

Module: M08 — Secrets in the Rocks Periods: 1 (53 minutes) NGSS: HS-LS4-1, HS-LS4-3 Lesson Type: Explain / Elaborate

Learning Objective

  • By the end of this lesson, students will be able to explain how DNA and protein sequence comparisons provide evidence for evolution by calculating genetic similarities and constructing a simple molecular clock model.

Phenomenon / Hook

Cold Case #3: “We’ve analyzed Lyuba’s bones and anatomy. Now we analyze her blood. Frozen for 40,000 years, mammoth DNA is still intact enough to sequence. When we compare mammoth DNA to elephant DNA… they’re 99% similar. What does that number tell us? And how can genetic code be a clock that tells us how long ago two species diverged?”

Pose the question: “If you had two books with nearly identical text, what would that tell you about their relationship? Is it the same with DNA?”

Materials

  • Projector for mammoth/elephant DNA comparison image
  • Chromebooks or printed sequences: [[resources/handouts/M08-L03-cytochrome-c-sequences]] (or digital access to NCBI)
  • [[resources/handouts/M08-L03-molecular-clock-activity]]
  • Calculators (one per pair)
  • Printed or digital: [[resources/handouts/M08-L03-similarity-data-table]] (DNA and protein similarities across species)
  • [[assessments/exit-tickets/L03-exit-ticket]]

Agenda

Opening (7 min)

  • Show mammoth/elephant DNA comparison image (2 min)
  • Think-Pair-Share: “If two species have DNA sequences that are 99% identical, what does that suggest about their relationship? What might explain the 1% difference?” (3 min)
  • Introduce concept: DNA as inherited code — changes accumulate over time (2 min)

Explore (20 min)

  • Part A: Cytochrome C Comparison (10 min)

    • Distribute cytochrome c amino acid sequences for 5–6 species (human, chimp, horse, tuna, wheat, yeast)
    • Students compare positions and count differences from human sequence
    • Create a simple similarity matrix: species vs. % identity to human
    • Guiding questions:
      1. Which species is most similar to humans? Least similar?
      2. Is the pattern consistent with what you know from anatomy? (e.g., chimp = closest, yeast = most distant)
      3. Why would a chimp and a human share more cytochrome c with each other than either does with yeast?
    • Discussion: “The pattern of molecular similarity matches the pattern of anatomical similarity — both tell the same evolutionary story.”

  • Part B: Molecular Clock Activity (10 min)

    • Introduce molecular clock concept: mutations accumulate at roughly constant rates → differences ∝ time since divergence
    • Given: Human-chimp cytochrome c = 0 differences. Human-horse = 12 differences. Assumed divergence time: human-horse = 60 million years ago.
    • Students calculate: If 12 differences = 60 million years, how many million years per difference?
    • Apply: If human-tuna = 18 differences, how long ago did the human-tuna lineage split?
    • Check: paleontology says ~400 million years for fish-tetrapod split. Is this close?
    • Emphasize: Molecular clocks are estimates, not exact measurements. Multiple clocks (different genes) are used for different timescales.

Explain (10 min)

  • Class synthesis:
    • DNA/protein similarities reflect shared ancestry: More similar = more recent common ancestor
    • Molecular clock: Genetic differences accumulate over time at roughly predictable rates
    • Mammoth confirmation: 99% DNA similarity to elephants suggests they share a recent common ancestor — the molecular clock puts this split at ~6 million years ago
    • Why 99%, not 100%: Mutations happen. Over 6 million years and many generations, mutations accumulate. Each mutation is a “tick” on the molecular clock.
    • Connecting all evidence: “Fossils show us what changed. Anatomy shows us how structures changed. DNA shows us exactly how similar we are at the most fundamental level. All three tell the same story.”

Elaborate (10 min)

  • Mini-Inquiry: “If you discovered a new species tomorrow, what molecular data would you collect to figure out where it fits in the evolutionary tree? How would you decide which genes to compare?”
  • Discuss: Ribosomal RNA (conserved), mitochondrial DNA (faster mutation rate), cytochrome c (moderate)
  • Preview L04: “Today we looked at genetic code. Tomorrow we look at something even more fundamental — development. How do organisms build themselves from a single cell?”

Closing (5 min)

  • Exit Ticket: [[assessments/exit-tickets/L03-exit-ticket]]
    1. Explain why the similarity of DNA sequences between two species provides evidence for evolution.
    2. If species A and species B have more similar DNA than species A and species C, what does that suggest about their evolutionary relationships?

Differentiation

SupportExtension
Provide a partially completed similarity matrix with some values filled inIndependent research: Find one example of a “molecular clock” study that changed our understanding of when two species diverged. Present to class.
Give a worked example: “If 10 differences = 50 million years, then each difference = 5 million years”Challenge: Design an experiment to test whether the molecular clock runs at the same rate in all organisms. What would you measure?

Assessment

  • Formative: Check similarity matrix calculations — are students correctly counting differences and interpreting patterns?
  • Exit Ticket: Understanding of DNA evidence and molecular clock logic

Teacher Notes

  • Tech note: If Chromebooks are limited, use the printed cytochrome c sequences — the activity works well with paper.
  • The 99% mammoth number: It’s approximately correct. Mammoth-elephant divergence is estimated at 6–7 million years. Use this as a specific anchor.
  • Molecular clock limitations: Stress that clocks are estimates. Different genes evolve at different rates. Fossil evidence is needed to calibrate the clock.
  • Bridge to L04: Embryology is sometimes considered “the fourth line” of evidence. It’s also the most visually striking — students are often surprised by vertebrate embryo similarities.