How Do We Prove the Gene Causes It?
How can a scientist prove that losing IRF6 causes clefting, instead of just appearing alongside it?
💡 When removing a gene breaks the process AND restoring it fixes the process, the gene is a cause, not a bystander; this is how the field proved IRF6 loss causes clefting.
Prerequisite check
- The is the sheet of cells covering surfaces; its outermost layer is the , a non-stick protective coating.
- is a cell maturing into a specialized type that does a specific job.
What you will learn
Goal: Use the logic of model-organism knockouts and rescue experiments to argue that IRF6 loss causes clefting rather than merely correlating with it.
- A is an animal studied to learn about a human process; mice and zebrafish are the workhorses for clefting.
- A is an animal with a chosen gene deliberately switched off, compared against a normal wild-type animal.
- Correlation means two things happen together; causation means one actually makes the other happen.
- A puts the gene back: if removing X breaks the process and restoring X fixes it, X is a cause.
Model: Knockout versus wild-type, then the rescue experiment
Scientists make a , an animal with a gene deliberately switched off, and compare it to a normal wild-type animal. For IRF6 the results line up across two species. A wild-type mouse differentiates its , fuses its , and lives; an Irf6-knockout mouse fails to form periderm, develops a palate with oral and skin adhesions, and dies perinatally. A wild-type zebrafish has a normal neurocranium (the fish analog) and mouth; an irf6-knockout zebrafish has a cleft of the anterior neurocranium and a cleft-like mouth, with the target esrp1 dropping about 80%. The same gene, knocked out in a mouse and in a fish whose ancestor we shared long ago, produces a cleft in both.
The closing argument is the : put the gene back and see if the goes away. In zebrafish, injecting normal irf6 mRNA into irf6-null embryos restored esrp1 and rescued the cleft. In mouse, re-expressing Irf6 partially rescued: the pups survived and skin adhesions resolved, though the cleft persisted because IRF6 was not restored in the cells themselves.
Explore (work the model before reading on)
- What is the difference between a and a wild-type animal?
- What did injecting irf6 mRNA back into the zebrafish do to (a) esrp1 and (b) the ?
- The same gene knocked out in mouse AND fish causes a in both. Why is matching the result across two distant species stronger than one species alone?
- Explain in your own words why the rescue step (putting the gene back) is what lets scientists claim cause rather than just "these two things happen together."
- The mouse rescue was only partial: the stayed because IRF6 was not restored in the . Does a partial rescue weaken or strengthen the claim that IRF6 acts in the periderm? Explain.
Guided notes
The trap and the two-step proof
- Step one, : remove IRF6, and the ____ in both mouse and zebrafish.
- Step two, rescue: put IRF6 back, and the is ____ (fully in fish, partly in mouse).
- When removing a gene breaks the process AND restoring it fixes the process, the gene is a ____.
Why cross-species matters
- Matching the result in two distant species (mouse and ____) is stronger than one species alone.
- The partial mouse rescue, where the stayed because IRF6 was missing from the , ____ (strengthens / weakens) the claim that IRF6 acts in the periderm.
Reading the Research
- Skim the title and abstract first to get the gist.
- Circle the one sentence that states the main claim.
- Box the evidence the authors give for that claim.
- Mark one sentence that confuses you, and move on.
Track your progress today
Check these off as you work through the lesson, then submit. This tells Mr. Mendoza how you're doing so he can help the class. It does not replace turning in your producible.
Use the code Mr. Mendoza gave you, not your name. Saved on this device.
- Read the Model and answered the Explore questions.
- Filled in the guided notes in my own words.
- Defined the new vocabulary with an example.
- Built the producible: A classmate argues: "Mateo has an IRF6 variant and a cleft, so IRF6 must cause his cleft." As the model researcher, write a two-part reply: (1) name what is missing from that argument (correlation vs causation), and (2) describe the knockout-then-rescue experiment in an animal that would actually test it.
- Wrote my Claim, Evidence, and Reasoning exit ticket.
Exit ticket (Claim, Evidence, Reasoning)
- Claim: Losing IRF6 causes clefting (agree or disagree).
- Evidence: In the , removing IRF6 made the ____ in mouse and fish; in the rescue, restoring IRF6 ____ the cleft.
- Reasoning: The remove-then-restore logic proves cause and not just correlation, because ____.
| Criterion | Proficient | Developing | Beginning |
|---|---|---|---|
| Complete | Every required part of the artifact is present and filled in. | Most parts are present, but one is missing or left blank. | Several parts are missing. |
| Accurate | The science and data are correct and match the evidence. | Mostly correct, with a small factual slip. | Key science or data is wrong. |
| Scientific reasoning (CER) | States a claim, backs it with specific evidence, and explains the reasoning. | Has a claim and evidence, but the reasoning is thin or missing. | Gives an answer with no evidence or reasoning. |
| Professional communication | Clear, organized, and labeled the way a clinician or scientist would write it. | Readable but disorganized or missing labels. | Hard to follow. |
| Submitted | Turned in the right way (Schoology for routine work) and confirmed. | Turned in, but in the wrong place or unconfirmed. | Not turned in. |
- CompleteProficient: Nothing is left blank: the model fills every part of "A classmate argues: "Mateo has an IRF6 variant and a cleft, so IRF6 must cause his cleft." As the model researcher, write a two-part reply: (1) name what is missing from that argument (correlation vs causation), and (2) describe the knockout-then-rescue experiment in an animal that would actually test it.".
- AccurateProficient: Every number and claim matches the case evidence.
- Scientific reasoning (CER)Proficient: It names a claim, cites the specific evidence, and explains the reasoning, not just the answer.
- Professional communicationProficient: It is organized and labeled like a real chart note.
- SubmittedProficient: It would be turned in on Schoology and confirmed.
Where this leads: careers
What's next: We proved IRF6 loss causes clefting using and rescue in mouse and zebrafish, so we now understand how the happens in one . But why is cleft lip and far more common in some human populations than in others? We chase that next, when the population geneticist takes the seat.