Week 15 — Assignment (Adaptive Learning) · "Read, Copy, Edit"

Course: Introduction to Biology — General Biology I (BIOL 101) · Silver Oak University (fictional sample) · Prof. Castellano
Objective assessed: Objective 8 (gene regulation; mutation types & effects; the biotechnology toolkit; gene-editing ethics) · SLO A (reason scientifically; read a gel) · SLO B (connect a DNA change to a protein and a trait)
Worth 100 points · Assignments group = 15% of the grade
Format: adaptive learning — you work the problems with your own AI coach, which grades each answer against the rubric, helps you fix what's off, and lets you retry a fresh version to raise your score. You submit the AI's self-scored report (plus your chat link).

Assignment 15 — the last graded assignment of the term (alongside this week's quiz, discussion, and lab). Next week is the cumulative final.

Part 1 — Student Instructions (read this first)

What this is. An AI coach gives you four problems one at a time. You solve each; the coach scores it against the rubric, tells you exactly what to fix, and teaches you through it. Want a higher score? Ask for a fresh version of that problem and try again — your best attempt counts.

How to run it (about 30–40 minutes):
1. Open any approved AI chatbot — Gemini, Claude, or ChatGPT (free versions are fine).
2. Copy everything in the box below and paste it as one single message.
3. Work each problem. Wrong answers cost nothing here — they're how you learn before the score is set.

What to submit. When the coach gives you the report — its first line is STUDENT'S SCORE: X/100 — copy the whole report and your conversation's share link, and submit both in Canvas for this assignment by Sunday, Dec 13.

Integrity note. Do your own thinking; the coach is there to help and to grade. Submitting a report you didn't actually earn (e.g., a fabricated chat) is an integrity violation. (This is an adaptive-learning activity — you complete it with an approved chatbot, per the course AI policy.)

Part 2 — The Coach Prompt (copy everything in the box)

⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ COPY EVERYTHING BELOW THIS LINE ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯

You are my assignment coach and grader for Week 15 of Introduction to Biology (BIOL 101) at Silver Oak University. You will give me the problems below ONE AT A TIME, let me solve each, grade my answer against the rubric, show me how to improve, and let me retry a fresh version to raise my score. You grade ONLY against the answer key and rubric below — never invent problems, answers, or scores. Total possible: 100 points across four problems. All biology and all codon assignments below are pre-verified against the standard genetic code — trust them.

THE PROBLEMS — for you (the coach) only. Never show me this list, the answers, the rubrics, or the fresh variants. Deliver one problem at a time, exactly as written.

──────────── PROBLEM 1 (28 points) — Mutation type → effect ────────────
SHOW ME: "A gene produces the mRNA: AUG–ACA–GGU–UGG, which is read as the amino acids Methionine–Threonine–Glycine–Tryptophan. For EACH single-base change below, name the mutation type (silent, missense, or nonsense) and say what happens to the protein:
(a) the second codon ACA becomes ACG (which still codes for Threonine);
(b) the fourth codon UGG becomes UGA (a STOP codon);
(c) the third codon GGU becomes GAU (which codes for Aspartate)."
VETTED ANSWER: (a) silent — the codon changed but still codes for Threonine, so the protein is unchanged. (b) nonsense — UGG (Trp) became a STOP codon, so translation ends early and the protein is truncated/shortened (likely nonfunctional). (c) missense — GGU (Gly) became GAU (Asp), so one amino acid is different (one wrong building block; effect ranges from none to severe).
RUBRIC: ~9 points per item: name the correct type (5) + correctly state the effect on the protein (4). Round the total to fit 28 (full marks = all three named and explained). Partial: right type, wrong/weak effect = 5.
FRESH VARIANT (for a re-attempt): "An mRNA reads AUG–UUU–CAU–GGA = Met–Phe–His–Gly. Classify each change: (a) UUU→UUC (still Phenylalanine); (b) CAU→UAU... wait, that becomes the first base of the codon — instead use: (b) a single base is DELETED right after AUG; (c) GGA→UGA." Answers: (a) silent (still Phe, protein unchanged); (b) frameshift — deleting one base shifts the whole reading frame downstream, garbling every codon after it; (c) nonsense — GGA (Gly) → UGA (STOP), protein truncated. Same rubric (name type + effect).

──────────── PROBLEM 2 (24 points) — Sort the biotechnology toolkit ────────────
SHOW ME: "Match each biotechnology tool to its job, in one short phrase each: (a) PCR; (b) gel electrophoresis; (c) recombinant DNA / plasmid; (d) CRISPR-Cas9. Then answer: in gel electrophoresis, do SMALLER or LARGER DNA fragments travel farther from the wells?"
VETTED ANSWER: (a) PCR = copies/amplifies a specific DNA segment (makes millions of copies). (b) Gel electrophoresis = sorts/separates DNA fragments by size. (c) Recombinant DNA / plasmid = combines DNA from two sources (a plasmid carries a new gene into a cell — e.g., the insulin gene into bacteria). (d) CRISPR-Cas9 = edits DNA at a specific location (cut/disable/fix/replace). Final: SMALLER fragments travel farther ("small and fast runs far").
RUBRIC: (a)–(d) 5 points each = 20 (correct job for each tool); the smaller-travels-farther answer = 4. Partial credit for a roughly-right job description. Confusing PCR (copy) with gel (sort) loses both (a) and (b).
FRESH VARIANT: "You have a single drop of dried blood from a crime scene — far too little DNA to analyze, and you want to compare its DNA fingerprint to two suspects. (a) Which tool do you use FIRST to make enough DNA to work with, and what does that tool do? (b) Which tool then produces the band pattern you compare, and what does it sort by? (c) On the gel, will the suspect's smallest fragment be near the wells or far from them?" Answers: (a) PCR — copies/amplifies the trace DNA into millions of copies; (b) gel electrophoresis — sorts the fragments by size into bands; (c) the smallest fragment ends up far from the wells (smaller travels farther). Same rubric idea (tool + job + the gel rule).

──────────── PROBLEM 3 (24 points) — Read the gel / DNA fingerprint ────────────
SHOW ME: "A forensic gel has four lanes: a Crime-Scene sample, Suspect 1, Suspect 2, and a size ladder. The Crime-Scene lane shows bands at the SAME positions as Suspect 2's bands, but DIFFERENT positions from Suspect 1's bands. (a) Which suspect's DNA best matches the crime scene, and how do you know? (b) One band in the crime-scene lane sits very FAR from the well; is that fragment relatively LARGE or SMALL, and why? (c) Why is it more reliable to say a gel EXCLUDES a suspect than to say it definitively proves guilt by itself?"
VETTED ANSWER: (a) Suspect 2 — in DNA fingerprinting you identify a match when the band patterns line up; the crime-scene bands align with Suspect 2's, not Suspect 1's. (b) Small — fragments farther from the well are smaller (they slip through the gel mesh and travel farther). (c) A non-matching pattern cleanly excludes a suspect, but a matching pattern is one line of evidence that can be affected by sample contamination, human error, or relatives with similar DNA, so it's strongest combined with other evidence (motive, other forensics). Either of those reasons earns credit.
RUBRIC: (a) 9 — names Suspect 2 + the band-matching logic; (b) 8 — "small" + the smaller-travels-farther reason; (c) 7 — a sound reason that exclusion is more certain than a stand-alone conviction. Partial credit throughout.
FRESH VARIANT: "On a gel, a 200-bp fragment and a 3000-bp fragment are run in the same lane. (a) Which one ends up farther from the well, and why? (b) Two siblings' DNA fingerprints look more similar to each other than to a stranger's — why does that make sense biologically? (c) Give one real benefit of DNA fingerprinting BESIDES convicting someone." Answers: (a) the 200-bp fragment travels farther (smaller = farther); (b) siblings share more DNA because they inherit alleles from the same two parents, so more of their fragment sizes match; (c) exonerating the wrongly convicted, identifying disaster victims or remains, paternity testing, tracking disease outbreaks — any one. Same rubric idea.

──────────── PROBLEM 4 (24 points) — Reason about a CRISPR scenario (SLO A) ────────────
SHOW ME: "A couple learns their future child has a 1-in-4 chance of inheriting a fatal childhood disease caused by a single recessive gene. A clinic offers to use CRISPR to edit the embryo so the disease gene is removed — a change that would be HERITABLE (passed to the child and all their descendants). In 5–7 sentences a thoughtful non-scientist could follow: (a) explain what CRISPR would actually do here (edit DNA — not copy or sort it); (b) explain why 'heritable / germline' makes this ethically different from treating a sick adult's own body cells; and (c) take a clear position — should this be allowed in this case? — and give ONE genuine reason for the OPPOSITE view."
VETTED ANSWER: (a) CRISPR edits DNA: a guide RNA directs the Cas9 protein to the disease gene in the embryo and cuts it so the sequence can be disabled or corrected (it does not copy DNA like PCR or sort it like a gel). (b) Editing an embryo is germline — the change is heritable, passed to that person and every descendant, and it's made on someone who cannot consent; treating a consenting adult's somatic (body) cells (e.g., approved sickle-cell gene therapy) affects only that one person and isn't passed on. (c) Any clear position earns credit — e.g., "allow it, narrowly, only for fatal single-gene diseases" OR "don't allow germline editing yet, given unknown off-target effects" — as long as the student also fairly states ONE real argument for the other side (e.g., for caution: unknown long-term/off-target effects, no consent from descendants, slippery slope to enhancement; for permitting: preventing certain, agonizing childhood death; medicine already prevents heritable suffering).
RUBRIC: (a) 8 — correctly says CRISPR EDITS DNA (not copy/sort); (b) 8 — explains heritable/germline vs. somatic and why that matters (consent / affects descendants / changes the gene pool); (c) 8 — a clear position (4) + a fair statement of one opposing reason (4). There is no "correct" side — grade the reasoning and the steelman, not the stance. Saying CRISPR "copies" or "sorts" DNA caps (a) at 2.
FRESH VARIANT: "A company wants to use CRISPR not to cure disease but to edit embryos for taller height and higher IQ ('enhancement'). In 5–7 sentences: (a) is this somatic or germline editing, and why does that matter; (b) name TWO concerns specific to enhancement (vs. curing disease); (c) take a position and give one fair reason someone might disagree with you." Answers: (a) germline (embryo) — heritable, no consent from future generations; (b) two of: it's not treating illness so the risk/benefit math is different; equity (only the wealthy could afford it, widening inequality); 'designer baby' / eugenics concerns; we don't even understand the genetics of traits like IQ; (c) any clear stance + a fair opposing reason. Same rubric idea (science + heritability + position with a steelman).

HOW TO RUN IT (with me, the student):
- Greet me in 1–2 sentences, ask my FIRST NAME, then give Problem 1 exactly as written. (NAME FALLBACK: if I answer without giving my name, keep going, but ask before the final report.)
- ONE problem at a time. Never show the whole set, the answers, the rubrics, or the variants.
- AFTER I ANSWER each problem:
• Grade my answer against that problem's rubric and state the score plainly ("That earns 22 of 28"). Judge MEANING, not wording.
• Say specifically what I got right, then TEACH the gap — explain the correct reasoning so I actually learn (full feedback is the point of this assignment).
• OFFER A RE-ATTEMPT: "Want to raise your score? I'll give you a similar problem." If I say yes, deliver the FRESH VARIANT (not the same problem), grade it, and set this problem's score to my BEST attempt (capped at full marks). I can retry as many times as I want.
• Move on when I'm satisfied.
- For Problem 4 (the ethics problem), stay neutral: grade the quality of the reasoning and whether I fairly stated an opposing reason — NEVER reward or penalize which side I pick.
- If I ask about the material, answer briefly, then return to the current problem. If I go off-topic, one friendly sentence, then — IN THE SAME MESSAGE — back to the problem.
- Until the final report, every message ends with a problem, a question, or a clear next step.
- Score HONESTLY against the rubric — don't inflate to be nice, and don't lowball; a wrong answer scores low, a strong answer earns full marks. Grade only against the vetted key above.

COMPLETION + REPORT. After I've finished all four problems (and any re-attempts), produce the report in EXACTLY this format — the FIRST LINE is my score:
STUDENT'S SCORE: X/100
WEEK 15 ASSIGNMENT — Read, Copy, Edit
Student: [name] | Date: ___
Problem 1 (Mutation type → effect): a/28 — [one line]
Problem 2 (Sort the biotech toolkit): b/24 — [one line]
Problem 3 (Read the gel / DNA fingerprint): c/24 — [one line]
Problem 4 (CRISPR scenario): d/24 — [one line]
Strongest skill: ___
Worth another look: ___
(The four problem scores must add up to the number on line 1.) Then say, verbatim: "Copy this entire report AND your share link to this chat, and submit both in Canvas for this assignment." End with one genuine sentence of encouragement (and, since the final is next week, a nudge that this is great review).

GETTING STARTED
Begin now: greet me, ask my first name, and give me Problem 1.

⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯ COPY EVERYTHING ABOVE THIS LINE ⎯⎯⎯⎯⎯⎯⎯⎯⎯⎯

Instructor grading note (Prof. Castellano)

• Record the STUDENT'S SCORE: X/100 from line 1 of the submitted report into the Assignments group.
• Spot-check a sample of chat share links against the reported scores; the embedded vetted key (with codon assignments pre-verified against the standard genetic code) means the coach grades the same way for every student and every chatbot, so checks are quick.
• The answer key + rubric live inside the student prompt (embed-don't-trust), so the score is consistent across Gemini / Claude / ChatGPT. Known weak point (H5/H7): an AI-self-scored grade submitted by share link is gameable; this is acceptable here as one assignment among many, but for high-stakes use pair it with an in-class or proctored check. Problem 4 is a values question — the key explicitly scores the reasoning and the steelman, not the side chosen.

Canvas placement block

canvas_object    = Assignment
title            = "Week 15 Assignment — Read, Copy, Edit (adaptive)"
assignment_group = "Assignments"
points_possible  = 100
grading_type     = points
assignment_type  = adaptive
submission_types = [online_text_entry, online_url]   # paste the report (score on line 1) + the chat share link
due_offset_days  = 6
published        = true
provenance       = "~ Prof. Castellano's edition · Fall 2026 · built with thecoursemaker.com"

Traditional variant — for comparison. This sample course is configured adaptive learning, so its actual Week-15 assignment is the AI-coached, self-scored version in I-assignment-and-rubric-week-15.md. This file shows the same Week-15 skills built the traditional way — the student completes the work and submits it, and the instructor grades against the rubric — so you can see both formats side by side. (Choosing assignment_type = traditional at course setup generates this style instead.)

Course: Introduction to Biology — General Biology I (BIOL 101) · Silver Oak University (fictional sample) · Prof. Castellano
Objective assessed: Objective 8 (gene regulation; mutation types & effects; the biotechnology toolkit; gene-editing ethics) · SLO A (reason scientifically; read a gel) · SLO B (connect a DNA change to a protein and a trait)
Worth 100 points · Assignments group = 15% of the grade

The Assignment

This is the last assignment of the term, and it pulls the molecular arc together. In four short parts, you'll connect a DNA mutation to its effect on a protein, sort the biotechnology tools by what each one does, read a forensic gel, and reason carefully about a real gene-editing scenario. Submit your answers as a document upload or text entry in Canvas. You'll be graded on the rubric below — read it before you start.

Part 1 — Mutation type → effect (28 pts). A gene produces the mRNA AUG–ACA–GGU–UGG, read as the amino acids Methionine–Threonine–Glycine–Tryptophan. For each single-base change below, name the mutation type (silent, missense, or nonsense) and say what happens to the protein:
- (a) the second codon ACA → ACG (which still codes for Threonine);
- (b) the fourth codon UGG → UGA (a STOP codon);
- (c) the third codon GGU → GAU (which codes for Aspartate).

Part 2 — Sort the biotechnology toolkit (24 pts). Match each tool to its job, in one short phrase each: (a) PCR; (b) gel electrophoresis; (c) recombinant DNA / plasmid; (d) CRISPR-Cas9. Then answer: in gel electrophoresis, do smaller or larger DNA fragments travel farther from the wells?

Part 3 — Read the gel / DNA fingerprint (24 pts). A forensic gel has four lanes: a Crime-Scene sample, Suspect 1, Suspect 2, and a size ladder. The Crime-Scene lane shows bands at the same positions as Suspect 2's bands, but different positions from Suspect 1's. (a) Which suspect's DNA best matches the crime scene, and how do you know? (b) One band in the crime-scene lane sits very far from the well — is that fragment relatively large or small, and why? (c) Why is it more reliable to say a gel excludes a suspect than to say it proves guilt all by itself?

Part 4 — Reason about a CRISPR scenario (24 pts). A couple learns their future child has a 1-in-4 chance of inheriting a fatal childhood disease caused by a single recessive gene. A clinic offers to use CRISPR to edit the embryo so the disease gene is removed — a change that would be heritable. In 5–7 sentences a thoughtful non-scientist could follow: (a) explain what CRISPR would actually do here (edit DNA — not copy or sort it); (b) explain why "heritable / germline" makes this ethically different from treating a sick adult's own body cells; (c) take a clear position — should this be allowed in this case? — and give one genuine reason for the opposite view.

Integrity & AI note. This is your own work, submitted for grading. You may use an approved chatbot (Gemini, Claude, or ChatGPT) to help you think — brainstorm, check a definition — but submitting AI-generated answers as your own is not allowed; if AI helped you think, add a one-line note of which tool and how. (Note: this is the traditional format. In this course's actual adaptive assignment, you work the problems with the chatbot and submit its self-scored report — see I-assignment-and-rubric-week-15.md.)

Rubric — 100 points

Levels describe observable differences so grading stays fast and consistent. Part 4 is a values question — grade the reasoning and the fairness of the opposing reason, not which side the student picks. (This same rubric is what the adaptive variant embeds for the AI to grade against.)

Instructor answer key — REMOVE BEFORE PUBLISHING TO STUDENTS

All codon assignments below are pre-verified against the standard genetic code (AUG=Met, ACA/ACG=Thr, GGU=Gly, GAU=Asp, UGG=Trp, UGA=STOP).

• Part 1: (a) silent — ACA→ACG still codes for Threonine, so the protein is unchanged (the genetic code is redundant). (b) nonsense — UGG (Trp) → UGA (STOP), so translation ends early and the protein is truncated / shortened (usually nonfunctional). (c) missense — GGU (Gly) → GAU (Asp), so one amino acid is different (one wrong building block; effect ranges from none to severe — sickle cell is a real missense example).
• Part 2: (a) PCR = copies/amplifies a specific DNA segment (millions of copies). (b) Gel electrophoresis = sorts/separates DNA fragments by size. (c) Recombinant DNA / plasmid = combines DNA from two sources (plasmid carries a new gene into a cell — e.g., the human insulin gene into bacteria). (d) CRISPR-Cas9 = edits DNA at a specific location (cut / disable / fix / replace). Final: smaller fragments travel farther ("small and fast runs far"). (Confusing PCR (copy) with the gel (sort) is the classic error.)
• Part 3: (a) Suspect 2 — DNA fingerprinting identifies a match when the band patterns line up; the crime-scene bands align with Suspect 2's, not Suspect 1's. (b) Small — fragments farther from the well are smaller (they slip through the gel mesh and travel farther). (c) A non-match cleanly excludes a suspect; a match is one line of evidence subject to contamination, human error, or similar DNA in relatives, so it's strongest combined with other evidence. (Independently re-verified for this week's lab: 500 bp travels farther than 2000 bp travels farther than 4000 bp; the crime-scene pattern {500, 2000, 4000} matches Suspect 2's, not Suspect 1's {1000, 2000, 4000}.)
• Part 4: (a) CRISPR edits DNA — a guide RNA directs the Cas9 "scissors" to the disease gene in the embryo and cuts it so it can be disabled/corrected (it does not copy DNA like PCR or sort it like a gel). (b) Editing an embryo is germline — the change is heritable (passed to the child and all descendants) and is made on someone who cannot consent; treating a consenting adult's somatic (body) cells (e.g., approved sickle-cell gene therapy) affects only that one person and isn't inherited. (c) No "correct" side — full credit for a clear position and a fairly stated opposing reason (for caution: unknown off-target/long-term effects, no consent from descendants, slippery slope to enhancement, equity; for permitting: preventing certain agonizing childhood death; medicine already acts to prevent heritable suffering).

Canvas placement block

canvas_object    = Assignment
title            = "Week 15 Assignment — Read, Copy, Edit (traditional)"
assignment_group = "Assignments"
points_possible  = 100
grading_type     = points
assignment_type  = traditional
submission_types = [online_upload, online_text_entry]
due_offset_days  = 6
published        = true
rubric_ref       = "week-15-assignment-rubric"
provenance       = "~ Prof. Castellano's edition · Fall 2026 · built with thecoursemaker.com"