Site By: @cgldevel

From Prompts to Protocols: AI in a Molecular Genetics Course

Penn State biochemist Karim Bouazoune, assistant research professor of biochemistry and molecular biology, has embraced artificial intelligence (AI) to upgrade how undergraduates learn biology by putting AI tools directly into both his students' hands and his course design. He has now used tools such as NotebookLM and ChatGPT to generate course overviews, lab protocols, and safety guidelines to support student learning for the spring 2026 semester.

Asking students to critique and create 

Last fall, Bouazoune invited students to use and interrogate AI tools themselves. They compared outputs from different AI models, explored how small prompt changes altered results, and examined where AI explanations of cloning steps fell short of disciplinary standards. Course assignments included using AI to compile lists of genome-editing tools, build interactive visualizations of enzyme kinetics, and create data visualizations. These tasks encouraged students to move beyond consumption toward creation, emphasizing data storytelling and scientific reasoning rather than mere technical novelty. The course also addressed ethical AI use, particularly questions of academic integrity when using such generative tools. 

AI‑generated materials as course design 

Bouazoune also used AI for his own instructional purposes, asking tools to draft infographic overviews of the semester, detailed lab procedures, and clear lab safety reminders. He then refined these outputs and integrated them into the lab manual and lectures, treating AI as a behind-the-scenes assistant that could help him prototype materials more efficiently. Having already explored AI's strengths and limitations with students the previous semester, he now applied those insights to make the course lab manual more visually compelling, reduce cognitive load, and help students grasp complex protocols at a glance. 

A step-by-step infographic titled “PCR Product Purification Using Spin Column” showing four main stages: A. Sample Preparation – Combine PCR reactions (pool 120 µL total), add 480 µL binding buffer, mix thoroughly, and spin to settle liquid. B. Binding to Column – Transfer sample to spin column, centrifuge for 1 minute at ≥10,000×g (11,000–13,000 rpm), discard flow-through, and return column to collection tube. C. Wash Steps – Add 700 µL DNA wash buffer, centrifuge, discard flow-through, repeat wash once more, dry spin for 2 minutes, and discard collection tube. D. Elution – Transfer column to a new tube, add 40 µL elution buffer, incubate for 2 minutes, centrifuge for 1 minute, and collect purified PCR product ready for downstream applications. The diagram uses color-coded panels (blue, orange, green, purple) with illustrations of tubes, pipettes, and centrifuges for each step.
Figure: An example of an AI produced figure for the lab manual

 

Accessibility and visual learning opportunities 

The AI-generated graphics that map the semester and illustrate lab guidelines can also support diverse learning needs. Visual summaries and flowcharts help students with reading difficulties or attention challenges to navigate complex procedures more easily. At the same time, AI opens new opportunities to assist in creating the accessibility features these materials require, such as generating descriptive text-based alternatives or creating audio versions, so that students with visual impairments can access the same information. This positions AI as a tool for making scientific communication both more visual and more inclusive, helping ensure course materials comply with accessibility requirements.

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