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Introductory Biology

  • “Phenology of a Dawn Redwood” – Images collected by students for this lesson pieced together illustrating a Metasequoia glyptostroboides changing color and dropping its leaves in the fall of 2017 on Michigan State University campus.

    Quantifying and Visualizing Campus Tree Phenology

    Learning Objectives
    The Learning Objectives of this lesson span across the entire semester.
    • Observe and collect information on phenological changes in local trees.
    • Become familiar with a database and how to work with large datasets.
    • Analyze and visualize data from the database to test their hypotheses and questions.
    • Develop a research proposal including empirically-driven questions and hypotheses.
    • Synthesize the results of their analysis in the context of plant biodiversity and local environmental conditions.
  • 3D Print Model of the Mars Curiosity Rover, printed from NASA 3D Resources (

    Exploring the March to Mars Using 3D Print Models

    Learning Objectives
    • Students will be able to describe the major aspects of the Mars Curiosity Rover missions.
    • Students will be able to synthesize information learned from a classroom jigsaw activity on the Mars Curiosity Rover missions.
    • Students will be able to work in teams to plan a future manned mission to Mars.
    • Students will be able to summarize their reports to the class.
  • Students present their posters to classmates and instructors during a poster fair.

    Discovery Poster Project

    Learning Objectives
    Students will be able to:
    • identify and learn about a scientific research discovery of interest to them using popular press articles and the primary literature
    • find a group on campus doing research that aligns with their interests and communicate with the faculty leader of that group
    • create and present a poster that synthesizes their knowledge of the research beyond the discovery
  • Society Logos with statement "At the end of my course students should be able to..."
  • Wikipedia in the Science Classroom. In this primary image, students are sharing their Wikipedia article evaluations and evaluation process with their peers.
  • Peterson MP, Rosvall KA, Choi J-H, Ziegenfus C, Tang H, Colbourne JK, et al. (2013) Testosterone Affects Neural Gene Expression Differently in Male and Female Juncos: A Role for Hormones in Mediating Sexual Dimorphism and Conflict. PLoS ONE 8(4): e61784. doi:10.1371/journal.pone.0061784

    Teaching RNAseq at Undergraduate Institutions: A tutorial and R package from the Genome Consortium for Active Teaching

    Learning Objectives
    • From raw RNAseq data, run a basic analysis culminating in a list of differentially expressed genes.
    • Explain and evaluate statistical tests in RNAseq data. Specifically, given the output of a particular test, students should be able to interpret and explain the result.
    • Use the Linux command line to complete specified objectives in an RNAseq workflow.
    • Generate meaningful visualizations of results from new data in R.
    • (In addition, each chapter of this lesson plan contains more specific learning objectives, such as “Students will demonstrate their ability to map reads to a reference.”)
  • Train tracks, image author: Mitya Ilyinov

    BioMap Degree Plan: A project to guide students in exploring, defining, and building a plan to achieve career goals

    Learning Objectives
    Students will be able to...
    • Identify their values and interests.
    • Identify careers that align with their values and interests.
    • Identify academic programs and co-curricular experiences that will prepare them for a career.
    • Create the first draft of a BioMap Degree Plan to support achievement of their career goals.
    • Articulate how their undergraduate academic experience will prepare them for their future career.
    • Use professional communication skills
  • pClone Red Makes Research Look Easy

    Using Synthetic Biology and pClone Red for Authentic Research on Promoter Function: Introductory Biology (identifying...

    Learning Objectives
    • Describe how cells can produce proteins at the right time and correct amount.
    • Diagram how a repressor works to reduce transcription.
    • Diagram how an activator works to increase transcription.
    • Identify a new promoter from literature and design a method to clone it and test its function.
    • Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments.
    • Design an experiment to verify a new promoter has been cloned into a destination vector.
    • Design an experiment to measure the strength of a promoter.
    • Analyze data showing reporter protein produced and use the data to assess promoter strength.
    • Define type IIs restriction enzymes.
    • Distinguish between type II and type IIs restriction enzymes.
    • Explain how Golden Gate Assembly (GGA) works.
    • Measure the relative strength of a promoter compared to a standard promoter.
  • Mechanisms regulating the lac operon system

    Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon

    Learning Objectives
    Students will be able to:
    • model how the components of the lac operon contribute to gene regulation and expression.
    • generate and test predictions using computational modeling and simulations.
    • interpret and record graphs displaying simulation results.
    • relate simulation results to cellular events.
    • describe how changes in environmental glucose and lactose levels impact regulation of the lac operon.
    • predict, test, and explain how mutations in specific elements in the lac operon affect their protein product and other elements within the operon.
  • The mechanisms regulating the trp operon system.

    Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon

    Learning Objectives
    Students will be able to:
    • Perturb and interpret simulations of the trp operon.
    • Define how simulation results relate to cellular events.
    • Describe the biological role of the trp operon.
    • Describe cellular mechanisms regulating the trp operon.
    • Explain mechanistically how changes in the extracellular environment affect the trp operon.
    • Define the impact of mutations on trp operon expression and regulation.
  • Using Place-Based Economically Relevant Organisms to Improve Student Understanding of the Roles of Carbon Dioxide,...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Describe the roles of light energy and carbon dioxide in photosynthetic organisms.
    • Identify the effect of nutrients on the growth of photosynthetic organisms.
    • Describe global cycles in atmospheric carbon dioxide levels and how they relate to photosynthetic organisms.
  • photo credit John Friedlein. Author (SRB) helps a student troubleshooting RStudio in the workshop session of class.
  • Monarch larvae

    Does it pose a threat? Investigating the impact of Bt corn on monarch butterflies

    Learning Objectives
    Students will be able to:
    • Apply genetics concepts to a relevant case study of Bt corn and monarch butterflies
    • Read figures and text from primary literature
    • Identify claims presented in scientific studies
    • Evaluate data presented in scientific studies
    • Critically reason using data
    • Evaluate the consequences of GM technology on non-target organisms
    • Communicate scientific data orally
  • A crossbill feeds on a pinecone

    Coevolution or not? Crossbills, squirrels and pinecones

    Learning Objectives
    1. Define coevolution.
    2. Identify types of evidence that would help determine whether two species are currently in a coevolutionary relationship.
    3. Interpret graphs.
    4. Evaluate evidence about whether two species are coevolving and use evidence to make a scientific argument.
    5. Describe what evidence of a coevolutionary relationship might look like.
    6. Distinguish between coadaptation and coevolution.
  • Adult female Daphnia dentifera. Daphnia spp. make a great study system due to their transparent body and their ease of upkeep in a lab.

    Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year...

    Learning Objectives
    Students will be able to:
    • Construct written predictions about 1 factor experiments.
    • Interpret simple (2 variables) figures.
    • Construct simple (2 variables) figures from data.
    • Design simple 1 factor experiments with appropriate controls.
    • Demonstrate proper use of standard laboratory items, including a two-stop pipette, stereomicroscope, and laboratory notebook.
    • Calculate means and standard deviations.
    • Given some scaffolding (instructions), select the correct statistical test for a data set, be able to run a t-test, ANOVA, chi-squared test, and linear regression in Microsoft Excel, and be able to correctly interpret their results.
    • Construct and present a scientific poster.
  • blind cave fish
  • 3D Print Models: A collection of 3D models printed from online repository files.
  • The mechanisms regulating the cellular respiration system.

    Discovering Cellular Respiration with Computational Modeling and Simulations

    Learning Objectives
    Students will be able to:
    • Describe how changes in cellular homeostasis affect metabolic intermediates.
    • Perturb and interpret a simulation of cellular respiration.
    • Describe cellular mechanisms regulating cellular respiration.
    • Describe how glucose, oxygen, and coenzymes affect cellular respiration.
    • Describe the interconnectedness of cellular respiration.
    • Identify and describe the inputs and outputs of cellular respiration, glycolysis, pyruvate processing, citric acid cycle, and the electron transport chain.
    • Describe how different energy sources are used in cellular respiration.
    • Trace carbon through cellular respiration from glucose to carbon dioxide.
  • Using phylogenetics to make inferences about historical biogeographic patterns of evolution.

    Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

    Learning Objectives
    Students will be able to:
    • Estimate phylogenetic trees using diverse data types and phylogenetic models.
    • Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
    • Use selected computer programs for phylogenetic analysis.
    • Use bootstrapping to assess the statistical support for a phylogeny.
    • Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
  • This collage contains original images taken by the course instructor. The images show a microscopic view of stomata on the underside of a Brassica rapa leaf (A), B. rapa plants in their growth trays (B), a flowering B. rapa plant (C), and different concentrations of foliar protein (D). Photos edited via Microsoft Windows Photo Editor and Phototastic Collage Maker.

    A flexible, multi-week approach to plant biology - How will plants respond to higher levels of CO2?

    Learning Objectives
    Students will be able to:
    • Apply findings from each week's lesson to make predictions and informed hypotheses about the next week's lesson.
    • Keep a detailed laboratory notebook.
    • Write and peer-edit the sections of a scientific paper, and collaboratively write an entire lab report in the form of a scientific research paper.
    • Search for, find, and read scientific research papers.
    • Work together as a team to conduct experiments.
    • Connect findings and ideas from each week's lesson to get a broader understanding of how plants will respond to higher levels of CO2 (e.g., stomatal density, photosynthetic/respiratory rates, foliar protein concentrations, growth, and resource allocation).
    Note: Additional, more specific objectives are included with each of the four lessons (Supporting Files S1-S4)
  • Format of a typical course meeting
  • Arabidopsis Seedling

    Linking Genotype to Phenotype: The Effect of a Mutation in Gibberellic Acid Production on Plant Germination

    Learning Objectives
    Students will be able to:
    • identify when germination occurs.
    • score germination in the presence and absence of GA to construct graphs of collated class data of wild-type and mutant specimens.
    • identify the genotype of an unknown sample based on the analysis of their graphical data.
    • organize data and perform quantitative data analysis.
    • explain the importance of GA for plant germination.
    • connect the inheritance of a mutation with the observed phenotype.
  • Pipets - photo by Magnus Manske

    Learning to Pipet Correctly by Pipetting Incorrectly?

    Learning Objectives
    • Students will be able to use analytical balances and micropipettes.
    • Students will be able to calculate averages and standard deviations.
    • Students will be able to use t-tests to compare two independent samples.
    • Students will be able to justify accepting or rejecting a null hypothesis based on an interpretation of p-values.
    • Students will learn to use spreadsheet software such as Microsoft Excel and/or Google Sheets
    • Students will be able to explain how pipetting incorrectly leads to errors.
  • Ecosystem

    Using Pathway Maps to Link Concepts, Peer Review, Primary Literature Searches and Data Assessment in Large Enrollment...

    Learning Objectives
    • Define basic concepts and terminology of Ecosystem Ecology
    • Link biological processes that affect each other
    • Evaluate whether the link causes a positive, negative, or neutral effect
    • Find primary literature
    • Identify data that correctly supports or refutes an hypothesis
  • Multiple sequence alignment of homologous cytochrome C protein sequences using Jalview viewer.

    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Define similarity in a non-biological and biological sense when provided with two strings of letters.
    • Quantify the similarity between two gene/protein sequences.
    • Explain how a substitution matrix is used to quantify similarity.
    • Calculate amino acid similarity scores using a scoring matrix.
    • Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).
    • Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.
    • Create a nearest-neighbor distance matrix.
    • Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.
    • Use appropriate bioinformatics sequence alignment tools to investigate a biological question.
  • Grow the Gradient game board. A student moves game pieces on the game board as they learn how the loop of Henle creates a salt concentration gradient in the medulla.

    Grow the Gradient: An interactive countercurrent multiplier game

    Learning Objectives
    • Students will be able to simulate the movement of water and sodium at each region of the loop of Henle.
    • Students will be able to associate osmosis and active transport with movement of water/solutes at each region of the loop of Henle.
    • Students will be able to model how the descending and ascending limbs of the loop of Henle maintain a concentration gradient within the medulla.
    • Students will be able to predict the effects of altering normal water and salt movement out of the loop of Henle on the salt concentration of the medulla, urine concentration, and urine volume.
    Advanced Learning Objectives for Extensions
    • Students will be able to predict the impact of the length of the loop of Henle on the magnitude of the concentration gradient within the medulla.
    • Students will be able to predict the length of the loop of Henle in organisms from different habitats.
  • American coot (Fulica Americana) family at the Cloisters City Park pond in Morrow Bay, CA. "Mike" Michael L. Baird [CC BY 2.0 (], via Wikimedia Commons,

    Knowing your own: A classroom case study using the scientific method to investigate how birds learn to recognize their...

    Learning Objectives
    • Students will be able to identify and describe the steps of the scientific method.
    • Students will be able to develop hypotheses and predictions.
    • Students will be able to construct and interpret bar graphs based on data and predictions.
    • Students will be able to draw conclusions from data presented in graphical form.
  • Students engaged in building the PCR model

    A Close-Up Look at PCR

    Learning Objectives
    At the end of this lesson students will be able to...
    • Describe the role of a primer in PCR
    • Predict sequence and length of PCR product based on primer sequences
    • Recognize that primers are incorporated into the final PCR products and explain why
    • Identify covalent and hydrogen bonds formed and broken during PCR
    • Predict the structure of PCR products after each cycle of the reaction
    • Explain why amplification proceeds exponentially
  • Human karyotype

    Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics...

    Learning Objectives
    Students successfully completing this lesson will:
    • Practice navigating an online bioinformatics resource and identify evidence relevant to solving investigation questions
    • Contrast the array of genes expected on homologous autosomal chromosomes pairs with the array of genes expected on sex chromosome pairs
    • Use bioinformatics evidence to defend the definition of homologous chromosomes
    • Define chromosomal sex and defend the definition using experimental data
    • Investigate the genetic basis of human chromosomal sex determination
    • Identify at least two genetic mutations can lead to sex reversal
  • A pair of homologous chromosomes.

    Meiosis: A Play in Three Acts, Starring DNA Sequence

    Learning Objectives
    • Students will be able to identify sister chromatids and homologous chromosomes at different stages of meiosis.
    • Students will be able to identify haploid and diploid cells, whether or not the chromosomes are replicated.
    • Students will be able to explain why homologous chromosomes must pair during meiosis.
    • Students will be able to relate DNA sequence similarity to chromosomal structures.
    • Students will be able to identify crossing over as the key to proper pairing of homologous chromosomes during meiosis.
    • Students will be able to predict the outcomes of meiosis for a particular individual or cell.
  • An active-learning lesson that targets student understanding of population growth in ecology

    Learning Objectives
    Students will be able to:
    • Calculate and compare population density and abundance.
    • Identify whether a growth curve describes exponential, linear, and/or logistic growth.
    • Describe and calculate a population's growth rate using linear, exponential, and logistic models.
    • Explain the influence of carrying capacity and population density on growth rate.
  • Two cells stained

    Bad Cell Reception? Using a cell part activity to help students appreciate cell biology, with an improved data plan and...

    Learning Objectives
    • Identify cell parts and explain their function
    • Explain how defects in a cell part can result in human disease
    • Generate thought-provoking questions that expand upon existing knowledge
    • Create a hypothesis and plan an experiment to answer a cell part question
    • Find and reference relevant cell biology journal articles
  • Sodium-Potassium pump

    Lights, Camera, Acting Transport! Using role-play to teach membrane transport

    Learning Objectives
    At the end of this activity, students should be able to:
    • Compare and contrast the mechanisms of simple diffusion, facilitated diffusion, and active transport (both primary and secondary).
    • Identify, and provide a rationale for, the mechanism(s) by which various substances cross the plasma membrane.
    • Describe the steps involved in the transport of ions by the Na+/K+ pump, and explain the importance of electrogenic pumps to the generation and maintenance of membrane potentials.
    • Explain the function of electrochemical gradients as potential energy sources specifically used in secondary active transport.
    • Relate each molecule or ion transported by the Na+/glucose cotransporter (SGLT1) to its own concentration or electrochemical gradient, and describe which molecules travel with and against these gradients.
  • Image from a clicker-based case study on muscular dystrophy and the effect of mutations on the processes in the central dogma.

    A clicker-based case study that untangles student thinking about the processes in the central dogma

    Learning Objectives
    Students will be able to:
    • explain the differences between silent (no change in the resulting amino acid sequence), missense (a change in the amino acid sequence), and nonsense (a change resulting in a premature stop codon) mutations.
    • differentiate between how information is encoded during DNA replication, transcription, and translation.
    • evaluate how different types of mutations (silent, missense, and nonsense) and the location of those mutations (intron, exon, and promoter) differentially affect the processes in the central dogma.
    • predict the molecular (DNA size, mRNA length, mRNA abundance, and protein length) and/or phenotypic consequences of mutations.
  • Students at Century College use gel electrophoresis to analyze PCR samples in order to detect a group of ampicillin-resistance genes.

    Antibiotic Resistance Genes Detection in Environmental Samples

    Learning Objectives
    After completing this laboratory series, students will be able to:
    • apply the scientific method in formulating a hypothesis, designing a controlled experiment using appropriate molecular biology techniques, and analyzing experimental results;
    • conduct a molecular biology experiment and explain the principles behind methodologies, such as accurate use of micropipettes, PCR (polymerase chain reaction), and gel electrophoresis;
    • determine the presence of antibiotic-resistance genes in environmental samples by analyzing PCR products using gel electrophoresis;
    • explain mechanisms of microbial antibiotic resistance;
    • contribute data to the Antibiotic Resistance Genes Network;
    • define and apply key concepts of antibiotic resistance and gene identification via PCR fragment size.
  • The Roc is a mythical giant bird of prey, first conceived during the Islamic Golden Age (~8th to 13th centuries CE), popularized in folk tales gathered in One Thousand One Nights. Rocs figured prominently in tales of Sinbad the Sailor. In this 1898 illustration by René Bull, the Roc is harassing two of Sinbad’s small fleet of ships. Illustration by René Bull is licensed under CC BY 2.0. (Source:

    A first lesson in mathematical modeling for biologists: Rocs

    Learning Objectives
    • Systematically develop a functioning, discrete, single-species model of an exponentially-growing or -declining population.
    • Use the model to recommend appropriate action for population management.
    • Communicate model output and recommendations to non-expert audiences.
    • Generate a collaborative work product that most individuals could not generate on their own, given time and resource constraints.
  • A three-dimensional model of methionine is superimposed on a phase contrast micrograph of Saccharomyces cerevisiae from a log phase culture.

    Follow the Sulfur: Using Yeast Mutants to Study a Metabolic Pathway

    Learning Objectives
    At the end of this lesson, students will be able to:
    • use spot plating techniques to compare the growth of yeast strains on solid culture media.
    • predict the ability of specific met deletion strains to grow on media containing various sulfur sources.
    • predict how mutations in specific genes will affect the concentrations of metabolites in the pathways involved in methionine biosynthesis.
  • Image adapted from :Image:Citric acid cycle noi.svg| (uploaded to Commons by wadester16)

    A simple way for students to visualize cellular respiration: adapting the board game MousetrapTM to model complexity

    Learning Objectives
    • Students will be able to describe the three stages of cellular respiration.
    • Students will be able to identify the reactants entering and the products formed during each stage of cellular respiration.
    • Students will be able to explain how chemical energy in carbohydrates is transferred to ATP through the stages of cellular respiration.
    • Students will be able to explain the effects of compartmentalization of cellular respiration reactions in different cellular spaces.
    • Students will be able to predict biological outcomes when a specific stage(s) of cellular respiration is altered. 
  • DNA barcoding research in first-year biology curriculum

    CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum

    Learning Objectives
    Students will be able to: Week 1-4: Fundamentals of Science and Biology
    • List the major processes involved in scientific discovery
    • List the different types of scientific studies and which types can establish causation
    • Design experiments with appropriate controls
    • Create and evaluate phylogenetic trees
    • Define taxonomy and phylogeny and explain their relationship to each other
    • Explain DNA sequence divergence and how it applies to evolutionary relationships and DNA barcoding
    Week 5-6: Ecology
    • Define and measure biodiversity and explain its importance
    • Catalog organisms using the morphospecies concept
    • Geographically map organisms using smartphones and an online mapping program
    • Calculate metrics of species diversity using spreadsheet software
    • Use spreadsheet software to quantify and graph biodiversity at forest edges vs. interiors
    • Write a formal lab report
    Week 7-11: Cellular and Molecular Biology
    • Extract, amplify, visualize and sequence DNA using standard molecular techniques (PCR, gel electrophoresis, Sanger sequencing)
    • Explain how DNA extraction, PCR, gel electrophoresis, and Sanger sequencing work at the molecular level
    Week 12-13: Bioinformatics
    • Trim and assemble raw DNA sequence data
    • Taxonomically identify DNA sequences isolated from unknown organisms using BLAST
    • Visualize sequence data relationships using sequence alignments and gene-based phylogenetic trees
    • Map and report data in a publicly available online database
    • Share data in a formal scientific poster
  • Hydrozoan polyps on a hermit-crab shell (photo by Tiffany Galush)

    A new approach to course-based research using a hermit crab-hydrozoan symbiosis

    Learning Objectives
    Students will be able to:
    • define different types of symbiotic interactions, with specific examples.
    • summarize and critically evaluate contemporary primary literature relevant to ecological symbioses, in particular that between hermit crabs and Hydractinia spp.
    • articulate a question, based on observations of a natural phenomenon (in this example, the hermit crab-Hydractinia interaction).
    • articulate a testable hypothesis, based on their own observations and read of the literature.
    • design appropriate experimental or observational studies to address their hypotheses.
    • collect and interpret data in light of their hypotheses.
    • problem-solve and troubleshoot issues that arise during their experiment.
    • communicate scientific results, both orally and in written form.
  • Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration Image File: QuickFixPrimImage.tiff Sources for images: Balance: Public Domain CCO Mitochondria: Pills:

    Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration

    Learning Objectives
    • Students will be able to explain how the energy from sugars is transformed into ATP via cellular respiration.
    • Students will be able to predict an outcome if there is a perturbation in the cellular respiration pathway.
    • Students will be able to state and evaluate a hypothesis.
    • Students will be able to interpret data from a graph, and use that data to make inferences about the action of a drug.
  • Using the Cell Engineer/Detective Approach to Explore Cell Structure and Function

    Learning Objectives
    Students will be able to:
    • Identify the major cell organelles
    • List the major functions of the organelles
    • Predict how changes in organelle/cell structure could alter cellular function
    • Explain how overall cellular function is dependent upon organelles/cell structure
    • Relate cell structure to everyday contexts
  • Figure 2. ICB-Students come to class prepared to discuss the text