Exam 1 Review

Exam Details

• The exam is on Tuesday of next week during normal class time (11:30 AM - 01:30 PM).

• The exam will be on Brightspace, and students must have their Zoom camera on during the test.

• The exam is located in the performance exam folder on Brightspace; the Zoom link is also located here.

• Your face must be visible during the test to be graded.

• The performance exams are similar to the activities completed in class.

• There will be three big questions, one from each unit: the nature of science, genetics, and evolution.

• Questions will be similar to those in the activities.

• Study the answer keys for the activities and review the activity and pre-activity materials.

• Be prepared to draw a model by hand, take a photo, and upload it to Brightspace.

• At random points during the exam, students will be pulled aside to show their environment and workspace to faculty proctors.

• Ensure a quiet workspace with no 02/2001-related materials visible.

• A working camera and microphone are required to take and have the exam graded.

Nature and Practice of Science

• The exam will assess the ability to apply knowledge by evaluating a news article and identifying accurate and inaccurate representations of the nature of science.

• Sloppy use of scientific terms (theory, law, observation, explanation, experiment) is common.

• Understanding the precise meanings of these terms is important for making informed decisions.

• Review definitions from early lectures, especially lecture number one, "The Language of Science."

• Be prepared to analyze if scientific terms are used correctly in articles or posts.

• Observations vs. Patterns vs. Causes:

  • Observations are single events.

  • Patterns are recurring events.

  • Science seeks to understand why patterns occur.

  • Processes and causes explain patterns.

  • Example: Phenotypic differences between male and female birds

    • The pattern is visible phenotypic differences.

    • Sexual selection is the cause of this pattern.

• Law and Theory:

  • Laws describe nature and are useful for making predictions.

  • Theories explain why laws work.

  • Laws describe "what," while theories explain "why."

  • Theories are complex and well-tested explanations.

  • A theory is not a hunch or guess but a robust explanation supported by evidence.

  • The theory of natural selection has been tested for over a century.

• Models:

  • A model is a tool for making sense of and advancing understanding of a phenomenon.

  • Models are not just depictions but tools to achieve useful things.

  • Types of scientific models: physical, mathematical, and conceptual.

• Types of Scientific Studies:

  • Association studies: Look for relationships between variables.

    • Example: Association between red meat consumption and cancer.

  • Comparison studies: Compare two groups to see how they differ.

    • Example: Comparing exercise patterns between lactose-intolerant and lactose-tolerant individuals.

  • Causation experiments: Randomly assign individuals to treatment and control groups.

    • Determine the cause or why something happens.

  • Natural experiments: Study the impacts of natural interventions.

    • Example: Studying the spread and impact of the COVID-19 pandemic.

  • The purpose of these studies is to test hypotheses or predictions.

• Boundaries of Science:

  • Science is not trying to prove or disprove the existence of the supernatural.

  • Science is one way of knowing about the world, distinct from morals and ethics.

  • Review the 17 common misunderstandings that students typically have (listed in the syllabus).

  • Be able to identify mistakes in articles and explain why they are mistakes.

Genetics

• Need to interpret data and use knowledge to explain it.

• Example: Research program studying fuspic variation in a population of flies.

  • Some flies have narrow wing spots, some have wide wing spots, and some do not have wing spots.

  • A protein-coding gene called WGG plays a role in forming this wing spot and encodes a protein (WGG).

  • Proteins were extracted from seven flies that varied in their wing spots.

  • Protein concentration measured and a western blot performed.

• Each individual has two alleles of this gene regardless of whether you see two bands.

  • Seeing two bands in some samples indicates that there are two different size-based alleles for this gene present among these seven flies.

• Data Analysis:

  • Note patterns in the data.

  • Protein concentrations:

    • Low numbers (~25) and high numbers (~52).

    • High concentration associated with wide spots.

  • Western blot:

    • Individuals 1 and 5 (no spots) have a single band of the smaller protein and similar concentration.

    • The rest of the individuals have two bands.

    • Individuals with narrow spots have two bands and a lower concentration of the protein.

  • Two homozygotes for the small protein version and five heterozygotes; no homozygotes for the large protein version.

• Develop a conceptual model in which the WGG wing variation gene variation is able to explain the phenotypic differences (wing pattern variation).

• Parts of the Model:

  • Two alleles: small encoding protein and large encoding protein.

  • Both alleles have noncoding DNA and coding DNA.

  • Coding DNA determines the length of the protein (differs between alleles.)

  • Noncoding has gene regulatory switches which control the amount of transcription.

  • The amount of mRNA determines the amount of protein.

• Small Encoding Allele:

  • Encodes a small protein and has a low amount of protein produced.

  • No variation among small protein encoding alleles in terms of amount.

  • Transcription → mRNA (amount controlled by noncoding DNA) → translation → small protein.

  • Present in both the small homozygotes and heterozygotes.

  • Homozygous for small proteins with low amounts results in spot-absent phenotype.

• Large Encoding Allele:

  • Variations in the amount of transcription.

  • Transcription → mRNA (amount controlled by noncoding DNA) → translation → large protein.

  • There are no large homozygotes.

  • Low amount leads to narrow spot; high amount leads to a wide spot in heterozygotes.

• Major Features:

  • Information about size differences between alleles.

  • Also, amount differences because both of those are playing causal roles in this pattern of variation.

  • Common Mistakes:

    • Not showing noncoding DNA for both alleles.

    • Not carefully noting both the size and the amounts associations with phenotypes.

    • Not showing that noncoding controls the amount of transcription.

    • The amount of mRNA determines the amount of protein.

    • Not getting the genotype-to-phenotype associations correct.

• Any mRNA that gets produced is translated.

  • The amount of mRNA and the amount of protein has a strong relationship.

Evolution

• When we see different patterns of phenotypes over time and trends in divergences, how do biologists figure out what's causing them?

• Looking at data and bringing some of the causes and mechanisms to explain the patterns.

• Typically ascribe genetic drift to situations when we don’t see any clear patterns.

• Unlikely that sexual selection is having an impact in cases where males and females are the same.

  • Because both males and females are being impacting similarly, so there’s no sex-specific sorting going on.

• When we see cases where males and females are diverging, we know that sexual selection is operating.

  • Sorting is based upon a sexual feature that is due to male competition or female choice.

• When we see trends rather than stability it is caused by selection.

  • Stabilizing Selection - population is stable.

  • Directional Selection - population is changing in a particular direction

• Look for patterns between males and females when you're interpreting the data.

• Even though you don't see divergence itself, can have sexual selection even if

• Common Mistakes in Models:

  • When building a model where you're having sex-specific sorting, and you might talk about how the environment is doing the sorting, ensure that your data matches the model that you have.

  • Clarify if the population is maintaining the distribution or it's changing the distribution of the trait.

    • Ensure to maintain the distributions through the cycles and generations of change.

• It's important that your data for these populations actually matches the model that you have.

Exam Details

• The exam is on Tuesday next week, during normal class time (11:30 AM - 01:30 PM) on Brightspace. Students must have their Zoom camera on.

• Located in the performance exam folder on Brightspace; the Zoom link is also here.

• Face must be visible to be graded.

• Exams are similar to in-class activities.

• Three big questions, one from each unit: nature of science, genetics, and evolution.

• Questions will be similar to those in the activities. Study the answer keys and review the activity materials.

• Be prepared to draw a model by hand, take a photo, and upload it.

• Students may be asked to show their environment to faculty proctors.

• Ensure a quiet workspace with no related materials visible.

• A working camera and microphone are required.

Nature and Practice of Science

• The exam assesses the ability to apply knowledge by evaluating a news article and identifying accurate/inaccurate representations of the nature of science.

• Understanding the precise meanings of scientific terms is important.

• Review definitions from early lectures, especially lecture number one, "The Language of Science."

• Analyze if scientific terms are used correctly in articles.

• Observations vs. Patterns vs. Causes:

  • Observations are single events.

  • Patterns are recurring events.

  • Science seeks to understand why patterns occur (processes and causes).

  • Example: Phenotypic differences between male and female birds, where sexual selection is the cause.

• Law and Theory:

  • Laws describe nature and are useful for making predictions (what).

  • Theories explain why laws work (why).

  • Theories are complex, well-tested explanations supported by evidence. The theory of natural selection has been tested for over a century.

• Models:

  • Models are tools for making sense of and advancing understanding of a phenomenon (physical, mathematical, and conceptual).

• Types of Scientific Studies:

  • Association studies: relationships between variables.

  • Comparison studies: Compare two groups.

  • Causation experiments: Random assignment to treatment/control groups.

  • Natural experiments: Study the impacts of natural interventions. Purpose: test hypotheses or predictions.

• Boundaries of Science:

  • Science does not prove/disprove the supernatural and is distinct from morals/ethics.

  • Review common misunderstandings (syllabus). Identify mistakes in articles and explain them.

Genetics

• Interpret data and use knowledge to explain it. Example: fuspic variation in flies.

• Some flies have narrow/wide/no wing spots. A protein-coding gene called WGG plays a role.

• Individuals have two alleles, indicated by bands in Western blot.

• Data Analysis:

  • Note patterns.

  • Protein concentrations: High concentration associated with wide spots.

  • Western blot: Individuals with no spots have a single band.

  • Two homozygotes for small protein; five heterozygotes; no homozygotes for large protein.

• Develop a conceptual model in which the WGG wing variation gene variation explains the phenotypic differences.

• Parts of the Model:

  • Two alleles: small and large encoding proteins.

  • Both alleles have noncoding and coding DNA.

  • Coding DNA determines protein length; noncoding controls transcription amount.

• Small Encoding Allele:

  • Encodes a small protein, low amount produced. Homozygous results in spot-absent phenotype.

• Large Encoding Allele:

  • Variations in transcription amount. No large homozygotes. Low amount leads to narrow spot; high amount leads to a wide spot in heterozygotes.

• Major Features:

  • Information about size and amount differences, noncoding controls transcription.

  • Common Mistakes:Not showing noncoding DNA, amount associations, transcription control, or correct genotype-to-phenotype associations.

• The amount of mRNA and protein has a strong relationship.

Evolution

• How biologists determine the causes of phenotype patterns over time.

• Typically ascribe genetic drift to situations when we don’t see any clear patterns.

• Sexual selection impacts cases where males and females are diverging.

• Sorting is based upon a sexual feature due to male competition or female choice.

• Trends rather than stability are caused by selection.

  • Stabilizing Selection - population is stable.

  • Directional Selection - population is changing in a particular direction

• Look for patterns between males and females.

• Common Mistakes in Models:

  • Ensure data matches the model.

  • Clarify if the population distribution is maintained or changing.

• It's important that your data for these populations actually matches the model that you have.