Biology 201: Genetics
Spring 2017, Davidson College

This is the public version of the syllabus. Davidson students should go here for the complete version (login required)

MWF 9:30-10:20 in Wall 320
Lab Mon 1:30 or Tues 1:40 in Dana 256

Dr. Karen Hales
Dana 201A, x2324


Course schedule 
go to Jan, Feb, Mar, Apr, May
lab syllabus
lab manual contents
Genetics news:
Science Daily Genetics
Genetics Literacy Project
The Scientist
New Scientist

Learning outcomes
By the end of the course, students will be able to explain, verbally and in writing, answers to the questions below. Students will be able to apply their knowledge toward formulating and articulating ethical arguments based on scientific evidence, as well as assessing the accuracy and plausibility of genetic descriptions in the news and in popular culture. In the laboratory students will be able to design and execute experiments that combine classical and molecular genetics of the fruit fly Drosophila melanogaster.

Resources and textbooks
We will use digital resources only for this class, with links in the course schedule below.
While no print book is required, you may benefit from having access to a recent Genetics text as background reference. Good options include Hartwell, Griffiths, Hartl, Hyde, Brooker, and Sanders and Bowman. I have several books I can loan out for the semester.

Office hours
Mondays 9:00-9:45 AM and Wednesdays 1-2 PM, as well as Tuesday Common Hours when I don't have other meetings. You will receive a link for an online signup process. I'll update that page with new dates and times as the semester progresses, adding extra slots according to demand. I can meet with you at other times, too--stop by if my door is open, or email for an appointment (list several possible dates/time ranges).

Email: You are responsible for all information I send by email, so check your messages each day.

Grading: Your final course grade will be calculated as follows. At the end of the semester I usually adjust everyone's average upward by the same amount before assigning the corresponding letter grade.

Two reviews
Short quizzes
Two writing assignments
Lab assignments
Lab report/poster
Final exam
Participation, effort, initiative
30% (15% each)
10%
15% (7.5% each) 5%
12%
20%
8%

%
94-100
90-93.9
87-89.9
83-86.9
80-82.9
77-79.9
73-76.9
70-72.9
67-69.9
60-66.9
0-59.9
Course grade
A
A-
B+
B
B-
C+
C
C-
D+
D
F

Attendance and participation
In class I do not record attendance. However, if you are not there to participate, your participation grade is affected. Laboratory sessions are mandatory. An unexcused absence from lab will result in a full letter grade deduction from your course grade.

Honor Code
You are to affirm your respect for and compliance with the Davidson Honor Code on every assignment. The full Honor Pledge reads as follows: "On my honor I have neither given nor received unauthorized information regarding this work, I have followed and will continue to observe all regulations regarding it, and I am unaware of any violation of the Honor Code by others." Plagiarism is an Honor Code violation and is defined as representing another person's words and ideas as one's own. Please carefully read the Davidson Department of Biology statement on plagiarism for comprehensive information on what constitutes plagiarism and how to avoid it.

Classroom etiquette and use of electronic devices
Do not leave the classroom in the middle of class unless it is a true emergency (in lab it's fine to step out briefly at appropriate stopping points). Set cell phones to silent/no vibration so that they do not disturb or distract you or others. Take handwritten notes unless you have received my permission to use a laptop (here's why). Laptops, tablets, and cell phones must be closed or face down on your desk unless I have assigned you to investigate something on the internet during class.

Policy on recording of class
Davidson College policy prohibits audio and video recording of classes by students without permission of the instructor. I will consider permission requests on a case-by-case basis. For students with a disability, permission will always be granted when the accommodations authorized by the Dean of Students Office include recording. Authorized recordings are for the sole use of the individual student and may not be reproduced, sold, posted online, or otherwise distributed.

Disabilities
I will do my best to provide accommodations for students with learning or physical disabilities. If you have a learning disability documented by Davidson College, please let me know during the first week of class so that arrangements can be made. I encourage students with other disabilities to self-identify (confidentiality guaranteed) so that we may explore ways to enhance your learning.

Class materials
PowerPoint files used in class will be posted online by the previous evening. I use PowerPoint only to provide illustrations and outline some topics; viewing a PowerPoint file does **not** substitute for attending class. Click the link from the schedule below to download; log in with email credentials. To print, please first set options to include multiple slides per page.

Assignments, study questions, daily quizzes
Assignments on the syllabus (reading, listening, viewing, etc.) relate to the topic of that day. You should be familiar with the material before coming to class. You may be quizzed on that material on the subsequent class day. Study questions are provided; they will not be collected, but they may show up as quiz questions.

Reviews
Reviews will be take-home, closed book, and closed notes.
Review #1 available 2/20, due 2/24 at 10:30 AM
Review #2 available 3/29, due 4/3 at 10:30 AM
The final exam will be in the Chambers self-scheduled exam center.

Writing assignments
There will be two short writing assignments later in the semester, one analyzing part of a journal article and one exploring popular culture depictions of genetics; see prompts within the schedule below.
Writing assignment #1 due 4/14 at 10:30 AM
Writing assignment #2 due 5/3 at 10:30 AM

Lab assignments
In lab you will turn in a short write-up or other assignment at the end of some lab sessions. The formal lab report at the end of the semester will be in the form of a research poster, due 5/8 or 5/9 at the beginning of your scheduled lab period. See lab syllabus for details.

Penalty for late assignments
Everyone gets a one-time pass to turn in one single review or assignment up to 24 hours late with no penalty (not counting the final exam, however). After that, the late penalty is ten percent per day or part thereof. The full ten percent penalty applies starting at the beginning of each day that the assignment is late; for example, an assignment that is one hour late will have a ten percent penalty applied.

Math and Science Center
The Math & Science Center (MSC) offers free assistance to students in all areas of math and science, with a focus on the introductory courses. Trained and highly qualified peers hold one-on-one and small-group tutoring sessions on a drop-in basis or by appointment, as well as timely recap sessions ahead of scheduled reviews. Emphasis is placed on thinking critically, understanding concepts, making connections, and communicating effectively, not just getting correct answers. In addition, students can start or join a study group and use the MSC as a group or individual study space. Located in the Center for Teaching & Learning (CTL) on the first floor of the College Library, drop-in hours are Sun-Thurs 8-11 PM and Sun/Tues/Thurs 4-6 PM, beginning the second week of the semester. Appointments are available at other times. For more information, visit the website or contact Dr. Mark Barsoum (mabarsoum or ext. 2796).

 

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Course schedule
Go to Feb, Mar, Apr, May

Date

Topic

Links active by the evening before class (use email credentials). If you print ppt slides, conserve by printing double-sided, multiple slides per page.

Assignments

Do assignments before class.

Everything is fair game for quizzing on the class day after we cover it.

Study questions

To guide you toward the most relevant concepts in the assignments. Will not be collected, but will likely show up as quiz questions.

W 1/18

DNA structure

Read the whole syllabus. You are responsible for all the information and requirements detailed therein.

How do we know DNA is important?

DNA structure


Special assignment to be fulfilled by Fri Jan 27 at 4 PM: come see me in my office for five minutes. Make an appointment via Slotted; use your personalized URL. The purpose is to familiarize you with the location of my office and to help me get to know you. A visit must take place for me to record your grade on the first review.


F 1/20

RNA structure and protein structure

RNA structure

Protein structure



M 1/23 Transcription, RNA processing, and translation Transcription 

mRNA processing


Translation


W 1/25

DNA replication, mitotic cell division, and packaging of the genome


DNA replication

Mitosis

DNA packaging and coiling in the nucleus

F 1/27

Genome projects Human Genome Project

The many non-human genome projects

DNA sequencing by the Sanger method

Special assignment (office visit) due today.

M 1/30

How genomes are sequenced now Next generation DNA sequencing (Illumina method)

Assembling whole genomes from short fragment reads

The $1000 genome and individual sequencing


W 2/1

Features and organization of genomes: how are we different and the same?

Landscape of genomes

F 2/3

Techniques for typing genomes

Surprises when typing someone--mosaicism and chimerism
Techniques for analyzing genomes

Mosaicism and chimerism

M 2/6

DNA fingerprinting

DNA fingerprinting: typing STRs and analyzing allele frequencies

Animal forensics

W 2/8

Intro to gene regulation: where, when, and why?

3D genome structure in the nucleus, and intro to epigenetics

Gene expression differences in time and space

3D genome structure in the nucleus

Epigenetics intro: DNA and histone modifications


F 2/10

Gene regulation: Epigenetics Epigenetic regulation that most genes undergo during development

For just a handful of a genes: imprinting

Epigenetics and X chromosome inactivation

Epigenetic changes from environmental effects


M 2/13

Gene regulation: transcriptional activation/repression

Transcriptional regulation

W 2/15

Gene regulation: RNA splicing and RNA interference Alternative splicing of RNA

RNA interference

F 2/17


Gene regulation: RNA localization, translation, and post-translational modifications

RNA localization within a cell

Translational regulation

Post translational modifications of proteins

M 2/20

Mutations--where, when, and how do they originally occur? How do we classify mutations at different levels?

Mutation mechanisms and DNA repair
Mutations 

DNA repair


Take home review #1 available today and due F 2/24 at class time

W 2/22

Catch up day

No new homework for today; take the take-home review early enough to leave time for Friday's homework.

F 2/24

Mutations and genetic disorders:
osteogenesis imperfecta case study
Take home review #1 due at 10:30 AM

Many genes can be associated with one disorder

One gene can be associated with many disorders
I
Extra or missing stop codons have unexpected effects


M 2/27

Mutations can affect gene regulation steps and cause disorders: prostate cancer and progeria case studies Mutations affecting gene regulation steps


W 3/1 Meiosis

Larger scale mutations at the level of chromosome number and  structure

Meiosis

Chromosome number mutations

Inversions

Translocations

F 3/3

Inheritance of mutations: Mendel's observations connect to meiosis and chromosome segregation

Chromosome segregation and allele frequencies in a population over time
Mendel and basic inheritance patterns

Connecting Mendel's observations to chromosome behavior

Extending Mendelian patterns to a population level

M 3/6

SPRING BREAK



W 3/8

SPRING BREAK    

F 3/10

SPRING BREAK



M 3/13

More on population genetics

The folly of the eugenics movement

Effects of selection on H-W equilibrium

Early 20th century eugenics movement


W 3/15

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Probability assessment for single gene disorders in an affected family and in a population

Pedigree analysis

F 3/17

Interactions among alleles of a single gene; variations on dominance and recessivity

Penetrance and expressivity

Dominance and recessiveness; also lethal alleles


M 3/20

Linkage and independent assortment
Linkage and independent assortment


W 3/22

Early gene hunts: linkage mapping
Linkage mapping

Variation on recombination: Mitotic recombination


F 3/24

Newer gene hunt techniques Exome or full genome sequencing

Genome wide association studies (GWAS) for complex traits

M 3/27

Uncovering the genetics of complex traits governed by many genes and the environment (aka
"quantitative genetics")

What is "heritability"?

Twin studies and controversies

Dissecting behavioral traits: OCD and autism


W 3/29

More on quantitative genetics and the genetics of behavior

Dissecting complex traits: artistic ability and sexual orientation

Take home review #2 on material through quantitative genetics distributed today and due M 4/3 at 10:30 AM.


F 3/31

NO CLASS--Dr. H at a conference Since there's no class, do the take-home review early so that you leave plenty of time for Monday's homework!   

M 4/3

Transgenerational epigenetic inheritance

Take home review #2 due at 10:30 AM.

How can epigenetic gene regulation pass through generations?


W 4/5

Genetic studies in model organisms are essential for understanding how human genes work

New gene editing techniques

Model organisms

CRISPR gene editing techniques


Planning ahead for Writing assignment #1 due F 4/14 (see 4/14 entry below for details)

F 4/7

Genetic therapies for single gene disorders and cancer Therapies via gene addition, splice modulation, or CRISPR


M 4/10

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Journal article discussion

CRISPR for sickle cell therapy


W 4/12

DNA testing: what happens at the doctor or at the online commercial service? Testing for disorders in adults and IVF embryos

Genetic tests during typical pregnancies

Direct-to-consumer DNA testing

F 4/14

Pharmacogenomics

Writing assignment #1 due today:

Pharmacogenomics
Grading rubric for writing assignment #1
Explanation of experimental goals: 15 pts
Explanation of techniques used: 15 pts
Explanation of graphical depictions of results: 15 pts
Explanation of why the results show what the authors claim: 15 pts
Proper use of terminology: 10 pts
Summary of what the paper went on to show: 5 pts
TOTAL 75 pts

M 4/17

NO CLASS--holiday break

W 4/19

Cloning as a reproductive or therapeutic option; link to stem cells.

Cloning organisms; therapeutic cloning and stem cell connection

Cloning pets? Can scientists bring back a mammoth?


Planning ahead for genetics in pop culture writing assignment due W 5/3
(see 5/3 entry below for details). See me by M 4/24 if your group cannot obtain or access your film through the library or other method.

F 4/21

Bacteria and our microbiome

Horizontal gene transfer

Bacteria and our microbiome

Horizontal gene transfer (HGT) in bacteria

HGT beyond bacteria

M 4/24

Genetic modification of microorganisms Recombinant DNA technology

What was the public discourse when genetic modification first began
?

Uses for genetically engineered microbes

W 4/26

Genetic modification of animals Transgenic animals for human health applications

Transgenic animals for food

Do gene-edited organisms count as transgenic?

F 4/28

Genetic modification of plants

How food has been genetically modified in traditional agriculture

More precise technologies--but which products should be called GM?

Engineering for pest/pathogen resistance

Engineering for other agricultural reasons

Engineering for human health benefits


M 5/1

Genetic modification of plants

Taking a science-based approach on a fraught topic


W 5/3

Genetics in pop culture

Writing assignment #2 due today: In advance, as a group watch a (previously chosen/assigned) film with genetics themes and discuss it. Each group will watch a different film--see list at right. Individually in writing, analyze one or two specific genetic issue(s) depicted in the film in detail. Cite specific scenes/examples. Explain what is accurate and what is not, and why. Frame your essay as an educational piece to high school students or the general public who may hold mistaken ideas about genetics from the film. 800 word maximum. Hard copy due at the beginning of class.

Before class, as a group find a link to a key relevant scene and send it to me so that in class we can view and discuss it.
Possible films: X-men, GATTACA, Multiplicity, The 6th Day, Boys from Brazil, Spiderman, Godsend, Splice, The Fly, The Island

Grading rubric for writing assignment #2
Choice of topic: 10 pts
Clarity/accuracy: 20 pts
Depth: 15 pts
Targeting the proper audience: 15 pts
Proper use of terminology: 15 pts
TOTAL 75 pts

F 5/5

Genetics in pop culture wrap up

Revisiting ethics of genetics issues

 
M 5/8 Genetics into the future. Course evaluations.

W 5/10
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Question and answer session in preparation for final.

F 5/12- Th 5/18

Take home final exam, due for SENIORS at 4 PM on Monday May 15th; for everyone else 4 PM Thursday May 12th.


 

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