Randall DeJong and Arlene Hoogewerf, Calvin College

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Integration of the GEP project with an upper level genetics course at Calvin College

Course Overview

GEP materials were integrated with a upper level Genetics and Development course in Fall 2009, 2010, and 2011. The course covers many topics, including advanced Mendelian considerations, recombination and gene mapping, deeper study of transcription and translation, recombinant DNA and bio-technology, modern genomics, developmental genetics, and elementary population and evolutionary genetics. The course meets for 3 lecture hours plus a 3 hour lab each week. The first six weeks of lab utilized traditional genetic laboratory exercises and the GEP project was implemented in the last six weeks. 


In 2009, the GEP materials used were:

Exercise #1: Detecting and Interpreting Genetic Homology

Exercise #2: Using mRNA and EST Evidence in Annotation

Worksheet: Chimp BAC Analysis: Genes and Pseudogene

  • There are now many more options in the GEP curriculum space that could be used!

Lessons Learned and Future Plans

All three years of implementation followed the general outline above, but differed in modest ways. Three different instructors were involved each of the years, and a trained or experienced TA was sometimes not available. The following were lessons learned:

  • It can be a bit difficult to engage three subpopulations of our Genetics and Development course: the focused pre-meds, the biochem majors, and the ecology/environmental students. Future inclusion of GEP may include more focused effort to establish the role of genomics in future medicine, to allow biochem majors to pursue additional avenues of investigation into protein structure (how informative/interesing would it be to compare 3D structure predictions for the same protein from two different species?), and to emphasize the use of DNA sequences in modern ecology and evolutionary studies. 
  • Students who already find molecular biology interesting are more engaged.
  • Having a trained TA (attended a workshop) or experienced TA (did well in the project in the previous year) is tremendously helpful. This was especially true in our laboratory sections, which had 16 students. This number of students will create more questions than a faculty member alone can handle.
  • Struggling students and even students with good understandings who have difficult projects require sustained help. It is easy to spend 20 minutes with just one student or student pair.
  • For most students, working in pairs works better than students working alone.
  • Six weeks of lab, with a introductory lecture or two beforehand, is just enough time to get a project done. Student work outside of lab time may be required.
  • The quality of student work was highly variable. 
  • Faculty and TA check of student work can be quite time-consuming.

Syllabus for Biology 321, Genetics and Development

(scroll down to bolded items pertinent to the GEP)

Biology 321: Genetics and Development
Calvin College
Course information and policies—Fall Semester 2009

Professor: Dr. Randall DeJong
Office: DH 109
Office phone: 526-7625
Email: rdejong@calvin.edu
Office hours: Mon. & Wed., 10:00 – 11:30 a.m. (please tell me after class you would like to meet)
Or whenever the door is open!

Course locations and times:
Lectures: Mon.-Wed.-Fri., 9 – 9:50 a.m., SB 202
Laboratory: Section LA: Tue., 8:30 – 11:20 a.m., Section LB: 1:30 – 4:20 p.m., SB 256
*Both sections will meet in Hekman Library Mac Lab for investigations in Bioinformatics and Genomics. See schedule for details and be alert for possible changes.

Genetics: Analysis and Principles, 3rd edition. Robert J. Brooker, McGraw-Hill, 2009. (Required)
Biology 321 Genetics Laboratory Manual. R. DeJong et al., Calvin College. (Provided)
Articles from the primary literature and popular press. (Provided)

Goals for the course:

1. To keep a focus on the “big themes and questions” of genetics and development. Like many areas of biology, the sub-disciplines of genetics and development are complicated, and contain many details. However, there are actually a relatively small number of basic, yet critical ideas that underlie our understanding of heredity and developmental biology.

2. To learn how this knowledge has been obtained. We need to know the key experiments, evidence, and reasoning behind the current theories in genetics and development. We should examine the data and understand how it is explained by the theories.

3. To discuss the implications of genetics and development. Genetics and developmental biology are critically relevant to current health, ethical, and political decisions we face as individuals, families, and societies.

4. To explore these disciplines from a Reformed Christian perspective. Scientific truth, if it is correct, reflects God’s truth. Yet, science can present new and challenging questions to all humans, including those who share a Christian worldview.

5. To strengthen our critical thinking skills. Scientific thought demands intellectual rigor.

6. To gain hands-on experience with laboratory and computational tools used in genetics. Our lab activities will reinforce concepts, but will also utilize real-world systems and strategies used in current scientific research.

7. To contribute scientific data to an ongoing study. Some of our in silico laboratory activities will be doing genome annotation in Drosophila species for current studies underway in the Genomics Education Partnership. Students who complete the annotation work will be eligible for authorship on a scientific publication.

Participation of this course in the Genomics Education Partnership
The Genomics Education Partnership (GEP) is a consortium of schools and instructors who have partnered with Sarah Elgin, a professor at Washington University in Saint Louis. She and her team of technicians and students, with funding from Howard Hughes Medical Institute, developed a joint project that brings real research and genomics into the classroom. Calvin College was admitted into the GEP in 2009. Two areas that you should be aware of regarding our participation in the GEP are:

1. Authorship: Since the GEP project allows students to analyze real genetic data, and their analysis will likely be used in a real scientific publication, this offers the opportunity for students to be included as co-authors. There are two requirements that must be met: 1) the student or team of students must complete their analysis of the data given them and submit all documentation and reports to the GEP, and 2) the student must provide their contact information such that they can reached in the future to view and sign their approval to the publication. More information will be provided when the GEP part of the course is begun.
2. Voluntary surveys:
The GEP needs to assess the effectiveness of the program. Students are requested to take two voluntary surveys each at the beginning of the semester and at the end of the semester. More information will be provided during the first class periods.


1. Office hours: My formal office hours are above, but you are welcome to see if I am available at any time.

2. Attendance in lecture is not required, but excellence in class participation can affect your final grade, and in-class activities cannot be made up. In addition to classroom discussion, in-class activities will include small group work and problem solving, and will not usually be announced in advance. Attendance in lab is required.

3. Assignments are due at the beginning of class for the due date given. Work that is turned in late will incur a penalty of 10% for the first day and 10% more for each additional day late.

4. Assistance is available to you in various forms, so talk to me if you need help. Also, Calvin will make reasonable accommodations for persons with documented disabilities. Notify a Coordinator of Services to Students with Disabilities located in Student Academic Services, HH 446, and notify me within the first two weeks of class.

5. Grades are assigned based on:

15% Writing (reflections, article review)
10% Quizzes, problem sets & in-class work
10% First test
10% Second test
10% Third test
20% Final exam
25% Laboratory assignments

% score Grade
95-100 A
90-94 A-
87-89 B+
83-86 B
80-82 B-
77-79 C+
73-76 C
70-72 C-
67-69 D+
63-66 D
60-62 D-
<60 F

6. Reading assignments (listed below) indicate the chapters and/or pages being covered in the corresponding class section (4:all = all of the chapter, 23.6 = section 23.6, 3: pp. 35-36 = pages 35-36). Additional handouts and any modifications to textbook reading will be provided in class. Please read all materials before class.

7. Tests and quizzes. Please note that test dates follow the Deans’ test schedule for the college. All tests must be completed on the day and time they are scheduled unless extenuating circumstances are present. These include illness, family emergency, etc. To take the test at an alternative time, you must 1) have a legitimate reason (e.g., illness) for missing it, 2) notify me by telephone or email of the problem as soon as you know of the problem, and 3) provide me with written documentation confirming the problem. Such documentation must be prepared by a physician or other disinterested party. If the justification for missing the test is satisfactory, you may take it at an alternative time, to be scheduled previous to the regular time where possible, or as soon after the regular time as possible. If the reason for the absence is not satisfactory, you will receive zero points for the test.

Date Topics Reading (ahead of lecture) Assignment
(due date provided when assigned)

Sep. 9 Welcome, overview, early Genetics, Mendel 1: all
Sep. 11 Mendelian genetics review, probability, chi-square analysis, binomial expansion 2: all Selected Ch. 2 problems.

Sep. 14 Chromosomes, meiosis, sex-linkage 3: all
Sep. 16 Chromosome variations, cytogenetics 8: 8.1, 8.2 Selected Ch. 3 & 8 problems.
Sep. 18 Cytogenetics wrapup / Begin Mendelian ext.

Sep. 21 Extensions of Mendelian genetics 4: all Selected Ch. 4 problems.
Sep. 23 Extensions of Mendelian genetics continued as above Writing assignment 1
Sep. 25 Genetic mapping 5 & 6: pp. 100-121, 134, 142, 150-155 Selected Ch. 5 & 6 problems. Drosophila exercise.

Sep. 28 Genetic mapping as above
Sep. 30 Quantitative genetics 25 Assignment of presentations
Oct. 2 Test 1

Oct. 5 DNA. Key experiments - Group presentations (3) 9: all, esp. pp. 222-227
Oct. 7 Chromosome structure. DNA replication. Presentations (2) 10: all, esp. p. 263 Selected problems from Ch. 9, 10, 11
Oct. 9 DNA replication. 11: esp. pp. 272-274, 277-280, 286-287

Oct. 12 Mutation and repair. 16: 424-442 Selected problems from Ch.16
Oct. 14 Transcription and translation. Presentation on deciphering genetic code (1) 12: all
13: 324-332
Oct. 16 Finish translation. Presentation on tRNA adaptor hypothesis (1) 13 339-355 Selected problems from Ch. 12 & 13

Oct. 19 Gene regulation. Presentation on Fire and Mello discovery of RNA silencing (1) 14: 360-376
Oct. 21 Gene regulation. 15: 388-414 Selected problems from Ch. 14 & 15
Oct. 23 Genomics 20

Oct. 26 Genomics 20 Writing assignment 2
Oct. 28 No class – Advising Recess
Oct. 30 Test 2

Nov. 2 Genomics 21
Nov. 4 Genomics and society 21
Nov. 6 Medical genetics and cancer 22

Nov. 9 Flex; Discussion of current paper in genomics
Nov. 11 Recombinant organisms and applications 18 & 19 Selected problems from 18 & 19
Nov. 13 Recombinant organisms and applications 18 & 19

Nov. 16 Recombination at the molecular level 17
Nov. 18 Population genetics 24 Selected problems from 17 & 24
Nov. 20 Population genetics 24

Nov. 23 Evolutionary genetics 26
Nov. 25 Evolutionary genetics handouts Selected problems from 26
Nov. 27 No class – Thanksgiving break

Nov. 30 Evolutionary genetics
Dec. 2 Flex; human genetic history handouts
Dec. 4 Test 3

Dec. 7 Non-Mendelian inheritance / development 7: pp. 160-177
Dec. 9 Developmental genetics 23
Dec. 11 Developmental genetics 23; 26.3

Dec. 15 Tuesday, Dec. 15
Final Exam, 1:30 p.m.
Please note that test dates follow the Deans’ test schedule for the college.

Date         Activity
Sep. 10    Live organism genetics: Setup cultures of C-fern, Sordaria, and yeast
Sep. 17    Live organism genetics: Monitor C-fern; observe and score Sordaria; setup yeast mutant screen
Sep. 24    Live organism genetics: Monitor C-fern; score yeast & repeat mutant screen
Oct. 1      Live organism genetics: Score C-fern; score yeast; collect class data
Oct. 8      Molecular techniques 1
Oct. 15    Molecular techniques 2
Oct. 22    Molecular techniques 3
Oct. 29    Chimp chunk– Mac Lab, Hekman 120
Nov. 5     Drosophila annotation– Mac Lab, Hekman 120
Nov. 12   Annotation work– Mac Lab, Hekman 120
Nov. 19   Annotation work– Mac Lab, Hekman 120
Nov. 26   No lab -- Thanksgiving
Dec. 3     Annotation work– Mac Lab, Hekman 120
Dec. 10   Presentation of final annotations & report submission