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Biol 3060 Spring 2017

SYLLABUS for PRINCIPLES OF GENETICS (BIOL 3060) L. Etchberger, 4 credits Face-to-Face at Utah State University Uintah Basin, Vernal Tuesdays and Thursdays / 5:15 – 7:15 pm / Room 129 Changed to: M & W / 2-4pm / Room B223K

“The problem [with genetic research] is, we're just starting down this path, feeling our way in the dark. We have a small lantern in the form of a , but the lantern doesn't penetrate more than a couple of hundred feet. We don't know whether we're going to encounter chasms, rock walls or mountain ranges along the way. We don't even know how long the path is.

— Francis S. Collins Quoted in J. Madeleine Nash, et al., 'Tracking Down Killer ', Time magazine (17 Sep 1990).

INSTRUCTOR Lianna Etchberger, Ph.D. Office: 221E, BEERC Bldg, USU Uintah Basin, Vernal / (435) 722-1783 / [email protected]

OFFICE HOURS Wed & Thu, 9:00 – 10:00 am, drop in, and by appointment I am happy to meet with you in person, by phone, or via Adobe Connect Conference in Canvas. Adobe connect is a great video conferencing medium where we can talk and share documents just as if we were in the same room together. I respond most quickly to Email or Canvas messaging. If you are in Vernal, stop by any time you find me in my office.

RATIONALE & COURSE DESCRIPTION This Quantitative Intensive (QI) course is required for and other majors. It provides an introduction to the basic principles of transmission, , and molecular aspects of modern genetics, and is intended for those pursuing further study in biology and related fields. This course prepares students for upper-division biology courses as well as professional programs such as medical, dental, and veterinary school. A problem-based, group learning approach is used to understand molecular mechanisms of inheritance, and how both genetic and environmental factors influence traits in . We will explore recent advances in biomedical research and its applications to disease. This course does not include a laboratory component; Genetics Laboratory (BIOL 3065) is a separate course that can be taken separately or concurrently. Prerequisite/Restriction: BIOL 1610; CHEM 1110 or CHEM 1210.

MATERIALS: OPEN EDUCATION RESOURCES To save students some money, we are using Open Educational Resources (OER) in this course; no need to purchase a textbook. OER can come in a variety of formats such as text, video, audio, and mixed media.

Most OER content requires some access to the Internet since most of the content is stored online. You can use either your own personal computer or a computer in a computer lab on campus to view OER online or to download it. Downloading OER onto your personal computer or laptop allows for quick and

Page 1 of 7 Biol 3060 Spring 2017 easy reference. When materials have been downloaded, you may:

• Access materials at any time with or without being connected to the internet • Have the ability to annotate and highlight material (with certain programs such as Adobe Reader) • Create a custom study sheet (copy and paste specific content from OER into a Word document and then customize it)

For questions, about OER, please contact Erin Davis, Regional Campus Librarian, [email protected] or 435-797-2075.

Our course will follow the organization of Open Online Genetics (OOG), an online textbook. Resources for each week’s content and learning will be organized in Canvas, our course management system.

Primary OER used in our course: • Open Online Genetics- online text (under development) by Nickle and Barrette-Ng at http://bio.libretexts.org/TextMaps/Map%3A_Online_Open_Genetics_(Nickle_and_Barrette-Ng) • Scitable by Education at at http://www.nature.com/scitable • Dolan DNA Learning Center- Resources at https://www.dnalc.org/resources/ • HHMI BioInteractive- Genetics at http://www.hhmi.org/biointeractive/genetics

COURSE LEARNING OBJECTIVES Learning outcomes in this course are driven by concept and competency recommendations from professionals across the nation. Our course closely follows of America’s Genetics Learning Framework. Also included are appropriate concept and competency recommendations in the 2011 Vision and Change in Undergraduate Biology Report from the American Association for the Advancement of Science.

After successful completion of this course, students will be able to: • Describe the molecular of genes and • Contrast different types of and predict how each can affect genes and the corresponding gene products, alter existing traits, and create novel traits • Describe the mechanisms by which an 's is passed on to the next generation • Describe the phenomenon of linkage and how it affects the assortment of genes during • Analyze phenotypic data from family histories to deduce patterns of inheritance • Design genetic crosses to test hypotheses about inheritance • Analyze the progeny from genetic crosses to extract information about genes, , linkage and gene functions • Apply the results of molecular genetic studies in model organisms to understanding aspects of human genetics and genetic diseases • Describe the processes that can affect the frequency of in a population over time • Interpret molecular data to determine the identities and inheritance patterns of human genes that can mutate to cause disease • Use data to investigate genetic traits and evolutionary relationships • Use quantitative reasoning • Use modeling and simulation • Tap into the interdisciplinary nature of genetics and its impacts on society

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COURSE : GROUP LEARNING I view my role as your instructor not to tell you what is in the readings by lecturing (you can read), but to provide opportunities for you to learn complex concepts and skills that you may not glean directly from the readings. I believe that our time together is better used to construct your knowledge of genetics. So, to achieve the genetics learning goals (listed above), and to develop the course skill objectives (listed below), I have designed this course to implement small group work.

Course objectives Individual and Small Group Learning Activities Used in IDEA course evaluation at USU For achieving objectives and learning goals Gain factual knowledge (terminology, Individual work: classifications, methods, ) • Guided reading (outside of class) Learn fundamental principles, • Individual Readiness Assurance Tests (; before class) generalizations, or theories • Homework problems (after class) • Exams (in Testing Centers) Learn to apply course material (to improve Group work in class: rational thinking, problem solving and • Application activities decisions) • Peer and instructor feedback

COURSE ASSESSMENT Readiness Assessment Tests (RATs). The success of this course relies on students coming prepared to class. RATs are intended to help you learn simple concepts before class, and to prepare you to learn more difficult concepts in class with the support of the instructor and your peers. Use the Reading Guides to focus your reading. The RATs are taken online in Canvas with a reasonable time limit to encourage you to do the reading before taking the test. You will have TWO attempts at the RAT, and your grade will be the highest attempt. The lowest 2 scores at the end of the semester will be dropped. RATs MAY BE ADDED TO THE COURSE IF NEEDED TO IMPROVE LEARNING. In-class Application Assignments. We will practice applying genetics concepts and skills in class with the help of feedback from your peers and me. Check Canvas before class to see what you need to bring to class for the various application activities. Homework Assignments. You will be assigned homework activities to help reinforce course material. Homework assignments include problems to solve and online quizzes. Check the Canvas calendar for due dates. Exams. You will take exams in the testing center at your site. Exams will assess concepts from the reading, lectures, activities and homework. All learning is guided by the learning objectives listed in the Reading Guides. Focus on these learning objectives as you study for the exams. Exams are comprehensive (will include concepts the class struggled with from the last exam), and may include multiple choice, fill- in-the-blank, matching, short essay questions and problems. The final exam includes a section on new material plus a comprehensive section on material from earlier exams.

LATE SUBMISSIONS All materials submitted late lose 10% of the possible points per day. For example, if you turn in an assignment two days late, I will deduct 20% prior to grading. To avoid losing points, submit your work on time or early if possible. If you cannot submit your assignment to me or to your site TA during class, then you can scan and email to me, or upload to Canvas. You can also submit to a TA at your site who will stamp the submission date and deliver the assignment.

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GRADING Your grade in this course depends on the percentage of total possible points you earn in weighted categories. The tables below describe how your final grade will be determined.

Total Points Possible Final Grade Contributions to Grade: 93-100% A 20 % Readiness Assessment Tests (RATs) 90-92% A- 87-89% B+ 20 % Homework and other assignments 83-86% B 60% Comprehensive Exams 80-82% B- 77-79% C+ 73-76% C Grade weights will be applied to the Canvas grade book so you 70-72% C- can follow your course grade as the semester progresses. Final 67-69% D+ 60-66% D grades will be determined using the scale in the table to the Below 60% F right.

INSTRUCTOR’S RESPONSIBILITIES I will help you learn by engaging you in the material and challenging you to think like a . You can expect me to attend all classes, and prepare RATs, activities and examinations that are fair and representative of the material covered in the reading and other assigned preparation materials. I will be available by email, telephone, or in my office during the day, and respond as soon as possible to answer specific questions and provide any needed assistance toward the learning objectives.

STUDENTS’ RESPONSIBILITIES You are expected to attend each class meeting. You will set up notifications to receive Canvas announcements. You will practice problem solving and reviewing concepts by using the Learning Objectives (study guides) to study for RATs, application exercises, and exams. You will make every effort to be a productive group member by applying the guidelines provided for useful discussion and helpful feedback (see Working In Groups on Canvas Study Tips page). Group conflicts should be addressed in the group. I will become involved only in extreme situations. In the event that there is any difficulty in keeping up with the pace of the course, it is YOUR responsibility to contact me for advice or assistance. If you cannot take an exam during the scheduled period, you must make other arrangements with me at least 48 hours before the exam is given. If you cannot attend a class, you are still responsible for all content. (I strongly suggest establishing contact methods with your genetics-buddies right now!)

ATTENDANCE Attendance is very important to be successful in this course. However, I do not keep track of attendance per se (other than clicker participation). Be aware that you are fully responsible for all announcements made and material covered in the lecture portion of the course. Use your biology-buddies!

USE OF MOBILE DEVICES AND LAPTOPS IN CLASS As research shows, multi-tasking and unexpected noises and movement automatically divert and capture people’s attention, which means that you are negatively affecting your everyone else’s learning experience if your phone goes off, images move on your laptop screen, etc. For this reason, I expect you to turn off your mobile devices (even vibrate can be distracting). If you must use a laptop, please mute it and sit behind other students. If you must answer your silenced mobile device in the case of an emergency, please leave the room before speaking. The bottom line- DO NOT DISTURB OTHERS.

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INCLUSIVITY We understand that our members represent a rich variety of backgrounds and perspectives. The biology department is committed to providing an atmosphere for learning that respects diversity. While working together to build this we ask all members to: • share their unique experiences, values and beliefs • be open to the views of others • honor the uniqueness of their colleagues • appreciate the opportunity that we have to learn from each other in this community • value each other’s opinions and communicate in a respectful manner • keep confidential discussions that the community has of a personal (or professional) nature • use this opportunity together to discuss ways in which we can create an inclusive environment in this course, at USU, and across the Uintah Basin community

UNIVERSITY POLICIES

The entire USU Student Policy Manual can be read online at http://catalog.usu.edu/content.php?catoid=12&navoid=3587 I highlight some of the most relevant policies below.

Students with Disabilities Please address any special needs or special accommodations with me at the beginning of the semester or as soon as you become aware of your needs. The Americans with Disabilities Act states: "Reasonable accommodation will be provided for all persons with disabilities in order to ensure equal participation within the program." If a student has a disability that will likely require some accommodation by the instructor, the student must contact the instructor and document the disability through the Disability Center (797- 2444), preferably during the first week of the course. Any request for special consideration relating to attendance, pedagogy, taking of examinations, etc., must be discussed with and approved by the instructor. In cooperation with the Disability Resource Center, course materials can be provided in alternative format, large print, audio, diskette, or Braille. For more information go to http://www.usu.edu/drc/

Withdrawal and Incomplete Grade Students are required to complete all courses for which they are registered by the end of the semester. In some cases, a student may be unable to complete all of the coursework because of extenuating circumstances, but not due to poor performance or to retain financial aid. The term 'extenuating' circumstances includes: (1) incapacitating illness which prevents a student from attending classes for a minimum period of two weeks, (2) a death in the immediate family, (3) financial responsibilities requiring a student to alter a work schedule to secure employment, (4) change in work schedule as required by an employer, or (5) other emergencies deemed appropriate by the instructor. If an incomplete grade is to be given, an Incomplete Grade Documentation Form must be filed by the instructor in the department or college office. Students may not be given an incomplete grade due to poor performance or in order to retain financial aid. An incomplete grade may be granted only if the student has completed the majority of the course and is passing the class at the time. http://catalog.usu.edu/content.php?catoid=12&navoid=3805

Classroom Incivility Utah State University supports the principle of freedom of expression for both faculty and students. The University respects the rights of faculty to teach and students to learn. Maintenance of these rights requires classroom conditions that do not impede the learning process. Disruptive classroom behavior will not be tolerated. An individual engaging in such behavior may be subject to disciplinary action.

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Faculty members of Utah State University have the responsibility and authority to determine, maintain, and enforce an atmosphere in their classrooms that is conducive to teaching and learning, in accordance with University policy and practice. Read more at http://catalog.usu.edu/content.php?catoid=12&navoid=3171

Academic Honesty and Integrity – The “Honor Pledge” Each student has the right and duty to pursue his or her academic experience free of dishonesty. The Honor System is designed to establish the higher level of conduct expected and required of all Utah State University students. To enhance the learning environment at Utah State University and to develop student academic integrity, each student agrees to the following Honor Pledge: "I pledge, on my honor, to conduct myself with the foremost level of academic integrity." Violations of the Academic Integrity Standard (academic violations) include, but are not limited to: 1. Cheating: (1) using or attempting to use or providing others with any unauthorized assistance in taking quizzes, tests, examinations, or in any other academic exercise or activity, including working in a group when the instructor has designated that the quiz, test, examination, or any other academic exercise or activity be done "individually"; (2) depending on the aid of sources beyond those authorized by the instructor in writing papers, preparing reports, solving problems, or carrying out other assignments; (3) substituting for another student, or permitting another student to substitute for oneself, in taking an examination or preparing academic work; (4) acquiring tests or other academic material belonging to a faculty member, staff member, or another student without express permission; (5) continuing to write after time has been called on a quiz, test, examination, or any other academic exercise or activity; (6) submitting substantially the same work for credit in more than one class, except with prior approval of the instructor; or (7) engaging in any form of research fraud. 2. Falsification: altering or fabricating any information or citation in an academic exercise or activity. 3. Plagiarism: representing, by paraphrase or direct quotation, the published or unpublished work of another person as one's own in any academic exercise or activity without full and clear acknowledgment. It also includes using materials prepared by another person or by an agency engaged in the sale of term papers or other academic materials. Read more about Academic Honesty and Integrity at http://catalog.usu.edu/content.php?catoid=12&navoid=3140

Grievance Process (Student Code) Students who feel they have been unfairly treated [in matters other than (i) discipline or (ii) admission, residency, employment, traffic, and parking - which are addressed by procedures separate and independent from the Student Code] may file a grievance through the channels and procedures described in the Student Code: Article VII Grievances at https://studentconduct.usu.edu/studentcode/article7

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Tentative Course Schedule Principles of Genetics (Biol3060), Spring 2017, L. Etchberger

OER Textbook: Open Online Genetics (OOG) by Nickel and Barrette-Ng at http://bio.libretexts.org/TextMaps/Map%3A_Online_Open_Genetics_(Nickle_and_Barrette-Ng)

Date Topic OOG RAT UNIT 1. The Genetic Material T Jan 10 Overview: DNA and Genes 1 RAT 1 R Jan 12 “ M Jan 16 No Class- MLK Holiday W Jan 18 , & Meiosis 2 RAT 2 Exam 1 in Testing Center (Jan 21&21) UNIT 2. Transmission Patterns & Variation in M Jan 23 of Single Genes 3 RAT 3 W Jan 25 “ M Jan 30** and Variation 4 RAT 4 W Feb 1 “ M Feb 6 Pedigrees & Populations 5 RAT 5 W Feb 8 Populations M Feb 13 “ Exam 2 in Testing Center (Feb 17&18) UNIT 3. Gene Interactions, Linkage and Mapping W Feb 15 Genetic Analysis of Multiple Genes 6 RAT 6 M Feb 20 W Feb 22 Linkage and Mapping 7 RAT 7 M Feb 27 Exam 3 in Testing Center (Mar 3&4) UNIT 4: & Studying Genes and Genomes W Mar 1 Techniques of Molecular Genetics 8 RAT 8 Mar 6-10 USU SPRING BREAK M Mar 13 Changes in Number and Structure 9 RAT 9 W Mar 15 M Mar 20 Molecular Markers and Quantitative Traits 10 RAT 10 W Mar 22 M Mar 27 and 11 RAT 11 W Mar 29 Exam 4 in Testing Center (Mar 31 & Apr 1) UNIT 5: The Importance of Regulating M Apr 3 Regulation of Gene Expression 12 RAT 12 W Apr 5 M Apr 10 Developmental Genetics Devo RAT Devo W Apr 12 M Apr 17 Genetics 13 RAT 13 W Apr 19 M Apr 24 Discussion: Genetics and Society TBA W Apr 26 Review May 1-4 Final Comprehensive Exam in Testing Center **M Jan 30 is last day to drop without notation on transcript Page 7 of 7