Bio 105. Ecology and Evolution Course Information

INSTRUCTOR: Conrad Toepfer, Office: 320S, Phone: 686-4221 (office),

e-mail: conrad.toepfer@brescia.edu MEETING TIMES: Lecture 10:00-10:50 MWF

Lab 2:00-3:50 W or Th OFFICE HOURS: 8:30-9:20 TTh, 1:00-4:00 F or by appointment Facebook Office Hours: 7:30-10:00 p.m. Sunday and Tuesday REQUIRED TEXTS: Lecture

Sadava, D., D.M. Hillis, H.C. Heller, and M.R. Berenbaum. 2014. Life: The Science of Biology, 10th ed. Sunderland: Sinauer Associates.

Lab Knisley, K. 2013. A Student Handbook for Writing in Biology, 4th ed. Sunderland:

Sinauer Associates.

COURSE DESCRIPTION: This is the first course in the five-course core for biology majors. It is intended to serve as an introduction to several concepts and skills that will be crucial for your success in later courses. It also is a prerequisite for several upper-level biology courses. Topics in this course include the scientific process, evolution and speciation and elements of population and community ecology. COURSE OBJECTIVES: At the completion of this course students will be able to:

Apply the scientific method to directed and independent projects.

Discuss the basics of evolutionary theory as a foundation for all of biology and apply the theory in predicting outcomes of natural selection and speciation.

Predict inheritance patterns at individual and population levels using Mendelian and population genetics.

Describe introductory concepts in ecology. NSTA Competencies:

Unifying Concept 2. Nature of scientific evidence and the use of models for explanation. Unifying Concept 4. Evolution of natural systems and factors that result in evolution or equilibrium. Unifying Concept 5. Interrelationships of form, function, and behaviors in living and nonliving systems. Science Content Requirement Analysis for Biology Core Competency 1. Life processes in living systems including organization of matter and energy. Science Content Requirement Analysis for Biology Core Competency 4. Theory and principles of biological evolutions. Science Content Requirement Analysis for Biology Core Competency 5. Ecological systems including the interrelationships and dependencies of organisms with each other and their environments. Science Content Requirement Analysis for Biology Advanced Competency 15. Molecular genetics and heredity and mechanisms of genetic modification. Science Content Requirement Analysis for Biology Advanced Competency 19. Historical development and perspectives in biology including contributions of significant figures and underrepresented groups, and the evolution of theories in biology. Science Content Requirement Analysis for Biology Advanced Competency 20. How to design, conduct, and report research in biology.

PREREQUISITES: none COURSE EXPECTATIONS AND POLICIES: Interact. Interaction with your peers and the instructor is an important part of learning. I intend to use small group and class discussions frequently. This is not meant to make you uncomfortable, but students who are more involved will gain more from the class. If you do not understand a concept, please ask a question. If you have an opinion, please express it. Be prepared. You need to be prepared to participate in class discussion and activities. It will be difficult to impossible for you to contribute and learn if you have not read assigned material and put some thought into it before arriving for class. In addition, you may be expected to develop new concepts based on previous material, which will be difficult if you fall behind in the class. Academic honesty. I expect that you will do your own work. You should be aware, however, that you may incorporate the ideas and thoughts of others as long as you give them credit. While I believe in second chances, cheating is unacceptable in the scientific community and will not be tolerated in this class. Cheating on exams or homework will result in an automatic zero on that assignment. Examples of cheating include plagiarism, working with other students on assignments intended for individual students, and copying during exams. You should assume that any assignment requires individual work unless I indicate that group work is allowed. Grading. I expect you to complete the assignments by the due date. Late work will be penalized 10% per day and will NOT be accepted more than one week after the due date. I do not put a high priority on grading late work so it may not be returned in a timely manner. In addition, if you disagree with a grade that has been given, you have one week after the assignment was returned to the class to discuss your grade with the instructor. Attendance. I will be following the school attendance policy. If you miss a class, you will be responsible for all notes, handouts, announcements of assignments, due dates, and any scheduling changes. I do notice individuals who are frequently absent and consider that when evaluating borderline grades at the end of the semester. Finally, coming late to class is disruptive to your peers and to me. If lateness becomes an issue, I will close and lock the classroom door at the start of class. Disability. Reasonable accommodations are available for students with a documented disability. If you have a documented disability and may need accommodations to participate fully in this course, please contact Dr. Dolores Kiesler (Office 254 on the second floor of the Administration Building.) All academic accommodations must be approved through her office. Please stop by or call 270-686-4259 to make an appointment. ASSESSMENTS: Assessments in this course will occur on a weekly basis. You are likely familiar with traditional assessments like exams. There will be additional assessments to gauge your understanding as we go through the course. These can range from pre/post concept inventories, “think-pair-share” discussions, to one-minute papers. Lecture Participation. We will have frequent assessments to gauge your understanding of major concepts. In some cases, you will be awarded points simply for participating in discussions or reflections. In other cases, you will be expected to write responses to course activities (e.g., answer follow-up questions after a case study). While many of these assessments are planned, many of them may appear unpredictably based on how well students are engaging with the course material. Biology thread. The Biology Department is responding to a call to take action concerning the “New Biology”. In the past biologists were trained in and operated as experts in increasingly specialized fields. The problems that the new generation of scientists will be called on to solve involve big questions, such as sustainable food production, treating the whole person in medicine, and balancing ecosystems simply do not lend themselves to this fragmented view of nature. We need a different way of thinking that will involve studying problems from multiple perspectives and synthesizing information from disparate sources. Each year there is a single topic (“thread”) that

will be addressed in most biology majors’ classes. At the end of each semester, all biologists will meet for a Biology Symposium in which classes will present their response to the thread topic. There will also be a common reflection (fall semester) and response paper (spring semester). This year’s thread will focus on dengue fever with the ultimate question of “Why should we be concerned about a tropical disease and how should be we respond?” The Symposium is 15 November (Friday, 1pm) and the reflection paper will be part of your grade for this class. Tests. This class will include three tests and a final. Tests primarily will consist of short and long essays and will be given during your regularly scheduled lecture time. A cumulative final will be given during the University scheduled time for this course. The final will be similar in style to the previous exams. Homework. As the semester progresses you will be assigned questions, additional writing assignments and problem sets. Again, unless indicated in the assignment, I expect that you will work individually on each assignment. If you fail to do so on an assignment, you will not receive credit for that assignment. Lab Short reports. There will be assignments during lab that will require responses on handouts or short write-ups outside of class. Some assignments can be finished during the lab time but others may require extra work and generally will be due the following week in lab. Directed projects. There will be a multi-week project at the beginning of the semester. We will be setting up the experiment as a class during lab times but students will be collecting data and continuing the experiment for two-three weeks outside of lab. After a presentation on formal scientific writing, you will be expected to use this project to practice writing selected sections of a scientific manuscript. Independent project. Later in the semester you will be expected to design and carry out an independent study. You will be required to develop a research proposal and conduct the experiment. After completion of the project, an oral presentation will be delivered to the class, and a formal written report will be expected. Extra Credit. If I decide to offer extra credit, it will be offered to the entire class. There will be NO extra credit available for individual students. SUMMARY OF GRADING: Lecture Lab Grading scale

Participation 100 Homework 100-150 A: 90-100% Homework 150-200 Directed project 75 B: 80-89% Thread 100 Project C: 70-79% Tests (3 @ 75) 225 Research proposal 25 D: 60-69% Final 125 Oral presentation 50 F: <60% Total 700-750 Formal report 100 Total 350- 400

Note: I reserve the right to change the number or structure of assignments or the total number of points assigned during the semester. Any changes will be announced in class or on handouts. If I make changes, I may offer options and let students vote on which option to do. BRESCIA UNIVERSITY EDUCATIONAL OUTCOMES

Skills—The scientific process is founded on the skills of thinking, research, communication, and creativity. New knowledge can only be generated through logical induction and deduction and the use of appropriate research techniques. During lectures, topics will frequently build on prior topics and students

will be asked to make predictions based on prior knowledge. Communication and creativity will be reinforced by oral and written projects in lecture and lab.

Value—This course will deal primarily with issues that affect global welfare. All organisms are intimately linked through descent from common ancestry and continue to interact on a daily basis at the ecological level. A recognition of this connectivity should begin to give students an appreciation for the value of every organism and their role in the global environment. Since humans are just one of many links in global ecosystems, an understanding of how other organisms interact will have some applicability to personal welfare. We cannot expect our use of resources and our manipulations of natural processes to continue unabated without some potentially detrimental affect in the future.

Knowledge—This course is primarily geared towards enhancement of scientific knowledge.

Information Literacy—Scientific knowledge is constantly changing so scientists are constantly accessing and evaluating information from a variety of sources. You will be expected to find, evaluate, and cite primary literature in the lab. All of these activities are important aspects of information literacy. In addition, you will be expected to communicate results in both written and oral forms.

TENTATIVE LECTURE OUTLINE, Fall 2014

Date Topics Assigned readings What is Science? Aug. 21 Course introduction none Aug. 23 Science? Biology? pp. 12-18 Aug. 26 Science? Biology? Aug. 28 NO CLASS Aug. 30 NO CLASS (Case study) handout Evolutionary Theory Sept 2 NO CLASS, LABOR DAY Sept. 4 Case study Sept. 6 Evidence for evolution Chapter 21 Sept. 9 Natural selection “ Sept. 11 Natural selection simulations Sept. 13 Natural selection case study Sept. 16 Adaptation Sept. 18 Sex selection “ Sept. 20 Sex selection Sept. 23 TEST Genetics and Speciation Sept. 25 Mitosis/Meiosis Chapter 11 Sept. 27 Mitosis/Meiosis Sept. 30 Genetics introduction Chapter 12 Oct. 2 Mendelian genetics “ Oct. 4 Mendelian genetics “ Oct. 7 Genetics case study Oct. 9 Population genetics reread pp. 436-8 Oct. 11 What is a species? Chapter 23 Oct. 14 Species II/models “ Oct. 16 Speciation simulation

Oct. 18 NO CLASS, FALL BREAK Oct. 21 NO CLASS, FALL BREAK Oct. 23 Catch-up/Review Oct. 25 TEST Ecology Oct. 28 What are populations? Chapter 55 Oct. 30 Population growth “ Nov. 4 Population regulation “ Nov. 6 Population regulation Nov. 8 What are communities? TBA Nov. 11 Foraging Nov. 13 Avoiding predation Nov. 15 Symbiosis Nov. 18 NO CLASS Nov. 20 Energy flow Chapter 57 Nov. 22 NO CLASS, THANKSGIVING BREAK Nov. 25 NO CLASS, THANKSGIVING BREAK Nov. 27 Energy flow Nov. 29 TEST Dec. 2-6 Grab-bag topics

TENTATIVE LAB OUTLINE, Fall 2014

Date Topic Sept. 3-5 Experimental design, Directed project planning Sept. 10-12 Set-up of directed projects Sept. 17-19 Finding and working with scientific literature Sept. 24-26 Scientific writing and data interpretation, Project report due by Fall Break Oct. 1-3 Independent project preparation Oct. 8-10 Independent project consultation Oct. 15-17 NO LAB, Fall Break Oct. 22-24 Caminacule speciation Oct. 29-31 Independent project proposals Nov. 5-7 Independent projects Nov. 12-14 Independent projects Nov. 19-21 Independent project presentations Nov. 26-28 NO LAB, Thanksgiving Break Dec. 3-5 Turn in final lab report

MOLECULAR/CELLULAR BIOLOGY Lecture: Bio115 12:30-1:50pm TR Room 325S Laboratory: Bio115L 2:00-4:00 pm W or R Room 333S Dr. Carol Maillet Office: 329S Phone: (270) 686-4284 Email: carol.maillet@brescia.edu Office hours: MTWRF: 9am-11am

Or by appointment Text: Brooker, RJ, Widmaier, EP, Graham, LE, Stiling PD. 2008 Biology 2nd ed. McGrawHill Publishing, Dubuque, IA. McMillan, VE 2006 Writing Papers in the Biological Sciences 4th ed Bedford/St. Martin’s, Boston, MA. (recommended for lab)

Other material, such a lab exercises, will be made available to students

Reasonable accommodations are available for students with a documented disability. If

you have a documented disability and may need accommodations to participate fully in

this course, please contact Dr. Dolores Kiesler (Office 254 on the second floor of the

Administration Building.) All academic accommodations must be approved through her

office. Please stop by or call 270-686-4259 to make an appointment.

Course description: Molecular/Cellular Biology is an introduction to the study of life at the molecular and cellular levels. It includes chemistry for the life sciences, cell structure and function, cellular utilization of energy including cell respiration and photosynthesis, and basic molecular biology including information flow from DNA to protein. Molec-Cell is the second course of a four-semester introductory sequence for biology and pre-professional health science majors. The laboratory will support and expand on topics covered in lecture and will include an independent research project. Prerequisites: There are no prerequisites for BIO115. However, I will assume that students have a basic high school level understanding of the topics and a working knowledge of college algebra. Instructional modes: Lecture time will include traditional lecture utilizing power point, transparencies as well as board work. Embedded in lectures are discussions, small group work and individual assignments and quizzes. Course objectives: After completing the course, students should

be conversant with the language and vocabulary associated with the fields of cell and molecular biology.

have a strong factual foundation to support central concepts.

appreciate that chemistry plays an enormous role in understanding biological systems.

recognize the similarities and differences between prokaryotic and eukaryotic cells.

correlate organelles and compartmentalization of metabolic function.

understand how radiant and chemical energy sources are harvested, converted and used in cells.

be aware of the chemical properties of DNA that support its biological function as heritable material.

understand the information pathway from DNA to protein and the processes of replication, transcription and translation.

NSTA Competencies:

Unifying Concept 1. Multiple ways we organize our perceptions of the world and how systems organize the studies and knowledge of science. Unifying Concept 2. Nature of scientific evidence and the use of models for explanation. Unifying Concept 3. Measurement as a way of knowing and organizing observations of constancy and change. Unifying Concept 4. Evolution of natural systems and factors that result in evolution or equilibrium. Science Content Requirement Analysis for Biology Core Competency 1. Life processes in living systems including organization of matter and energy. Science Content Requirement Analysis for Biology Core Competency 2. Similarities and differences among animals, plants, fungi, microorganisms, and viruses. Science Content Requirement Analysis for Biology Core Competency 3. Principles and practices of biological classification. Science Content Requirement Analysis for Biology Core Competency 7. General concepts of genetics and heredity. Science Content Requirement Analysis for Biology Core Competency 8. Organizations and functions of cells and multi-cellular systems.

Science Content Requirement Analysis for Biology Core Competency 10. Regulation of biological systems including homeostatic mechanisms. Science Content Requirement Analysis for Biology Core Competency 11. Fundamental processes of modeling and investigating in the biological sciences. Science Content Requirement Analysis for Biology Core Competency 12. Applications of biology in environmental quality and in personal and community health. Science Content Requirement Analysis for Biology Advanced Competency 13. Bioenergetics including major biochemical pathways. Science Content Requirement Analysis for Biology Advanced Competency 14. Biochemical interactions of organisms and their environments. Science Content Requirement Analysis for Biology Advanced Competency 15. Molecular genetics and heredity and mechanisms of genetic modification. Science Content Requirement Analysis for Biology Advanced Competency 16. Molecular basis for evolutionary theory and classification. Science Content Requirement Analysis for Biology Advanced Competency 17. Causes, characteristics, and avoidance of viral, bacterial, and parasitic diseases.

Science Content Requirement Analysis for Biology Advanced Competency 18. Issues related to living systems such as genetic modification, uses of biotechnology, cloning, and pollution from farming. Science Content Requirement Analysis for Biology Advanced Competency 19. Historical development and perspectives in biology including contributions of significant figures and underrepresented groups, and the evolution of theories in biology. Science Content Requirement Analysis for Biology Advanced Competency 20. How to design, conduct, and report research in biology. Science Content Requirement Analysis for Biology Advanced Competency 21. Applications of biology and biotechnology in society, business, industry, and health fields. Science Content Requirement Analysis for Biology Supporting Competency 23. Biochemistry Science Content Requirement Analysis for Biology Supporting Competency 24. Basic chemistry laboratory techniques. Science Content Requirement Analysis for Biology Supporting Competency 31. Thermodynamics. Science Content Requirement Analysis for Chemistry Core Competency 1. Fundamental structures of atoms and molecules. Science Content Requirement Analysis for Chemistry Core Competency 2. Basic principles of ionic, covalent, and metallic bonding. Science Content Requirement Analysis for Chemistry Core Competency 3. Physical and chemical properties and classification of elements including periodicity. Science Content Requirement Analysis for Chemistry Core Competency 4. Chemical kinetics and thermodynamics. Science Content Requirement Analysis for Chemistry Core Competency 5. Principles of electrochemistry. Science Content Requirement Analysis for Chemistry Core Competency 6. Mole concept, stoichiometry, and laws of composition.

Course policy:

Eating in class: I try to keep the lectures casual. You may eat or drink during class, but please don’t bring items that are noisy and will disrupt your fellow students (or me). Crunchy things in crinkly packaging are a bad idea. Electronic communication during class: Turn off your cell phone when you enter the classroom or lab. Taking calls during class or checking your cell to see who just called or updating your status on Facebook is not allowed. No texting. These activities are disruptive for your colleagues and rude for everyone involved. If there is a situation where you need to be able to be contacted during class, please talk to me ahead of time. Such situations would include return calls by a physician or potential employer. Attendance: Although I may not take attendance, you are expected to be here. Attendance enters into your grade in 2 ways: (1) you cannot do well in this course without being in class because of the information dissemination and in-class exercises, and (2) attendance can be a deciding factor should your final grade be on the cusp. A note on lab attendance: there are no makeup labs. If you are unable to

attend a lab, please see the instructor about attending another lab section. Lab reports can only be based on your data. You cannot use data from another student for your lab report. Late work: Assignments are due at the beginning of the class or lab period on the due date. Pages must be stapled or clipped together. Late work is not given any points but will be corrected at the student’s request. Exams: Exams are multiple choice, short answer, essay and applied problems. I will announce the format of an exam before the day of the exam. Review sessions are scheduled at the request of the students. Make-up exams are given only in emergency situations. Documentation is required to qualify for a make-up and notification must be given before the exam begins. Leaving a message or sending an email is not sufficient. You must talk to me. Make-up exams are comprised entirely of essay questions. Cheating and plagiarism: Neither is tolerated in my class. Essentially all work that you present as your own (quizzes, exams, papers, or lab reports) must be your own. If you are unclear what constitutes plagiarism, please see me. Violation of the rules will result in a minimum penalty of a ZERO on the assignment in question.

Evaluation: Grades will be determined as follows: Lecture (Bio115): Exams (2) 200 pts Final exam*: 150 pts Class preparation assignments**: 50 pts Quizzes: 100 pts Participation***: 25 pts Thread application paper: 25 pts Total: 550 pts *Final exam will be comprehensive.

** Class preparation assignments (CPAs) will be explained in the introduction to the course. For full credit, you must turn in 90-100% of the CPAs. You will receive no points if you turn in less than 50%. The remainder is prorated. *** Participation points are earned by attending Celebration of Excellence presentations or other presentations in the Division.

Grading scale: 90-100% A Superior 80-89% B Above average 70-79% C Average 60-69% D Passing, but below average <59% F Failure

TENTATIVE CALENDAR

Week Topic 1 (1/15) Introduction to Molec/Cell

Identification, location and organization of genetic material Lab: Syllabus and safety review; figures and tables 2 (1/22) Structure of DNA DNA structure, cont Lab: Isolating DNA 3 (1/29) Cell cycle; DNA replication DNA replication, cont. Lab: PCR 4 (2/5) Cell division

Cell division, cont. Lab: Gel electrophoresis 5 (2/12) Cell cycle control and cancer

EXAM 1 Lab: Mitosis 6 (2/19) Membrane structure Homeostasis and transport Lab: Macromolecules 7 (2/27) Transport, cont.

Transport, cont. Lab: Membrane disruption 8 (3/5) Proteins and protein synthesis Protein synthesis, cont. Lab: Lab practical; planning for project 9 (3/12) SPRING BREAK

Lab: No lab 10 (3/19) Protein synthesis, cont. Protein synthesis, cont. Lab: Group project, cont. 11 (3/26) Metabolic pathways EASTER BREAK Lab: Group project, cont. 12 (4/2) Metabolic pathways, cont.

Cell communication 13 (4/9) EXAM 2

Cellular energy 14 (4/16) Photosynthesis Photosynthesis, cont. Lab: Group project, cont. 15 (4/23) Cell respiration Cell respiration, cont.

Lab: Research project report due 4/26 16 (4/30) Cell specialization Review

Lab: Oral reports; clean up 5/7 FINAL Tuesday 7 May – 1:05-3:00

General education outcomes: Brescia students will be skilled in: Thinking:

Students are expected to think critically, which involves identifying salient facts, integrating facts into a conceptual framework, and predicting outcomes. They will apply these steps to their own work in the laboratory setting, as they generate data and analyze it to form conclusions.

Research: Students will form and test hypotheses in settings involving studies experiments that the students perform themselves. Data will be generated by both traditional as well as current techniques and will be frequently require information literacy for analysis.

Communication: Students will communicate their understanding of material in several ways. Oral in-class discussions, written essay questions on exams and analysis and presentation of data generated in lab require effective oral and written communication as an individual or in small group communication. Each student will also establish skills in effective listening in lecture and small group interactions and effective reading in completing various assignments.

Creativity: Creativity in the sciences tends to be creative thinking or “thinking outside the box”. Of course, this requires initially establishing the contents of “the box”. But, as students examine data, they see where this data may fit into an established concept or they may see how their data and the data of others may challenge current thought. Examining historical experiments as a class exercise is one way that they will learn to appreciate the dynamic process that is science.

These skills will be evaluated in essay questions on exams, concept maps, formal lab reports, and problems in cell biology.

Brescia students will value: Global, human and personal welfare. Students are encouraged to consider advances in science in terms of social

gain as well as social or environmental cost. As students begin to understand the biological and chemical foundation of disease and treatment, they are better qualified to make judgments concerning their own or other’s welfare. As they appreciate cell physiology, they also begin to understand the basis for cellular development, ultimately leading to an understanding of stem cells, and the effects of loss of regulation in cellular process, one outcome of which is cancer. Perhaps, more importantly, they can bring critical thinking, as demonstrated in the sciences, to many of the problems and decisions that they will face in other aspects of their lives.

These values will be assessed both subjectively using class discussions and objectively by asking students to respond to thought questions on exams.

Brescia students will possess a knowledge of: Science

This course deals with building a foundation in cell biology. They will gain this knowledge by active reading and listening, but also by laboratory exercises in which they test hypotheses using current technology. Students will demonstrate their knowledge in class discussion, small group projects, and exams.

215 Biological Diversity Course Information

INSTRUCTOR: Conrad Toepfer, Office: Sci 320, Phone: 686-4221 (office), e-mail: conrad.toepfer@brescia.edu MEETING TIMES: Lecture 12:30-1:50 TTh; Lab 2:00-3:50 T OFFICE HOURS: 9-11 MWF, 8-10 p.m. (virtual hours on Facebook) or by appointment TEXT: Brooker, R.J., E.P. Widmaier, L.E. Graham, and P.D. Stiling. 2008/2010. Biology. Dubuque:

McGraw-Hill.

COURSE STRUCTURE: This is the fourth course in the biology core for majors and is intended to build on previous training in evolution, molecular/cellular biology and human anatomy and physiology. This course will focus on the classification of plants and animals, plant and animal anatomy, and comparative physiology. The course will be delivered in an open-ended, inquiry-based format this year. Students will be involved in determining the direction of their own learning in this course. COURSE OBJECTIVES:

Gain knowledge of the classification of organisms from the Kingdoms Fungi, Protista, Plantae, and Animalia.

Determine anatomical, physiological, and behavioral traits that distinguish organisms at multiple levels of classification. Develop an understanding of the evolutionary development and adaptive value of those traits.

Gain more intensive exposure to plant diversity, structures and functions.

Extend prior exposure of human biology to comparative anatomy and physiology of other animals. NSTA Competencies:

o Unifying Concept 5. Interrelationships of form, function, and behaviors in living and nonliving

systems.

o Science Content Requirement Analysis for Biology Core Competency 2. Similarities and

differences among animals, plants, fungi, microorganisms and viruses.

o Science Content Requirement Analysis for Biology Core Competency 3. Principles and practices

of biological classification.

o Science Content Requirement Analysis for Biology Core Competency 5. Ecological systems

including the interrelationships and dependencies of organisms with each other and their

environments.

o Science Content Requirement Analysis for Biology Core Competency 10. Regulation of biological

systems including homeostatic mechanisms.

COURSE EXPECTATIONS AND POLICIES: Interact. Interaction with your peers and the instructor is an important part of learning. I make frequent use of questions both to gauge student understanding and to encourage students to deduce new concepts. This is not meant to make you uncomfortable, but students who are more involved will gain more from the class. Be prepared. You need to be prepared to participate in class discussion and activities. It will be difficult to impossible for you to contribute and learn if you have not read assigned material and put some thought into it before arriving for class. In addition, you may be expected to develop new concepts based on previous material, which will be difficult if you fall behind in the class.

Academic honesty. I expect that you will do your own work. You should be aware, however, that you may incorporate the ideas and thoughts of others as long as you give them credit. While I believe in second chances, cheating is unacceptable in the scientific community and will not be tolerated in this class. Some assignments may be group assignments and will be announced as such; do not assume that all assignments are group work. Working with a partner or partners on homework that is not a group assignment will result in a grading penalty. After one warning, the points for each assignment will be split among all participants who worked together on the assignment. Cheating on exams or homework will result in an automatic zero on that assignment. Behavior. There are two specific items of personal behavior that I will not accept in this class. Electronic devices, including and especially cell phones, may not be used during class without prior permission. Devices that are used without approval will be confiscated and returned to the student at the end of the class period. I also will not tolerate the use of smokeless tobacco or snuff during class. Safety. Behavior that endangers fellow students or Brescia facilities will result in your dismissal from the class period or lab in which the behavior occurs. You will receive a zero on any graded assignments or activities from that period or lab. Depending on the severity of your actions, additional penalties, up to but not limited to expulsion from the course and/or lab, may be imposed. Attendance. I will be taking attendance in lecture, although no grade will be associated with your attendance. You will be responsible for all notes, handouts, announcements of assignments, due dates, and any scheduling changes. Although attendance is not graded formally, if you choose to miss class on a regular basis it will not serve you well if you end up with a borderline grade at the end of the semester. Assignments. I expect you to complete the assignments by the due date. Work to be turned in will be collected at the beginning of lecture. Late work will be penalized 10% per day until it is received; late work will not be accepted one week after the original due date. This penalty will begin one hour after the end of a class period in which the assignment was due. If you disagree with a grade that has been given, you have one week after the assignment was returned to the class to challenge your grade. Disability. Reasonable accommodations are available for students with a documented disability. If you have a documented disability and may need accommodations to participate fully in this course, please contact Dr. Dolores Kiesler (Office 254 on the second floor of the Administration Building.) All academic accommodations must be approved through her office. Please stop by or call 270-686-4259 to make an appointment. ASSIGNMENTS: Lecture Journal and participation. Since the majority of the material in this semester will be generated by you, it is critical that I am able to trace your learning through regular entries in a journal. You are expected to show both content and process in your journal. Details will be provided early in the semester. Tests.This class will include three tests and a final. Tests will include a mix of objective (fill-in-the-blank, definitions) questions as well as short answers and essays. A cumulative final will be given during the University scheduled time for this course. The final will be similar in style to the previous exams. Lab Practicals. There will be two lab practicals during the semester. The content of each practical will be determined by the material that students have discovered up to that point in the semester. Journal. While your “lecture” journal needs to be more reflective and is used to document your intellectual development through the course, the lab journal is intended to document your observation and classification skills. As you handle specimens, you need to draw and label what you observe. I will be looking for your attention to detail and your ability to identify relevant features of each specimen.

Unknown identifications. Near the end of the semester, you will be provided with unknown specimens. Using the classification schemes and content that you have identified during the semester, you will be expected to determine where in the classification scheme the specimens fit and develop an argument for your placement of those placements. SUMMARY OF GRADING: GRADING SCALE: Lecture A: 90-100%

Exams (3 @ 75) 225 B: 80-89% Final 125 C: 70-79% Journal 200 D: 60-69% Participation 100 F: <60% Thread 75 Total 725 Lab Participation 100 Lab Journal 100 Lab practicals 150 Unknown id’s 100 Total 450

Note: I reserve the right to change the number or structure of assignments or the total number of points assigned during the semester. Any changes will be announced in class or on handouts. If I make changes, I frequently offer options and let students vote on which option to do. BRESCIA UNIVERSITY EDUCATIONAL OUTCOMES

Skills—The scientific process is founded on the skills of thinking, research, communication, and creativity. New knowledge is generated through logical induction and deduction and the use of appropriate research techniques. Any decision in biology must include a critical analysis of relevant scientific research or the development of a suitable scientific study. In addition, communication is particularly important because biologists often must deal with a wide variety of people from fellow scientists to politicians to a reporter from the newspaper. This requires that the scientific information be communicated differently for each prospective audience. Finally, creativity is one of the primary traits necessary to be a good scientist. If you are unable to figure out a new angle to a previous question or put together just the right combination of variables and/or equipment, you will not be successful as a practicing scientist.

Value—With recent advances in biology such as molecular analyses of DNA, an awareness of ethical issues has become increasingly more important. Issues of personal welfare may include such things as elevated disease risks associated with societal changes. An understanding of issues such as resource availability and use fall under human welfare. Finally, issues like sustaining biodiversity have an impact on all of life (global welfare) and require difficult decisions that cross political boundaries and project far into the future.

Knowledge—In addition to the obvious application to scientific knowledge, biology does require ethical decisions (religion and philosophy) as well as analyses of economic impacts (cultural and communication knowledge).

TENTATIVE OUTLINE, Spring 2013

Date Topics Jan. 15 Introduction, Cladistics Jan. 17 Cladistics and classsifcation

Jan. 22 Where do we begin? Jan. 24-Mar. 7 Working on our classification Mar. 12/14 SPRING BREAK Mar. 19- Apr. 25 Working on our classification Mar. 28 EASTER BREAK Apr. 30-Mar. 2 Wrapping up any uncovered concepts Given the student-driven and open-ended nature of this course, I cannot provide a detailed schedule of topics. However, you should be aware that we will cover taxonomy (e.g., Kingdoms Protista, Fungi, Plantae, Animalia and subgroups), distinguishing traits of each group, and comparative physiology of both plants (e.g., evapotranspiration and water transport) and animals (e.g., osmoregulation).

GENETICS Lecture: Bio300 12:30-1:50 pm Tues/Thur Room 325S Laboratory: Bio300L 2:00-4:00 pm Wed Room 333S Dr. Carol Maillet Office: 329S Phone: (270) 686-4284 Email: carol.maillet@brescia.edu Office hours: 9:00-11:00amTR; 10:00-10:45am MWF; 2:00-4:00pm MR or by appointment

Reasonable accommodations are available for students with a documented disability. If

you have a documented disability and may need accommodations to participate fully in

this course, please contact Dr. Dolores Kiesler (Office 254 on the second floor of the

Administration Building.) All academic accommodations must be approved through her

office. Please stop by or call 270-686-4259 to make an appointment.

Biology Curriculum Focus: As will be more fully explained in class, the Biology Department is

responding to a call to take action concerning the “New Biology”. In the past biologists in all

areas were trained in and operated as experts in increasingly specialized fields. The problems

that the new generation of scientists will be called on to solve involve big questions, such as

sustainable food production, treating the whole person in medicine, balancing ecosystems, etc.,

simply do not lend themselves to this fragmented view of nature. We need a different way of

thinking that will involve studying problems from multiple perspectives and synthesizing

information from disparate sources. This is our plan: Each year there will be a single topic (i.e.

“thread”) that will be addressed in all biology majors classes. At the end of each semester, all

biologists will meet for a Biology Symposium in which classes will present their response to the

thread topic. There will also be a common reflection (fall semester) and response paper (spring

semester). This year’s thread is “Why should we be concerned about a tropical disease and

how should we respond?” The Symposium is 15 November (Friday, 1pm). The reflection

paper will be part of your grade for this class and will be due finals week.

Text: Brooker, RJ 2005 Genetics: Analysis & Principles 4th ed McGrawHill Dubuque, IA Other material, such a lab exercises, will be made available to students Course description: Genetics is required for a biology major or minor and for some pre-professional programs. This course will explore the four subcategories of genetics: transmission genetics (patterns of inheritance including Mendelian and non-Mendelian patterns), cytogenetics (the study of chromosomal structure and transmission), molecular genetics (the chemical basis of inheritance) and population genetics (the study of genes in populations). We will utilize a variety of organisms (viruses, bacteria, fungi, plants and animals) in our study in order to demonstrate the universality of the heritable material. Our basic understanding of genetics supports a deeper understanding of current topics, such as heritable diseases, effects of environmental mutagens, or genetic engineering. The laboratory will support and expand on topics covered in lecture. Prerequisites: Bio115 or permission of the instructor. In addition, a working knowledge of basic algebra is necessary. You should also be familiar with cell structure; the chemistry and structure of nucleic acids and proteins; the processes of replication, transcription and translation; and the basics of mitosis and meiosis. Many of these subjects will be examined in greater detail in genetics, but some fundamental knowledge is simply assumed. You should also be able to communicate effectively in written or oral styles. Instructional modes: Lecture time will include traditional lecture utilizing power point, transparencies as well as utilizing the board. Embedded in lectures are discussions, small group work and individual assignments and quizzes. The laboratory will use models, live organisms and computer generated exercises. Course objectives: After completing the course, students should

be conversant with the language and vocabulary associated with the field of genetics.

have a strong factual foundation to support the genetics concepts.

be able to predict the probability of a genotype or phenotype from experimental data, which include results from controlled matings, pedigrees and molecular analyses.

understand the chemical properties of DNA that support its biological function as heritable material.

recognize how mutations introduce changes in DNA, which, in turn, may impact gene expression or gene product structure and affect the organism at the cell and organismal levels.

realize the consequences of increasing or decreasing diversity within the gene pool. NSTA Competencies:

Unifying Concept 2. Nature of scientific evidence and the use of models for explanation. Unifying Concept 3. Measurement as a way of knowing and organizing observations of constancy and change. Unifying Concept 4. Evolution of natural systems and factors that result in evolution or equilibrium. Unifying Concept 5. Interrelationships of form, function, and behaviors in living and nonliving systems. Science Content Requirement Analysis for Biology Core Competency 1. Life processes in living systems including organization of matter and energy. Science Content Requirement Analysis for Biology Core Competency 2. Nature of scientific evidence and the use of models for explanation. Science Content Requirement Analysis for Biology Core Competency 4. Theory and principles of biological evolutions. Science Content Requirement Analysis for Biology Core Competency 6. Population dynamics and the impact of population on its environment. Science Content Requirement Analysis for Biology Core Competency 7. General concepts of genetics and heredity. Science Content Requirement Analysis for Biology Core Competency 8. Organizations and functions of cells and multi-cellular systems. Science Content Requirement Analysis for Biology Core Competency 11. Fundamental processes of modeling and investigating in the biological sciences.

Science Content Requirement Analysis for Biology Core Competency 12. Applications of biology in environmental quality and in personal and community health.

Science Content Requirement Analysis for Biology Advanced Competency 15. Molecular genetics and heredity and mechanisms of genetic modification. Science Content Requirement Analysis for Biology Advanced Competency 16. Molecular basis for evolutionary theory and classification. Science Content Requirement Analysis for Biology Advanced Competency 19. Historical development and perspectives in biology including contributions of significant figures and underrepresented groups, and the evolution of theories in biology. Science Content Requirement Analysis for Biology Advanced Competency 20. How to design, conduct, and report research in biology. Science Content Requirement Analysis for Biology Advanced Competency 21. Applications of biology and biotechnology in society, business, industry, and health fields. Science Content Requirement Analysis for Biology Supportive Competency 39. Statistics Science Content Requirement Analysis for Chemistry Core Competency 1. Fundamental structures of atoms and molecules.

Science Content Requirement Analysis for Chemistry Core Competency 2. Basic principles of ionic, covalent, and metallic bonding.

Course policy:

Eating in class: I try to keep the lectures casual. You may eat or drink during class, but please don’t bring items that are noisy and will disrupt your fellow students (or me). Crunchy things in crinkly packaging are a bad idea. Attendance: Although I don’t take attendance, you are expected to be here. It will enter into your grade in 2 ways: (1) you cannot do well in this course without being in class because of the information dissemination and the in-class exercises, and (2) attendance can be a deciding factor should your final grade be on the line. There are no make-up labs. If you are unable to attend a lab, please see the instructor. Lab reports can only be based on your data. You cannot use data from another student for your lab report. Electronic communication during class: Turn off your cell phone when you enter the classroom or lab. No taking calls during class or checking your cell to see who just called. No texting. These activities are disruptive for your colleagues and rude for everyone involved. If there is a situation where you need to be able to be contacted during class, please talk to me ahead of time. Such situations would include return calls by a physician or setting up a job interview. Late work: Papers, lab assignments, etc are due at the beginning of the class or lab period on the due date. Pages must be stapled or clipped together. Late work is penalized 50% of the earned grade; this policy is in effect for one week. Work that is submitted after 1 week is not given any points but will be corrected at the student’s request. Exams: Exams are multiple choice, short answer, essay questions and applied problems. I will announce the format of an exam before the day of the exam. Review sessions before exams are scheduled at the request of the students.

Make-up exams are given only in emergency situations. Documentation is required to qualify for a make-up and notification must be given before the exam begins. Leaving a message of sending an email is not sufficient. You must talk to me. Make-up exams are comprised entirely of essay questions. Extra credit: Extra credit may be earned by attending student research seminar. Cheating and plagiarism: Neither is tolerated in my class. Essentially all work that you present as your own (quizzes, exams, papers, or lab reports) must be your own. If you are unclear what constitutes plagiarism, please see me. Violation of the rules will result in a minimum of a ZERO on the assignment in question.

Evaluation: Grades will be determined as follows: Lecture (Bio300): Exams (3) 300 pts Final exam*: 150 pts Homework problems: 100 pts Dengue fever project**: 100 pts Reflection paper 25 pts

Total: 625 pts *Final exam will be comprehensive. **A description of this project will be provided separately. Grading scale: 90-100% A Superior 80-89% B Above average 70-79% C Average 60-69% D Passing, but below average <59% F Failure

lTENTATIVE CALENDAR

Week Topic Reading Assignment 1 (8/22) Introduction; DNA, genes, chromosomes and mitosis Ch1.1, 2.1, 3.2 2 (8/27) Meiosis Ch3.2,3.3 Project 3 (9/3) Simple monohybrid inheritance Ch4.1 Sex-linked inheritance; dihybid inheritance 4 (9/10) Exam Material from weeks 1-3

Gene interaction – epistasis Ch4.2 5 (9/17) Epistasis; multigene traits Ch4.2; 25.1-2 Quantitative genetics Ch25.1-2 6 (9/24) Environmental effects on gene expression-sex influence, etc Ch4.1; 5.1 Epigenetics Ch5.2 7 (10/1) Exam 2 Material from weeks 4-6

DNA/RNA structure; genes Ch9 8 (10/8) Replication (and mitosis and meiosis) Ch11 Transcription/Translation Ch12;13 9 (10/15) Regulation of gene expression Ch14

FALL BREAK 10 (10/22) Regulation of gene expression Ch15 RNAi Ch15.5

11 (10/29) Dengue GMO Ch18 Dengue genetics 12 (11/5) Exam 3 Material from weeks 7-11 Mutation and mutation repair Ch16 13 (11/12) Transposition Ch17.3 Genes in populations Ch24 14 (11/19) Population genetics Ch24 Hardy-Weinberg Ch24 15 (11/26) Changes in allele frequency Ch24 THANKSGIVING BREAK 16(12/3) Developmental genetics Ch23 Review 12/10 FINAL Tuesday, 1:05-3:00 pm

General education outcomes: Brescia students will be skilled in: Thinking:

Students are expected to think critically, which involves identifying salient facts, integrating facts into a conceptual framework, and predicting outcomes. They will apply these steps to their own work in the laboratory setting, as they generate data and analyze it to form conclusions. They will also critically analyze studies by other scientists and will identify the steps in the scientific method and ultimately determine whether or not the authors of a study have supported or rejected their hypothesis.

Research: Students will form and test hypotheses in settings involving studies

from published journal articles or experiments that the students perform themselves. Data will be generated by both traditional as well as current techniques and will be frequently require information literacy for analysis. Students will identify appropriate information sources (electronic and print). As part of the exercise, students will design an effective search and retrieve the information on a topic of interest. As students find and retrieve information, they will evaluate the quality of the information and determine if it is appropriate for the assignment. In addition, students will synthesize the information to present a cohesive argument or discussion on the chosen topic. Using one of several potential forums, the student will present the results of the research before his/her peers. The student will properly acknowledge the sources of information as both ethical and legal issues.

Communication: Students will communicate their understanding of material in several ways. Oral in-class discussions, written essay questions on exams and a written analysis of a published paper require effective oral and written communication either individually or in small group communication. Each student will also establish skills in effective listening in lecture and small group interactions and effective reading in completing various assignment.

Creativity: Creativity in the sciences tends to be creative thinking or “thinking outside the box”. Of course, this requires initially establishing the contents of “the box”. But, as students examine data, they see where this data may fit into an established concept or they may see how their data and the data of others may challenge current thought. Examining historical experiments as a class exercise is one way that they will learn to appreciate the dynamic process that is science.

These skills will be evaluated in essay questions on exams, projects, formal lab reports, and genetics problems.

Brescia students will value: Global, human and personal welfare. Students are encouraged to consider advances in science in terms of social

gain as well as social or environmental cost. A class discussion concerning genetically modified plants (particularly rice) is one platform for students to understand our impact on global welfare. In addition as students begin to understand the genetic and biochemical foundation of disease and treatment, they are better qualified to make judgments concerning their own or other’s welfare. As they trace pedigrees and analyze the results of diagnostic testing, they will gain understanding of the impact of genetics on individuals. They will also increasingly appreciate the diversity that defines our human and environmental global communities, which will promote celebrating diversity and understanding its value. Perhaps, more importantly, they can bring critical thinking, as demonstrated in the sciences, to many of the problems and decisions that they will face in other aspects of their lives.

These values will be assessed both subjectively using class discussions

and objectively by asking students to respond to thought questions on exams. Brescia students will possess a knowledge of:

Science This course deals with building a foundation in genetics. They will gain this knowledge by active reading and listening, but also by laboratory exercises in which they test hypotheses using current technology. Analysis requires mathematical reasoning and an understanding of key concepts and uses computer analysis.

Students will demonstrate their knowledge in class discussion, small group projects, and exams.