INVESTIGATIVE BIOLOGY LABORATORY (BioG 1500) SYLLABUS



INVESTIGATIVE BIOLOGY LABORATORY (BioG 1500) SYLLABUS This course is designed to provide lab experience with emphasis on the processes of scientific investigation and to promote collaboration, communication, and literacy in science. The goal of this lab course is to teach skills, especially critical thinking and problem solving, that students can apply in research laboratories during their time at Cornell and after graduation. These skills go far beyond learning how to use particular laboratory equipment. The course introduces students to a laboratory research environment, teamwork, hypothesis formation, experimental design, statistics, and ethics in research. Students gain information and science literacy skills and practice many forms of science communication, from presentations to proposal writing and scientific poster preparation. Students first fill their scientific toolbox and then develop the capacity to solve increasingly challenging problems with greater independence. In this inquiry-based lab course students can choose between two main research fields for a final project: the development of antibiotic resistance and biofuel production using green algae. The expectation is that students finish the course as well-rounded scientists, equipped with all the skills needed in real research environments.The course employs a number of student-centered pedagogies including case studies, formative assessment using a web-based response system (poll everywhere), problem-based learning, reflection, role playing, presentations, hands-on activities, peer-teaching, peer-review, and inquiry-based learning.By the end of the course, students will be able to:1. Design hypothesis-based experiments, choose appropriate statistical test(s), analyze data, and interpret results.2. Demonstrate mastery of lab techniques and scientific methods that can be applied across biological systems and scales.3. Find and evaluate relevant scientific information using appropriate library tools. 4. Effectively contribute to work within their research groups and reflect on the ethics, benefits and challenges of collaborative work. 5. Use discovery science to explore patterns in nature, and apply accuracy and precision to the scientific process. 6. Apply fundamental biological information to increasingly novel and complex situations.7. Author and produce scientific content using digital, oral, visual, audio and written communication formats. TEACHING STAFFLectures are given by the Course Director, Dr. Mark Sarvary, and Co-Instructor, Dr. Frank Castelli. Drs. Sarvary and Castelli are Cornell alumni and passionate about teaching biology. Lab sections are led by graduate student Lab Instructors who may be assisted by Undergraduate Teaching Assistants. The teaching staff strives to be supportive of our students and welcome you to approach them for assistance. The course also has an amazing logistical support staff. To learn more about the course staff, visit our website (InvestigativeBiology.cornell.edu).HOW TO REACH USWe provide answers to frequently-asked questions and other information on our website: InvestigativeBiology.cornell.edu Please email our course address (biolabs@cornell.edu) with any questions and we will get back to you, usually during business hours. This address should also be used for scheduling issues, reporting excused absences, and any course related issues.CLASS MEETINGS In Fall 2020 we are an online course. Log into Canvas and click on the appropriate Zoom link to attend class. If the circumstances allow, we are also planning for an entirely optional opportunity to gain hands-on experience with lab equipment in our lab rooms on campus.Weekly Lecture: First two lectures will be live, Tuesday 9:10-10:00 am. The other lectures will be pre-recorded and released at the beginning of each week.Weekly Lab: All lab sections will be held live. See your online course roster for the section times.Video camera feeds during class meetings: We understand that there are circumstances under which students may feel very uncomfortable turning on their video feed during class meetings, so we do not require that they be turned on. However, we strongly encourage video to be turned on because turning on cameras helps class to feel more engaging and more like a community. Also, turning on cameras makes it easier for instructors to receive non-verbal feedback that greatly improves teaching. Many students last semester suggested that we more strongly encourage students to turn on their cameras to improve the remote class meeting experience. With this in mind, please prepare for class meetings in ways that maximize your comfort with being on camera. If you have concerns about turning your camera on during class, please privately communicate this to your lab instructor. Diversity statement: The staff and instructors of BIOG 1500 are committed to encouraging diversity, inclusivity, and equity, and we urge our students to practice the same habits. Since this course is a collaborative learning environment featuring a diverse group of people, we encourage all of you to engage thoughtfully and professionally, be generous in listening to each other, and cherish the diversity of thoughts and ideas. We hope to create a learning environment where all feel welcomed, respected, supported, valued, and therefore, able to participate fully. Please feel free to let course instructors or staff know if any circumstances arise that affect your ability to participate. Accommodations: We all learn differently, and we want every student to succeed in the course. If you have a learning need or disability, please register as soon as possible with Cornell Student Disability Services () so they can provide us with the appropriate documentations for accommodations. FOUR IMPORTANT THINGS YOU WILL NEED IN THIS COURSE1.The "Lab Manual": Investigative Biology - a Laboratory Text (Sarvary, Fall, 2020) – available through Canvas2.Open access books. – free and available onlineBiology: : : Everywhere classroom response system – free and available online at Poll Everywhere produces a tool that allows you to interact with your instructor(s) through your own mobile devices or computers. The intended goal is to improve student engagement in the classroom through the use of interactive learning. During each lecture you will use Poll Everywhere to answer multiple-choice and short answer questions based on the assigned readings and your understanding of the lecture. You must log in with your NetID every time! If you are not logged in, your answers will not count toward your grade!How to register:Go to: will be asked to provide your name and Cornell email address (other email addresses will not be accepted in the course). Create a unique password.If you plan on using your cell phone to text the responses, you must enter and certify your cell phone number in your profile (profile/edit) to ensure that you receive credit for responding.?Check if you are connected to BIOG1500 under settings/voter registration. Follow the instructions for “Register as a Participant” to check if your account is connected to the course. It may prompt you to enter Dr. Sarvary’s email address: mas245@cornell.edu. If you have any questions, please visit the Poll Everywhere User Guide (guide).Your information is protected and Poll Everywhere will never share emails or phone number with any third party.Answering poll questions:Questions will appear on BioG1500.Make sure you are signed in before answering the questions. This will ensure that you receive credit for responding. Signing in is your responsibility. Without signing in, you will not receive any credit for your answers.Without completing the steps above, Dr. Sarvary & Dr. Castelli will not be able to see your responses.4.“R” is a free statistical software that will be needed for data analysis and graphing throughout the semester. You can download this software for your PC or Mac from r-. Choose one of the US Mirrors. Please also download R-studio from ide/download. Create a folder on your computer called “RBioG1500”, where you may wish to store all the datasets used in BioG 1500.Download this software to your computer. On Chromebooks and tablets you can use the web based version: TO SUCCEED IN THIS COURSE:Participate in the online dialogues and come prepared to the lab sessions: The content knowledge required for the laboratory sessions will be discussed during the lectures. The online participation grade will be based on Poll Everywhere Questions (multiple choice and short answer) asked during and at the end of the lectures. These questions will test whether you have completed the assigned readings and whether you acquired the necessary information to complete the laboratory exercises. Completing the assigned readings prior to lecture will help you to learn more and more deeply from the lecture. Poll Everywhere questions from the pre-recorded lectures are due on TUESDAYS AT 11 AM (Ithaca, NY time). A total of 10% of the polling scores will be dropped, in case you cannot watch a lecture or you run into technical difficulties. Using the Discussion board of Canvas you will need to respond to prompts and provide feedback to your peers. After watching an Elephant communication study, you will need to answer the questions and discuss it in class. Your participation in science communication using Twitter will also count towards the lab participation grade. Lastly, after guidance and discussion, you will need to submit and discuss a mock email that you write to a professor to ask to join their research lab -maybe you'll want to actually send it!Gain useful lab skills: Your success in the lab section depends on your preparation for each new lab. A thorough reading of the relevant lab manual chapter, and attending and actively engaging in lecture should adequately prepare you for each lab session. Please log into Zoom on time so you can actively participate in the lab. If you need to miss a lab, contact Irena Horvatt (biolabs@cornell.edu). This will enable our course staff to better assist you. In cases where two or more labs have been missed, course withdrawal is suggested. Take advantage of the course learning tools: Questions to prepare you for each module, and questions to test your knowledge are in the assigned readings of the lab manual. Meet your lab instructor during office hours to discuss the answers to these questions. Apply your skills questions in the lab manual and worksheets are designed to help you solve problems related to a lab topic or help you learn a particular skill in science, such as searching for scholarly literature. Some of them will be completed in lab, others outside of lab. Use these questions as smart learning tools! These questions may appear on the open book exam at the end of the semester. Instructional videos and Tutorials were developed or sought out by our staff to help you gain certain lab skills. Please be on time and don’t procrastinate: Some assignments are due at the beginning of lecture and others are due at the beginning of your lab section. Please consult the calendar at the end of the syllabus. To maintain fairness, the lab instructor cannot change deadlines. If you have a valid reason to receive an extension without penalty, please contact Dr. Sarvary. If you cannot finish your assignment by the deadline, you can submit a late assignment, but to be fair to those students who submitted on time there will be a grade reduction. Late assignments carry a 25% reduction of grade per day: for example if you turn in your assignment within 24 hours after its deadline, you cannot receive more than 75% of the maximum score. If you are 25-48 hours late, your maximum score can be 50%. Since providing timely feedback is important for learning, no assignment is accepted after 48 hours passed the deadline. Please also realize that submitting late work may result in a delay in receiving a grade for that work. Some assignments, because of their nature, cannot be turned in late. For example, submitting a peer review late would not be fair to your classmate who is waiting for that feedback to proceed with their assignment, or the correct answer to a poll question may be provided shortly after responses are collected. We are here for you! So please ask for help when you need it! It Is very difficult for us to help you if you wait until the end of the course to raise problems/issues. We welcome you to come and talk to us. If you are experiencing undue personal or academic stress at any time during the semester or need to talk with someone about a personal problem or situation, please seek support as soon as possible. Monitor your assignments and the posted grades on Canvas. Please look at answer keys and your graded assignments as soon as they are posted . “Errare humanum est”, therefore if you notice a grading error on your assignments, please notify your Lab Instructor within 48 hours of the receipt of the grade. Due to the fast pace nature of this course, we cannot honor re-grading requests after 48 hours. Please always provide a clear and detailed explanation of why you disagree with an answer key or how something was graded. The BioG 1500 Staff is available to talk with you about stresses related to your work in this class. Additionally, we can assist you in reaching out to any one of a wide range of campus resources: Cornell Learning Strategies Center ()Gannett Health Services (gannett.cornell.edu)Peer Support provided by Empathy Assistance and Referral Service (EARS, )Office of Undergraduate Biology (OUB, )Student Disability Services (SDS, ) HOW WE WILL ASSESS YOUR KNOWLEDGE AND LABORATORY SKILLS:We use a wide variety of assessment techniques to form a realistic picture of your understanding of the course content and the scientific skills you gained in this course. ComponentLab skills and content knowledge (total 47%)Percent of GradeOpen book final exam15Statistics worksheet8Online participation grade (discussion boards, etc.)12Lab attendance & etiquette 4Animal Behavior worksheet4Transferable skills worksheet4Communicating Science (total 53%)Paper dissection worksheet10Choosing a journal worksheet4 Proposing your research project:First draft of proposal for peer-review4Peer-review and self-review3Final version of the proposal12 Going to a conference:Poster itself (visuals and content)10Poster oral presentation3Poster Supplementary materials3Climate change forum participation4Total100%Final letter grades: We do not grade on a curve, i.e. we do not lower individual grades based on the class average nor do we limit the number of students that receive high grades. The general guidelines for letter grades: 90-100%: (A+, A, A-); 80-90%: (B+, B, B-); 70-80%: (C+, C, C-); 60-70%: (D+, D, D-); below 60% is F. Exact cut-off points will not be known until the day of letter grade assignment. We do not offer extra/bonus assignments. Incompletes: We understand that sometimes it is not possible to complete a course. Please be aware that according to university policy, incompletes can only be arranged only when a student has substantial passing equity in the course (e.g., all requirements for the course have been completed satisfactorily except for a term paper or final exam) and the reason for not completing all course requirements is reasonable to the instructor and beyond the student's control. If you feel that you are eligible for an incomplete, you must contact Dr. Sarvary or Dr. Castelli and provide supporting documentation when appropriate. HOW TO STAY CONNECTED AND BE INFORMED:1. Course website and social media: You can find valuable course information on our website (InvestigativeBiology.cornell.edu). Use our social media outlets to receive real-time information about the course, staff and your fellow students. Find @Cornellbiolabs on Twitter, Facebook, and Instagram. Please use #CUintheLab in your posts regarding the course.2. Canvas: Instructors and course staff will post links to Zoom meetings and course related materials to Canvas. Assignments must be submitted through Canvas and you will use Canvas to view course documents, to view slides of course lectures, to receive statistical codes for R, and to watch online tutorials for statistics, literature searches, and other topics. You can also monitor your grades throughout the semester. Access to Canvas requires that you sign in with your Cornell NetID, which is the first part of your Cornell email address, and your self-chosen password (these are the same credentials you use to check your Cornell email). OTHER INFORMATION:Academic Integrity: We value integrity and fairness and we encourage you to as well. Acts which lack academic integrity like plagiarism and cheating are not fair to other students or yourself. Students tend to be tempted when overwhelmed or stressed, usually close to deadlines. Please plan to avoid this temptation by pacing your work and asking for help as early as possible. We are here to help you succeed in this course and can work with you to improve your learning or working habits. Helping another student to plagiarize or cheat also lacks academic integrity. We encourage students to learn from each other when a course component calls for it, but if you are approached for inappropriate assistance (e.g., asked to cheat on an individual assessment or assignment), the fair thing to do would be to decline. If you have participated in an act of academic integrity and later feel regret, we welcome you to come forward and explain. With all of that said, we are required to also remind you of the official university policy which we abide by. Plagiarism: According to the Cornell University Code of Academic Integrity, a student shall be guilty of violating the code of academic integrity if she/he knowingly represents the work of others as her/his own [or helps another student to do so]. For additional information, refer to . If you are accused of plagiarism, a primary hearing is scheduled at which the evidence is considered and a decision rendered. If you are found guilty, the academic integrity officer of your college is notified.Using pedagogical data for publications: The instructors of this course are passionate about teaching and are always seeking new, modern pedagogical methods to improve the education of our students. Instructors may use data from exams or from poll questions in aggregate form (without identifiers of any sort) to evaluate our pedagogy. Analysis of exam or poll questions may be published in pedagogical journals. We value and always maintain our students’ confidentiality, but students can request verbally or via email (biolabs@cornell.edu) to opt out if they have concerns. Please do not hesitate to contact the instructors if you have specific questions.CALENDAR FOR LECTURE AND LAB ACTIVITY Week ofActivityReadings and AssignmentsOAB = Open access book, IB = Investigative Bio Lab Manual All lab sections are held live. Only 2 lectures are live and the rest are recorded.Week of August 31Lecture 0recordedCourse Introduction, pre-course questions, undergraduate research opportunitiesWatch intro video to become familiar with the course. Week of September 7Lecture 1liveThe scientific process, “Science is…”; How science is produced and consumed.OAB: Biology 1.1 The Science of BiologyDUE: CANVAS DISCUSSION BOARD ON 5 SCIENTISTS OR SCIENCE NEWS SOURCES ON TWITTERLab 1Experimental Design Workshop: the scientific process, Student and TA research experienceIB: Ch. 1; Download SimUtext software on your laptop DUE: ELEPHANT COMMUNICATION STUDY WORKSHEETDUE: CANVAS DISCUSSION BOARD ABOUT FAVORITE SCIENTISTWeek of September 14Lecture 2liveExperimental design: the naked mole rat exampleIB: Ch. 1.DUE: WATCH ASSIGNED VIDEOSLab 2Lab Skills Workshop: Discussing Microscopy, spectrophotometry, serial dilutions, pipetting. IB: Ch. 2DUE by Friday at noon (Ithaca, NY time): ANIMAL BEHAVIOR WORKSHEETWeek of September 21Lecture 3recordedStatisticsOAB:Statistics 1.1Statistics 2.1 and 2.4Statistics 9.1 and 9.2 and 9.4Lab 3Statistics workshop: statistical methods and intro to R. IB: Ch. 3 Download R-project and R-Studio.Week of September 28Lecture 4recordedScientific communicationLab 4Communication workshop: digital footprint, paper discussion (jigsaw), library tutorial, Twitter: Ch. 5 DUE: READ ASSIGNED PAPER AND COMPLETE PAPER DISSECTION WORKSHEET.Download Zotero and visit the library guide: of October 5Lecture 5recordedIntroduction to Antibiotic resistance and Limiting NutrientsOAB: Biology 14.4 DNA Replication in ProkaryotesBiology 25. 2 Green algae: precursors of land plantsMicrobiology 1.3 Types of MicroorganismsMicrobiology 14 Antimicrobial drugsLab 5Become familiar with the projects,Mid-semester eval, Liebig’s barrel simulation, start designing your experiment. Complete the outline. IB: Ch. 6; Ch. 7 DUE: FIND A PRIMARY RESEARCH JOURNAL ARTICLE RELATED TO EACH OF THE RESEARCH TOPICS, AND FOR EACH ARTICLE, POST A 3+ STEP TWITTER THREAD: INTRODUCTION, METHODS AND RESULTSDUE: CHOOSING A JOURNAL WORKSHEETWeek of October 12Lecture 6recordedWriting a research proposal IB: Ch. 5DUE: STATISTICS WORKSHEETLab 6No labs. Work on your research proposal.Week of October 19Lecture 7 recordedHow to conduct Peer-reviewIB: Ch. 5DUE: EXPAND THE OUTLINE INTO A RESEARCH PROPOSAL AND INDIVIDUALLY WRITE THE INTRO, METHODS, PREDICTED RESULTS AND REFERENCES FOR PEER REVIEWLab 7Finalize and present experimental design. Start peer-review.Week of October 26Lecture 8recordedData analysis and conclusion drawing: revisit statistical analysis; show examples of drawing conclusions based on stat results. DUE: COMPLETE THE REVIEW OF TWO PROPOSALS AND SELF REVIEWLab 8Receive experimental data. Data analysis. Start poster preparation.Week of November 2Lecture 9recordedNew science communication: AR, VR, Media labs and makerspaces.DUE: USE THE REVIEWS TO IMPROVE YOUR INDIVIDUAL PROPOSAL. SUBMIT IT ON CANVAS.Lab 9Reviewing the semester. Finalize your poster.Week of November 9Lecture 10 recordedBiology research at CornellLab 10Virtual poster presentations; Tweet out your experiment; What are the next steps following your research project? DUE: POSTER PDF AND SUPPLEMENTARY MATERIALSWeek of November 16 (and until November 24)Lecture 11No lecture. Open book exam question release.Lab 11Open lab: lab rooms are set up with microscopes, pipettes and spectrophotometers. You can go and practice (optional to students on the Ithaca Campus).November 25 – November 29 Thanksgiving breakWeek of November 30Lecture 12 recordedThe importance of climate change. Lab 12Answering questions about the Open Book Exam. Climate change forum preparation.Week of December 7Lecture 13recordedResponsible conduct of research and open science I.B.: Ch. 5.DUE: OPEN BOOK EXAMLab 13Climate change forum. How can you use the skills you gained in this course?DUE: MOCK EMAIL TO A PROFESSORDUE: TRANSFERABLE SKILLS WORKSHEETWeek of December 14Lecture 14No LectureDUE: TWEET ABOUT A TRANSFERABLE SKILL YOU LEARNED IN THE COURSE AND HOW IT RELATES TO YOUR SCIENTIFIC CAREERNo labs ................
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