Fundamentals of Scientific Inquiry in the Biological Sciences I Syllabus—Fall 2021 PDF

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This is the syllabus for the Fall 2021 academic year for Fundamentals of Scientific Inquiry in the Biological Sciences I also known as Bio 204...

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BIO204 Syllabus—Fall 2021 Fundamentals of Scientific Inquiry in the Biological Sciences I Stony Brook University Undergraduate Biology, College of Arts and Sciences This course satisfies the SBC category SPK (Speak Effectively before an Audience). You must sign up for BIO458-T02. Course Director: Marvin O’Neal III, PhD Faculty and Instructor Office Hours will be held in-person in CMM/BLL Room G10 and/or online using Zoom. Semester schedules are posted in the lab manual and on the recitation Blackboard (Bb) site. Any questions, email [email protected]

Part 1: Course Information UNDERGRADUATE BULLETIN COURSE DESCRIPTION: This is the first course in the foundational laboratory sequence for all biology students and students in related fields. Students will experience the laboratory process, research process, a wide range of laboratory tools, methods, skills, learn to read and write scientific presentations, and collaborate in formal inquiry. This course has been designated as a High Demand/Controlled Access (HD/CA) course. Students registering for HD/CA courses for the first time will have priority to do so. This course has an associated fee. Please see www.stonybrook.edu/coursefees for more information. 2 credits Prerequisite: CHE123, CHE129, CHE131, CHE141 or CHE152. Pre- or Corequisite: BIO201, BIO202, or BIO203. COURSE COMPONENTS: Required Materials: ● Access to Blackboard, Stony Brook University’s course management system ● Access to online Lab Manual: Fundamentals of Scientific Inquiry in the Biological Sciences I (Garcia, O’Neal, and Spikes, current edition, 2020) from Hayden-McNeil ● University Adopted Clicker Software: Turning Point App ● Goggles: impact resistant, UV protection, ANSI certified ● Computer with audio and video capability ● Proficiency with Zoom, the primary platform for SBU virtual meetings Course Delivery Mode and Structure: This is an in-person course. The Lab component is in-person, scheduled in laboratories in the Centers of Molecular Medicine/Biology Learning Laboratories (CMM/BLL) at SBU. Recitation is in-person, scheduled in Frey lecture hall room 100 at SBU. Links to all online meetings are found in the Blackboard learning management system (LMS) and the online lab manual. The lab manual is the best resource to use to fully understand all course expectations, deliverables and due dates, especially because the course requires significant time management. Some assignments and course interactions will utilize software with which you may not be familiar. See “Technical Requirements” section for more information. We will provide a computer for your use in the lab; however, we recommend that you bring in your personal laptop. How We Will Communicate: Check Blackboard course websites (BIO 204.R# and BIO 204.L#) regularly for information regarding administrative changes, lab instructor communication, and course updates. Logging in daily to the Blackboard announcement page ensures that you are able to remain an active member of the course. Carefully read emails and announcements. Email course-related questions to your instructor’s email or to [email protected]. Your Stony Brook University email must be used for all University-related communications. All instructor correspondence will be sent to your SBU email account. To log in to Stony Brook Google Mail, go to http://www.stonybrook.edu/mycloud and sign in with your NetID and password.

Technical Requirements: This course uses Blackboard for communication between faculty and students, submission of assignments, and posting of grades. Access the Blackboard course site at https://blackboard.stonybrook.edu. If you are unsure of your NetID, visit https://it.stonybrook.edu/help/kb/finding-your-netid-and-password for more information. You are responsible for having a reliable computer and Internet connection throughout the term. Assignments will require the use of email, a word processor, spreadsheet program, and presentation software to complete this course successfully. The following list details a minimum recommended computer set-up and the software packages you will need to have access to, and be able to use: ❖ PC with Windows 10 or higher or Mac with OS 10.11 or higher with 250 GB Hard Drive ❖ Intel Core i5 or higher with 8 GB of RAM ❖ Latest version of Chrome or Firefox; Mac users may use Chrome or Firefox. A complete list of supported browsers and operating systems can be found on the My Institution page when you log in to Blackboard. ❖ High speed internet connection ❖ Word processing software: Microsoft Office -Word, Excel, PowerPoint minimally- and Google Drive. ❖ Headphones/earbuds, microphone, and webcam/internal camera ❖ Ability to download and install software applications and plug-ins (note: you must have administrator access to install applications and plug-ins). Technical Assistance: If you need technical assistance at any time during the course or to report a problem with Blackboard you can call 631-632-9800 (client support, Wi-Fi, software and hardware), submit a help request ticket at https://it.stonybrook.edu/services/itsm, or if you are on campus, visit the Walk-Up Tech Support Station. COVID Protocols: All Federal, State, and Stony Brook University protocols will be followed without exception. Any student, whether they are vaccinated or not, found violating lab safety protocols will be asked to leave and will not be permitted to make up any work or assignments. Repeated violations will result in failure of the course. Students must read all placards before entering labs and respond quickly to faculty, instructor, and undergraduate teaching assistant compliance requests. Students may be required to socially distance, wear a mask, wear provided gloves, sterilize work stations and/or use campus compliance software and apps, like Campus Clear.

Part 2: Course Goals and Assessments COURSE GOALS: This course is designed to be an introduction to your career in the biological sciences and prepare you for upper division biology courses. The most critical aspect of this preparation is to develop scientific thought and process. In addition, you will be introduced to common laboratory practices and procedures and practice experimental design using scientific reasoning. For each lab there are learning objectives which are used to construct the activities, assessments, assignments, and quizzes. Please use these to guide your preparation, lab work, and studying. In other words, successful completion of the learning objectives demonstrates that you have achieved a level of mastery of the knowledge and skills required for this course. The following goals are further divided in your lab manual into specific Learning Objectives and placed at the beginning of each lab activity. After completing this course, you will be able to: 1. Explain and apply fundamental principles of the scientific process to extrapolate accurate conclusions from scientific data and design basic experiments. 2. Access information using effective, well-designed search strategies and appropriate information sources. 3. Organize, synthesize, and communicate scientific information in verbal and written forms. 4. Constructively engage in teamwork to facilitate collaboration and a high-quality group product. 5. Convert quantitative information between various forms including graphs/tables/equations/words and accurately perform calculations including appropriate statistical tests. 6. Discuss ethical issues in science with depth and clarity, presenting multiple perspectives.

The SPK (Speak Effectively before an Audience) category of Stony Brook’s General Education Curriculum can be satisfied by completing all three of the following objectives in the Scientific Literature Project, see Table below. You must be enrolled in a separate course, BIO458 T02, in order to receive credit. SPK Learning Objective (LO)

Scientific Literature Project

Assessment

(LO1) Research a topic, develop an oral argument and organize supporting details

Apply a reading strategy to an article from the primary literature and prepare a scientific poster

Reading Strategy Worksheet

(LO2) Deliver a proficient and substantial oral presentation for the intended audience using appropriate media

Present Scientific Literature Poster Presentation and answer questions from lab group during Q&A

Oral Poster Presentation

(LO3) Evaluate oral presentations of others according to specific criteria.

Assess student poster presentations

Sci Lit Survey

GRADING What will I do each week in BIO204? 1. Prepare - Read the lab manual and take notes in your Excel notebook 2. Pre Quiz - Complete the pre quiz in the Blackboard Recitation site by 9AM each Monday. 3. Recitation - Attend Recitation at your scheduled time. Take notes, participate in problem-solving activities, and answer quiz questions via the Turning Technologies clicker or mobile app. You may not use both during the same recitation period as this will negatively impact your grade. 4. Lab - Attend Lab at your scheduled time in CMM/BLL in-person lab. Participate in all lab activities, both group and individual as prompted by your Instructor. Follow all COVID protocols provided by SBU. 5. Excel Notebook - Maintain a record of your activities (notes, data analysis, and answers to questions) in your Excel notebook. Revise and submit your lab notebook within 24 hours of the start of lab. 6. Projects/Exams - Prepare for upcoming Projects and Exams. Submit on time, using SafeAssign. Assessment

Points

CIQ and SPK

15

Complete the Course Information Quiz (CIQ) to test your knowledge of this syllabus and complete the SBU Curriculum Speak Survey (SPK) to determine if you should sign up for BIO458-T02.

Pre Quiz

48

Pre quizzes assess your preparation for the upcoming recitation and lab. You should review the lab manual and complete the pre quiz on the Recitation Blackboard site by 9AM each Monday. These are independent quizzes and you are expected to work on your own.

192

Clicker questions will be given during each recitation using the Turning Point app, clicker, or polling. These questions are designed to determine if you understand the concepts presented in the Lab Manual for the upcoming lab but may also include material from previous recitations. You may use notes from your own Lab Notebook; however, these are independent quizzes and you are expected to work on your own. No make-up quizzes will be given. Report any issues with clickers immediately to the [email protected]. Each clicker question is worth 4 points if correct, 2 points if incorrect, 0 points if you do not answer.

Recitation Quiz

Description

Excel Notebook

165

The Excel notebook is a record of your notes from each week’s lab activities and group work. Complete the lab’s Excel notebook (worth 15 points; completed as a group) and upload it into Blackboard Assignments in your Lab Section. Complete a Teamwork Assessment (worth 5 points; completed as an individual) for the labs noted in the schedule below, found in the Lab Manual. You will be graded on the quality (accuracy, organization, thoroughness, etc.) of a particular component (such as a written description, response to a question, graph, analysis, etc.) for each lab.

Excel Competency

25

An understanding of Excel is a key component of many scientific laboratories. Appropriate formatting and statistical methodologies will be explored. This is a take home exam which you are expected to work on individually.

120

This project is designed to teach you how to read primary scientific literature. This project includes four major steps: 1) applying a reading strategy, 2) completing a worksheet, 3) presenting a poster summarizing your assigned article to your peers, and 4) peer-reviewing other presentations. You will receive feedback on your worksheet (25 pts.), meet with your instructor to review your poster (10 pts.) and present your final poster (85 pts.). Because different articles are assigned to each student, your section’s instructor will not grade all parts of this project. Topic specialists, instructors teaching other BIO 204 sections, will grade the accuracy of your poster. A list of the articles and topic specialists will be posted in the lab manual. It is important that you meet with the topic specialist if you have any content questions about your assigned article. You are expected to work on your own for this assignment.

160

The Midterm Exam (60 pts.) will be online and given through the course management system, Blackboard. You will have 1 hour to complete the exam within an 18-hour window (6:00AM-midnight). Although this is an open-book exam, you should work independently to complete it. The midterm exam must be submitted by 11:59 PM and includes multiple choice, calculations, and short answer questions. The Final Exam is cumulative and will occur during final exam week. This exam is closed book and will be held in-person during common exams.

75

This exam is a practical, conducted in-person. You will be required to demonstrate to an instructor how to use the micropipettor, balance, compound microscope, caliper, centrifuge, and how to make solutions. This is a timed, independent exam. You will be graded on correct answers as well as proper use of each piece of equipment. The specific exam questions can be found in the Lab Manual.

100

You will write a full lab report using data from Labs 3 and 4, for the Biochemistry Enzyme experiments. The report should follow a standard scientific format of title, introduction, methods, results, discussion and references. This course requires a particular format (adopted from a scientific journal format), called Knisely.

Experimental Design Proposal and Review

100

During this multi-week assignment, you will demonstrate how to design a behavioral experiment using isopods. As a group of 3-4 students, design and present your experiment to your lab section (50 pts.). Then, individually and using the supplied rubric, you will evaluate other group proposals (25 pts.) and submit a proposal analysis (25 pts.).

Total Points

1000

Scientific Literature Project

Exams

Tools Competency Exam

Biochem Lab Report

In order to request a regrade, you should do the following within 2 weeks of receiving the graded assignment: ● Email the grader a written statement describing why the grade is incorrect. ● You must attach and reference the rubric. ● You must attach your graded assignment. ● If you do not receive a confirmation from the grader, email [email protected] ● Be mindful that regrades take time and are secondary to grading of recently submitted assignments.

How are letter grades determined? Letter grades are assigned following a meeting between all of the instructors and faculty at the end of the semester. Letter grades are based on your final point total. The following table will help you determine the MINIMUM letter grade that you will receive based on accumulated points. However, we typically add points to a section based on its performance relative to other sections and to the overall averages in each category for the entire class. Therefore, your letter grade may be higher than this scale. Historically, the average letter grade in this course has been approximately a C+/B−. Course grades are not curved. If every student accumulates greater than 933 points by the end of the semester, then everyone will receive an “A.” It is therefore possible for all students within a section to receive an “A” (24/24), although historically, the highest number has been 17/22. If extra credit is given, then the letter grade will still be calculated based on the 1,000-point scale and not a percent score, even if the total exceeds 1,000 points.

Part 3: Attendance and Absence Policy ATTENDANCE POLICY You are expected to attend and participate in every recitation and lab for the full period. During lab and recitation, you should be engaged, listening, and ready to participate with audio, video, or both. For any quizzes given in recitation, on Bb, or in lab, NO MAKE-UP QUIZZES WILL BE OFFERED . Lateness

Penalty

Reason

between 5-45 minutes

-10 pts.

Lack of professionalism, immaturity, irresponsibility, impede group dynamic, safety concerns, etc.

more than 45 minutes

absence

Lack of professionalism, immaturity, irresponsibility, impede group dynamic, safety concerns, etc.

loss of points

Disruption to group, class, or posted resources can result in a loss of any/all lab points as well as additional penalties from faculty or university.

Disruption of any lab or event

Planned Absences, such as Religious Holidays and University-sponsored events If you have an official, pre-scheduled university event, such as an athletic competition or an exam in another class, OR if you observe one of the approved religious holidays, then you must complete this online form by the end of the Add/Drop. Last minute requests will not be honored. There are no regularly scheduled make-up recitations or laboratories for excused absences; instead, students will be responsible for making up all work outside of class. If in-class quizzes or participation grades are missed due to an excused absence, this grade will be prorated based on work received from other laboratories and recitations. BIO204 is a high-demand course and therefore most sections are full; however, if it is possible to place you into another recitation or lab, it is your responsibility to email the faculty or instructor of that section, on the day you attend, so that your grades can be migrated to the appropriate section. Excused Absences We understand that emergencies occur during the semester, which might result in an absence. You are still responsible for all work missed and all assignments are still due by the original date/time. Please communicate with your lab instructor and/or recitation faculty member of your absence within one week. Technical difficulty with internet connections, Zoom or Blackboard is not a sufficient reason for an extended lack of participation or completion of work. Per University policy, faculty will not view medical documentation related to your absence. If required, contact the Student Support Team in SAC 222 (https://www.stonybrook.edu/commcms/studentaffairs/studentsupport/, Phone: (631) 632-7320, Fax: (631) 632-6756, Email: [email protected]) if extenuating circumstances are impacting your academic attendance and performance. Permission to make up assignments or exams will be decided on a case-by-case basis. The

Exams should be taken at regularly scheduled times. Requests to make up an exam should be submitted, in writing, to the Course Director, Dr. O’Neal using [email protected]. Unexcused Absences For each unexcused absence from recitation, zeros will be given for quizzes. For each unexcused absence from the lab, zeros will be given for the lab notebook assignment as well as any assignment related to that lab. Any assignments that are due on the day of an unexcused absence can and should still be submitted electronically by the beginning of the lab to be accepted as “on time.” BIO204 is a high-demand course and therefore most sections are full. It may not be possible to place you into another recitation or lab. Even if we are able to do so, making up a laboratory in another section does not negate an unexcused absence. Late Assignment Submission Option Ontime assignments must be submitted by the beginning of lab on the day that they are due unless otherwise noted on the course schedule. Any designated assignments that are NOT submitted through Blackboard in t...