Bio 371L – Spring 2017

Biology 371L - Experimental Physiology

INTRODUCTION

This lab could do more to change your thinking about science than any other course you will take at UT.
You will be given wide open opportunities and learn new skills, not just facts. The physiology in the
laboratory experiments may be new or unfamiliar to you, even if you have taken a physiology class in the
past. Regardless of your background, you will research and read primary scientific literature, design and
execute experiments, analyze your data, and present thoughtful and detailed explanations of the entire
process. In the final weeks of the semester each lab team will design and execute its own experiment.
During the last week of classes, each team will present its project in a 10-minute oral presentation and
each individual will submit a full written paper.

Because you will be working in teams to design and execute your own protocols, there will be times when
your experiments do not work perfectly. We don’t expect them all to work perfectly, so don’t worry about
your grade early in the semester. Try not to be frustrated. Troubleshooting and finding solutions are a
major part of what "real science" is all about. For the most part you will not be graded on getting “good”
results unless it is the result of an oversight that you should have already learned about in this course.

This course consists of a weekly one-hour lecture that all lab sections attend together, one four-hour
laboratory session, plus at least 2-3 hours of library or computer work per week. You will also need to
find time to meet with your team to plan protocols and analyses. BIO 371L is a Substantial Writing
Component class and you will be writing and rewriting assignments in the format of scientific papers
submitted for publication. BIO 371L also carries a Quantitative Reasoning flag and an Independent
Inquiry flag: the meanings of all three are detailed below.

Writing
Writing Flag courses are designed to give students experience with writing in an academic
discipline. In this class, you can expect to write regularly during the semester, complete substantial
writing projects, and receive feedback from your instructor to help you improve your writing. You
will also have the opportunity to revise one or more assignments, and to read and discuss your
peers’ work. You should therefore expect a substantial portion of your grade to come from your
written work.

Quantitative Reasoning
Quantitative Reasoning courses are designed to equip you with skills that are necessary for
understanding the types of quantitative arguments you will regularly encounter in your adult and
professional life. You should therefore expect a substantial portion of your grade to come from
your use of quantitative skills to analyze real-world problems.

Independent Inquiry
This course carries the Independent Inquiry flag. Independent Inquiry courses are designed to
engage you in the process of inquiry over the course of a semester, providing you with the
opportunity for independent investigation of a question, problem, or project related to your major.
You should therefore expect a substantial portion of your grade to come from the independent
investigation and presentation of your own work.

We hope that you have fun in this course and we welcome your comments, critiques, and suggestions.
Many of the best modifications of the course have come from conversations with students.

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COURSE OBJECTIVES FOR Biology 371L

Students who complete this class should be able to:

1. describe how model systems demonstrate basic physiology that is shared by humans and other
mammals.
2. search the primary literature to find relevant experiments.
3. read, evaluate, and properly reference the primary literature.
4. design and execute a well thought out experiment.
5. analyze and critique the design of experiments of others.
6. write a protocol for an experiment and execute it.
7. collect appropriate data.
8. analyze data from their own or others' experiments.
9. use simple statistical analysis, including Student t-test and linear regression.
10. interpret a p-value correctly.
11. read and interpret graphs in different formats.
12. present data in the most appropriate form (graph or table).
13. relate their results to what has been found in the past.
14. say where they would go with a project given unlimited time and resources.
15. write a scientific paper, with all parts from abstract to references, in correct format.
16. present an experiment as an oral presentation.
17. use Excel for spreadsheet, data analysis, and graph construction.
18. use a word processing program such as Word to write and import graphics.
19. use basic lab equipment including computer data acquisition systems.
20. make solutions and dilutions using proper glassware and technique
21. cooperate with classmates and work effectively in teams.
22. be able to concisely define all words and concepts used in the course

WHAT DO I NEED FOR BIO 371L?

Lab manual (required): Departmental Lab Manual will be available from Co-op Custom Publishing.
This will include an additional fee for access to AD Instrument’s Lt program.

Texts (suggested): A Short Guide to Writing about Biology 7/e by Pechenik (Longman).
A Pocket Style Manual 5/e by Diana Hacker (Bedford St. Martin)

SUPPLY LIST:
Required:
1. Lab coat or scrubs – required for entry into the lab (UT rules)
2. “iClicker” These will not be used on the first of classes. Please register your clicker through
Canvas
3. Non-memory (ie. super-cheap) calculator

Optional:
1. Dissecting kit with fine dissecting instruments if you do not want to use the communal equipment.
We have plenty for you, though.
2. Safety glasses if you don’t want to use the communal glasses in the lab.

F You should bring your clicker and a calculator to lecture each week.

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THINGS TO NOTE:
Electronics: No cell phone or tablet or smartwatch use is allowed in lecture or lab.

Attire: Students must wear closed-toe shoes, scrubs or lab coat, and have legs protected at all times in
lab (no shorts). Safety goggles, gloves, and other protective equipment may also be required at times
depending upon the activity. You may not participate in lab if you are not wearing appropriate clothing.

WHO IS HELPING ME SUCCEED IN THIS COURSE?

BIO 371L is a course that will teach you how to approach problems and how to solve them. It is taught
in an inquiry-based manner, meaning that we will often not tell you the answer to your question if we
believe that you have the evidence before you to sort it out yourself. This type of learning environment
has been shown to create far deeper learning and understanding, but is not always easy or fun. We
appreciate that it is hard work and we appreciate your effort. Our goal is to have you learn the
maximum amount of useful understanding that we can manage in one semester and we view ourselves as
facilitators and enablers, not encyclopedias or content delivery vectors.

Course Director: Dr. Peter English.

HOW ARE GRADES CALCULATED IN BIO 371L?

This class is not graded on a strict 90-80-70 scale due to variations in grading rigor among the different
graders. If you have an “easy” grader, it is possible that you can get a C with an 83% overall average.
Conversely, if your grader is demanding, it is possible to get an A- with an 88% average. As Course
Director, I standardize the grading among the different lab sections. We will use the +/- grading system.

Please note that the workload in this class is distributed so that there is a lot of work on the front end
(first 3-4 weeks) but that the grading is weighted to the end of the semester, with nearly a third of your
grade based on your final project. Early scores are usually not predictive of final grades unless they are
very low or very high.

Lecture components:
2 lecture tests 10%
iClicker points, lecture homework 5%

Lab components
Design scores
protocol design (5) 5%
results and discussion design (5) 5%

Writing scores
protocols (2) 15%
results and discussion (2) 15%

Final project
oral presentation 10%
full write-up 20%

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Lab performance
Daily performance score 10%
Peer evaluations, homework, quizzes 5%

Use of iClicker You must arrive at lecture each day with a functioning, turned on iClicker. Points will be
earned for answering questions (earns one point - whether answered correctly or incorrectly), for correct
answers (for those questions that have correct answers, the correct answer is worth an additional 0.5
points), and for answering all questions in a given day (an additional three points). If your iClicker is not
functioning, you obviously cannot participate in these points, so please be sure that it works.

SCIENTIFIC REPORT WRITING:

Writing assignments in this class will consist of:
(1) protocols with background research from the scientific literature and detailed methods
(2) results with data analysis, statistics, and appropriate data presentation and an appropriate
discussion of the results that compares the obtained results with the predicted results and with
the journal articles that helped generate the expected results
(3) one full write up of your independent project, including all sections of a scientific paper

Writing: Clear writing is an extremely important skill. Your TA is available to answer specific questions
before your assignment is due, but will not “pre-grade” your assignment. We will work with you as much
as possible but we cannot be expected to correct long-standing writing deficiencies. You are encouraged
to take your papers to the Writing Center for assistance with writing skills - see the Canvas site for
additional information.

F Plagiarism warning! Even though you may contribute ideas and background research to a
protocol, you MAY NOT use the written text from a protocol in your final paper or scientific
write-ups unless you were the person who wrote the protocol and received the protocol writing
grade. You may discuss your work with other team members but you must write your own papers
and protocols. Failure to follow this requirement is considered academic dishonesty.

Attendance: UT policy is to expect registered students to attend all scheduled meetings of the courses to
which they are registered. We agree. Students who miss quizzes or tests or other scored activities
(announced or unannounced) without an excused absence will receive a zero. Students with an excused
absence will have their next (or previous, at instructors discretion) equivalent quiz or test grade counted
double or be graded out of fewer total points. If you miss lab, there is a high likelihood that you will be
unable to produce the assignments tied to that lab (so your design score would be zero, for example).

Weekly quizzes: Unannounced and announced short quizzes may be given haphazardly in lecture and
lab – any section can have a quiz independent of any other section. The quizzes can include any material
covered in the course up to that point, including the prep you should have done to get ready for today’s
lab. Quizzes may include in-class writing assignments. You may use non-programmable calculators and
should always have one with you.

Preparation: During the beginning of the course we will be working on skills that are necessary for the
rest of the semester such as graphing, making dilutions, writing protocols, and proper data analysis. Learn
these skills while they are the focus of the class, as later in the semester we will assume that you have
mastered them. Uncorrected problems in these crucial areas can make this class a painful experience, so
PLEASE ASK FOR HELP. Try to remember that our goal is to have you master the material and
succeed – we will work with you to help you achieve the goals of the course. That said, no amount of
effort on our part can make up for a lack of effort or poor decision making from a student.

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It is important that you come to lab fully prepared to do the exercise assigned for that week. You should
know not only what equipment you will be using, but how to use it, what you will be measuring, and why.
You should have sufficient depth of knowledge about your system to solve problems that might arise.
You should arrive at lab prepared to begin immediately, knowing the all aspects of the experiment well
enough to ace a quiz over it! Your daily performance score is dependent on you being prepared and is ten
percent of your semester score – a string of zeros typically translates into an undesirable letter grade.

Homework: Homework, lab reports, protocols, and any other assignments are due at the beginning of the
period or as scheduled in Canvas. Assignments are considered late if they are not in the TA’s or Canvas’
possession at the start of class. Papers turned in late will be penalized 10% of the total point value for
each day or partial day the report is late. For some assignments, like protocols, no late assignments are
accepted. Extensions, when possible, will be granted only for exceptional circumstances, such as a
documented illness, death in the family, or apartment complex burning down. The usual load of
coursework is not grounds for an extension.

All lab reports must be computer-generated, double-spaced, and printed on white paper. This includes
graphs (you cannot just pencil these in later). Most assignments are turned in via Canvas, so that must
be done before coming to lab. Technical difficulties using the official UT course management system is
not an acceptable reason for a late assignment.

Grading issues and resolution: We believe that grading is a multi-part event. First we assign values to
assignments or quiz responses and then you review those values to understand (a) what you did
incorrectly and (b) what you will need to do differently in the future to earn higher values. Sometimes
graders make errors, more often students make errors as they work to understand new material and
thought processes. We absolutely want to correct any grading errors and also help you understand student
errors, so just ask. We are less interested in debating the point values of wrong answers. Any
disagreements between students and TAs will be resolved by the course director.

Examinations: There will be two full-period tests in lecture. There is no final examination.

Oral presentations: The last week of the semester each team will present a ~10-minute talk on its final
project. The presentation and the experimental design/results will be graded by the other students as well
as the TA and the course director.

Communication by E-Mail: A valid, functioning e-mail address is required! If you do not receive a
Canvas message because your address is incorrect, you are STILL RESPONSIBLE for the information in
the email. You can change your directory email by logging into UT Direct, then going to PERSONAL
INFORMATION, CHANGE EMAIL.

Use of Canvas: The UT Canvas site will be used extensively during the semester to disseminate
information, administer quizzes, receive assignments, and will be a primary source for announcements.
You should plan to check this frequently and/or set up notifications. The calendar view is often a great
way to stay organized, so check it out.

Electronics: LAPTOP, CELL PHONE, SMART WATCH OR OTHER ELECTRONICS USE IS NOT
ALLOWED IN LECTURE OR LAB unless required for special accommodations. You should read the
article posted in Canvas under “Files” if you think that computer use is helpful to you – study after study
has shown that it is devastating to comprehension

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USE OF CLASS MATERIALS – COPYRIGHT CONCERNS

The materials used in this class, including, but not limited to, exams, quizzes, handouts, the lab manual,
and homework assignments are all copyright protected works. Any unauthorized copying of the class
materials is a violation of federal law and may result in disciplinary actions being taken against the
student. Additionally, the sharing of class materials without the specific, express, written approval of the
instructor may be a violation of the University's Student Honor Code and an act of academic dishonesty,
which could result in further disciplinary action. This includes, among other things, uploading class
materials to websites for any purpose, including sharing those materials with other current or future
students. Please read the section below about our approach to academic dishonesty in 371L.

ACADEMIC DISHONESTY
The penalties for academic dishonesty at UT can range from a zero on the assignment or test to an "F" in
the course. In BIO 371L we believe that you have spent enough time in higher education to know better,
and so we will always recommend an F for the semester, no matter the infraction. Academic dishonesty
includes (but is not limited to) cheating on tests and quizzes, altering tests and assignments after they have
been returned, lying in order to get an extension, failing to cite references, plagiarizing from references,
and uploading course material to anywhere other than the course Canvas site.

Students who violate any of the above, or any other type of misconduct not specifically addressed above,
may be called to a meeting with the course director and if a violation of the honor code is suspected the
matter will be referred to Student Judicial Services (SJS).

The UT Honor Code (or statement of ethics) is here and linked on the Canvas site:
http://catalog.utexas.edu/general-information/the-university/#universitycodeofconduct

Academic accommodations: Students with disabilities may request appropriate academic

accommodations from the Division of Diversity and Community Engagement, Services for Students with
Disabilities, 471-6259, http://www.utexas.edu/diversity/ddce/ssd/

Planned absences for religion: By UT Austin policy, you must notify your instructor of your pending
absence at least fourteen days prior to the date of observance of a religious holy day. If you must miss a
class, an examination, a work assignment, or a project in order to observe a religious holy day, you will
be given an opportunity to complete the missed work within a reasonable time before or after the absence.
In a lab course with team work such as this it may be impossible to complete missed work for a number
of reasons, in which case you will be evaluated out of fewer total points so that you are not penalized for
the absence.

Safety notice: The following recommendations regarding emergency evacuation from the Office of
Campus Safety and Security, 512-471-5767, http://www.utexas.edu/safety/ 
 Occupants of buildings on
The University of Texas at Austin campus are required to evacuate buildings when a fire alarm is
activated. Alarm activation or announcement requires exiting and assembling outside.
 Familiarize
yourself with all exit doors of each classroom and building you may occupy. Remember that the nearest
exit door may not be the one you used when entering the building.
 Students requiring assistance in
evacuation shall inform their instructor in writing during the first week of class.
 In the event of an
evacuation, follow the instruction of faculty or class instructors.
 Do not re-enter a building unless given
instructions by the following: Austin Fire Department, The University of Texas at Austin Police
Department, or Fire Prevention Services office.
 Link to information regarding emergency evacuation
routes and emergency procedures can be found at: www.utexas.edu/emergency


Behavior Concerns Advice Line (BCAL): 512-232-5050


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Campus Carry and BIO 371: Students can now legally carry concealed handguns with proper
certification, and if you plan to do so there are some aspects of this course that you should consider when
you plan your day. First, your backpack or purse and other items will be out of reach when you are in
lab. If you plan to carry your handgun in your backpack or purse or in a way that it will not be attached
to your body, you will not be able to legally do that in the lab. Similarly, on lecture test days your
backpacks and other items will be out of reach. Dr. English will provide all students with oral notice,
but know that handguns are not allowed in his office.

Persons allowed to carry concealed handguns must keep them concealed at all times, so if you see a gun
there is a problem. If you see a gun anywhere on campus carried by anyone other than a police officer,
please immediately call 911. You should report a “person with a gun.” Of course, in such an
emergency situation the class rules about cell phones and electronics are irrelevant.

12th Class day: February 1, 2017 : Last day an undergraduate student may add a class except for rare and
extenuating circumstances. Last Drop or Change Status Date: April 3, 2017.

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Lecture is on Miscellaneous due this week

Week Lecture topic Lab activity Writing Due in lab this week
Wednesday (lecture and lab – check Canvas)

1 18 Jan Design experiments - - no lab - -

Statistics and Your first protocol.
2 25 Jan Syllabus quiz on Canvas All: First protocol assignment (see Canvas)
problem solving Reading assessment.

Safety & MSDS. Graphing Compliance training proof.
3 1 Feb Photosynthesis All: Solutions on top of page 31
and Excel. Solutions. Annotated bibliography.

Photosynthesis All: Solutions and Variability homework.
4 8 Feb Osmolarity Fake knee data.
experiments All: Intro + protocol for today

All: Photosynthesis results & discussion,
5 15 Feb Tonicity Osmolarity experiments Osmolarity calculations
C :Intro + protocol for today

A: Osmolarity results & discussion;
6 22 Feb Epithelial transport Tonicity experiments Tonicity calculations
D: Intro + protocol for today

Tubule design questions
7 1 Mar **Lecture Test** Epithelial Transport 1 C: Tonicity results & discussion
Insect saline calculations

8 8 Mar Smooth Muscle Epithelial Transport 2 B: Intro + protocol for today


15 Mar - SPRING BREAK - - - - - - -

9 22 Mar Final project Cardiac Muscle 1 D: Tubule results & discussion


10 29 Mar Analyzing data Cardiac Muscle 2 A: Intro+ protocol for today

Written Proposal,
11 5 Apr Samples Project proposals B: Smooth muscle results & discussion
equipment/materials list

12 12 Apr **Lecture Test** Individual projects - - Final project protocol (ask TA about this)

13 19 Apr Presentations Individual projects - -

14 26 Apr - - no lecture - - Individual projects - -


All: Intro, materials & methods, results,
15 3 May - - no lecture - - Presentations Sensible presentation
discussion due 1 week after presentation