COMPARATIVE ANIMAL PHYSIOLOGY COURSE SYLLABUS
Biol. 334A; FALL 2015
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Instructor: Alexa Tullis
Office: 257E Thompson Hall
Phone: x2857
E-mail: atullis@ups.edu
Office hours arranged on an individual basis to fit your schedule. Additional office
hours will be scheduled before exams.
Objectives:
Biology 334 is an upper level course designed to:
• teach basic principles of animal physiology
• promote good laboratory skills and teach aspects of physiological experimentation
• promote intellectual and laboratory independence
• refine data analysis and scientific writing skills
Upon completion of this course, you should have acquired:
• an understanding of basic principles in animal physiology,
• the ability to apply these principles to understand novel situations,
• the basic tools necessary for writing a solid biological research paper,
• many skills necessary to perform laboratory experiments in animal physiology
Required Texts:
• Animal Physiology 3rd ed (2012) by Hill, Wyse, and Anderson.
• A short guide to writing about biology, 6th - 8th ed, by Pechenik (others are probably fine,
too, but most of you will have the 6 – 8th ed.)
Lectures: MWF 9:00-9:50 AM in Thompson 171
Class sessions are primarily an interactive lecture format, with some class
discussion. In some cases you will be asked to do specific problems or other short
assignments prior to coming to lecture. Although these assignments may not be collected
they are important for keeping up with the lecture and may be considered when
evaluating your class participation.
• The lecture schedule lists pages in your text associated with each lecture. Read these
pages before lecture; it will enable you to get more out of the lecture and will help
you answer questions when called upon. Re-read the associated pages after lecture,
focusing on the material covered in lecture.
Course Moodle Page:
The course Web/Moodle page can be accessed through the UPS Moodle page
http://moodle.pugetsound.edu/moodle/. Our site contains essential material for both lecture and
lab, including lecture slides, laboratory exercises, exam study materials, worksheets, and outside
readings.
• To save paper and for a faster turnaround time, you will be turning in most assignments
through Moodle. IMPORTANT: Unless otherwise stated, I will only accept
Microsoft Word files for written work and Excel files for data. If I cannot open your
file or if there is something wrong with it such that I cannot read it after I open it then I
may consider the assignment not turned in.
1
Exams:
There will be two mid-term exams and one final exam. IMPORTANT: To ensure that
you are not rushed when you take the mid-terms, they will be given in the evening from 5:30 –
7:30 PM on the scheduled day*. Please make arrangement now to reserve those times. Lectures
on those days will be devoted to last minute questions on exam material. Exams will primarily
cover lecture material but may also contain questions relating to the laboratory.
IMPORTANT: Make-up exams will not be given but adequate consideration may be
given and adjustments may be made if there is a medical or family related emergency. Written
documentation of the nature of the emergency may be required. The final exam will be given on
Monday December 15th from 8-11am. As per university policy, the final exam must be taken
during this time.
* If the entire class can agree on another 2 hr block of time that works for everyone, I’m open to
changing this.
Classroom Conduct
• As a courtesy to me and your classmates, please put cell phones on vibrate and in
your bags during lecture. I am not asking you to turn them off since during a campus
emergency, the university will contact us through our cell phones. If only your phone
goes off during lecture, silence it; if everyone’s goes off during lecture, answer it.
• As long as it does not distract other students, I do not mind if you eat or drink in
lecture.
Late Policy:
Unless otherwise stated, assignments are due at the start of lecture or lab as indicated on
the individual assignments and in the lecture schedule. Turning in an assignment late will reduce
the maximum credit available by 10% per day, including weekend days. Work turned in late on
the same day that it is due will be considered ½ day late and 5% of the points possible will be
deducted from your earned grade. Late assignments will not be accepted (a) after 7 days past the
due date, and/or (b) if not turned in with enough time to be evaluated before a follow up
assignment is due, and/or (c) after 5pm on the last day of reading period. TO BE FAIR TO ALL
STUDENTS, THIS LATE POLICY WILL BE STRICTLY ENFORCED. I will waive the late
penalty only if there is a medical or family related emergency. Written documentation of the
nature of the emergency may be required.
University Student Bereavement Policy:
Upon approval from the Dean of Students’ Office, students who experience a death in the family,
including parent, grandparent, sibling, or persons living in the same household, are allowed three
consecutive weekdays of excused absences, as negotiated with the Dean of Students’. For more
information, please see the Academic Handbook, http://www.pugetsound.edu/studentlife/personal-safety/student-handbook/academic-handbook/bereavement-policy/
Sports Related Absences:
If you are going to miss an exam or laboratory due to an athletic event, please inform me
AT LEAST ONE WEEK before that date. If you need to make up a laboratory in another section
it is your responsibility to make prior arrangements with me and the other Animal Physiology
professor. As stated earlier, no make up exams will be given. However, it is possible that
arrangements can be made with your coach so that you can take the exam. Due dates will not be
adjusted due to an athletic-related absence so plan ahead.
In keeping with university policy, athletic practices are not excuses for missing or coming
late to class or labs. Coming late or leaving early from lab or lecture due to sports-related events
may result in a lower class participation grade.
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Official Classroom Emergency Response Guidance
Please review university emergency preparedness and response procedures posted
at www.pugetsound.edu/emergency/ <http://www.pugetsound.edu/emergency/> . There
is a link on the university home page. Familiarize yourself with hall exit doors and the
designated gathering area for your class and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor
at the designated gathering area so she/he can account for your presence. Then wait for
further instructions. Do not return to the building or classroom until advised by a
university emergency response representative.
If confronted by an act of violence, be prepared to make quick decisions to protect
your safety. Flee the area by running away from the source of danger if you can safely
do so. If this is not possible, shelter in place by securing classroom or lab doors and
windows, closing blinds, and turning off room lights. Stay low, away from doors and
windows, and as close to the interior hallway walls as possible. Wait for further
instructions.
University Policy on Academic Accommodations
If you have a physical, psychological, medical or learning disability that may impact your course
work, please contact Peggy Perno, Director of the Office of Accessibility and Accommodation,
105 Howarth, 253-879-3395. She will determine with you what accommodations are necessary
and appropriate. All information and documentation is confidential.
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ANIMAL PHYSIOLOGY LABORATORY
Laboratories: Harned Hall 235
Laboratory work is an important part of any course in animal physiology. The laboratory
exercises are designed to introduce you to some important physiological techniques. You will be
given an opportunity towards the end of the semester to use these techniques in an experiment of
your own design. Another aspect of lab work that we want to expose you to in Comparative
Animal Physiology is trouble shooting, which is one of the most important skills a scientist
learns. Since this is not the aim of most college science laboratories, many of the lab exercises
you have done in the past have been specifically designed to be foolproof. Because we are often
working with live animals or preparations, it is virtually impossible to design foolproof animal
physiology labs.
Labs are scheduled for 4 hours (please do not ask if you will get out early).
Laboratory investigations during weeks 1 - 7 will be structured labs. Weeks 9 – 14 will
be devoted to independent laboratory research, data and statistical analysis, and
interpretation of results. All laboratory exercises are available on Moodle.
Laboratory Conduct
• As a courtesy to me and your classmates, please put cell phones on vibrate and in
your bags during lab. I am not asking you to turn them off since during a campus
emergency, the university will contact us through our cell phones. If only your
phone goes off during lab, silence it; if everyone’s goes off, answer it.
• As per department policy there is to be no food or drink in the lab room. There will be a
place to put these items outside of the lab room.
• Animals must be treated with care and respect. It is a privilege to be able to work with
them. Any instance of animal abuse will lead to a failing grade in this course.
Structure of the standard labs
All lab exercises for this course will be available on Moodle. Most of the time you will be
working in groups of two, although a few labs will involve groups of four. All standard lab
exercises will be preceded by a short introductory lecture and are designed to be completed in
one lab period.
• Pre-labs: Pre-labs are due through Moodle by the start of your lab period, and each
student must complete their own pre-lab. I’ve designed these questions to help prepare
you for the experiment. Reading appropriate sections of the text will help you understand
the physiological processes we are studying in each experiment.
• Post-labs: Standard labs have Post-labs associated with them. Each post-lab is slightly
different and is described at the end of each lab exercise. Unless otherwise stated, these
will be due by the start of your next lab period through Moodle.
• Lab notebook: Everyone must have an individual lab notebook, the type is up to you.
The quality of your lab notes directly influences your ability to analyze your data and,
thus, indirectly influences the quality of your post-labs and research papers. Because I
feel so strongly that good notes are a major key to good science there may (or may not)
be surprise checks on your lab notes.
• Lab preparation and performance: Throughout the term I will be assessing your lab
preparation and performance. It is usually readily apparent if a student has not prepared
adequately for lab because performance will be suboptimal.
Independent projects
You will have the opportunity halfway through the semester to design and execute a
study that you and your research partner have designed. In designing your independent project,
we encourage you to integrate and expand upon techniques you learned during the standard lab
exercises, although you can also use a new technique if it is practical and informative. This is a
time to further investigate physiological phenomena that peaked your interest or apply
techniques that you found particularly enjoyable (more info on the "Independent Projects"
handout).
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Research Papers
Each student must submit 2 written research papers, one on a standard lab and one on
your independent project. Each paper includes some kind of revision. The specifics for these
papers vary and are outlined in the "Writing Assignments" handout. Completion of both papers
is required for a passing grade in this class.
Lab make-ups
All labs are required and missed labs may result in a lower final course grade unless there
is a family or medical emergency, proof of which may be required. Because labs are designed
specifically for 8 people and constrained by equipment availability, no switching of lab sections
will be allowed except in the case of a family or medical emergency. If you must miss a lab, you
may make it up in any of the other lab sections, including those run by the other Animal
Physiology professor (Sue Hannaford, shannaford@pugetsound.edu, x2959). It is your
responsibility to clear any changes with the professors in advance. Due to the time involved in
setting up each lab, you will only be able to make up labs during the same week that your missed
lab exercise is scheduled – no exceptions.
Schedule of lab sections
Instructor
Day
Tullis
Monday
Tullis
Monday
Hannaford
Tuesday
Hannaford
Wednesday
Time
12 - 4 PM
5 - 9 PM
1 - 5 PM
1 - 5 PM
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Academic Integrity and Plagiarism
Several forms of academic misconduct are especially relevant to this class and deserve
highlighting:
• Cheating on exams or quizzes.
• Alteration, fabrication or misrepresentation of data.
• Plagiarism on any assignment, including lab exercises. This includes written work and
laboratory drawings.
The following pages on the Puget Sound web site are your sources for information on Academic
Integrity:
• What constitutes plagiarism?
(http://research.pugetsound.edu/c.php?g=304242&p=2028010):
Every semester I have had to deal with incidences of student plagiarism. In almost all cases,
the student stated that they did not know that they plagiarized. To help prevent you from
accidently plagiarizing during this and other classes, you are all required to study the
information about plagiarism on the Collins Library web site and take the Academic
Integrity Quiz associated with this page (link on the right side of the page).
• What happens if a student plagiarizes or otherwise violates the rules of academic integrity?
(http://www.pugetsound.edu/student-life/personal-safety/student-handbook/academichandbook/academic-integrity/):
This page contains general information on academic integrity and the policy for dealing with
violations of academic integrity. Please note the university requires every incident of
academic dishonesty to be reported to the Registrar.
• I am obligated to report any incident of academic dishonesty. Any penalty applied with
respect to this course will depend on the severity of the violation. Again, it is your
responsibility to make sure that you understand this issue. Please ask me if you have any
questions.
When you sign the Student Contract for this course, you are stating that you have read the
information on this page and that you fully understand what constitutes plagiarism and
what the penalties for violations of academic integrity.
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Grading (subject to slight changes):
Midterms (2 x 100 pts)
Final
Graded homework assignments (approx.)
Lab research paper: first submission
Lab research paper: final submission
Summary of primary references #1
Summary of primary references #2
Introduction & Methods Draft for Independent Project Paper (completeness)
Peer reviews of Intro. & Methods
Final Independent Project Research Paper
Pre-labs (5 @ 5 pts each)
Post-labs (5 @ 10 pts each)
Lecture preparation and participation*
Lab preparation and performance**
TOTAL
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Points
200
200
35
25
50
10
10
5
10
100
25
50
15
15
750 pts
This category refers to your apparent preparation and participation in lecture. I will
assess your performance in this area by taking into consideration your attendance,
the extent to which you do the assigned readings and assignments (even those that
are not graded), and how readily you participate during lecture.
** I will assess your lab preparation and performance during every lab session by
observing your level of preparation and how directed and independently you work
during lab. I will also be observing how thoughtfully you treat the lab animals and
how clean you leave the lab space.
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STUDENT CONTRACT
Comparative Animal Physiology (BIOL334) Fall 2015
Please sign the contract and return it to your professor by Friday, September 4th.
Signed contracts are required to receive grades in this course.
I have carefully read the syllabus and know the correct answers to all of the questions on
the Course Self-Test. I understand the content of the syllabus.
• I am aware of the term exam and final exam dates and that the term exams will be given
in a 2-hour block of time outside of the regularly schedule lecture time.
• I understand that no make-up exams will be given.
• I am aware of the assignments, and I understand that assignments are due on the date and
time stated. I understand that preparation assignments are not accepted late and that there
is a penalty for any other assignment turned in late.
• I understand that labs are mandatory and that failure to attend lab for something other
than a documented medical or family emergency may lead to a lower final course grade.
I have read the University’s policy on violations of academic integrity and the penalties
associated with such violations.
• I understand these policies and penalties.
I have read the material about academic integrity and plagiarism contained on the Collin’s
Library website as outlined in the syllabus.
• I have taken the Academic Integrity Quiz associated with the Library’s web page on
Academic Integrity.
• I understand what constitutes plagiarism.
• I pledge to refrain from any act of academic dishonesty, plagiarism or scientific
misconduct.
• I understand that all written work must be completed individually by me unless the
assignment specifically states otherwise. I understand that if I violate this policy,
penalties will be applied.
NAME (PRINT) ________________________________________________
SIGNATURE ________________________________________________
DATE __________________________
7
BIOL334 COMPARATIVE ANIMAL PHYSIOLOGY
TENTATIVE LECTURE SCHEDULE FALL 2015
Wk
1
Date
M 8/31
W 9/2
F 9/4
2
3
M 9/7
W 9/9
F 9/11
LABOR DAY – no class
Temp and body mass continued
The cellular basis for endothermy
M 9/14
Principles of gas exchange & design of
respiratory structures
(Complete Gasses in Air & Water worksheet
before coming to class)
Continued
Blood: Respiratory pigments and oxygen
transport
W 9/16
F 9/18
4
M 9/21
W 9/23
F 9/25
5
Topic
Major themes in animal physiology
Overview of animal metabolism; aerobic and
anaerobic pathways
The importance of temperature & body mass
on metabolism
Continued
Carbon dioxide transport and body fluid pH
* Circulatory System Assignment due
through Moodle by 9am
Continued
M 9/28
Does temperature acclimation influence the
oxygen binding of crayfish hemocyanin?
W 9/30
Water & salt balance: Basic problems and
principles
(Complete Water & Salt Balance worksheet
prior to class)
Water & salt balance in aquatic environments
First Submission of Research Paper 1
uploaded to Moodle by 9am
Water balance in terrestrial environments &
the importance of body size
EXAM I^
Terrestrial water balance cont.
Cellular muscle physiology: Regulation of
muscle contraction
(Complete Muscle Cell Structure Refresher
before coming to class)
Whole muscles at work
continued
F 10/2
6
M 10/5
7
W 10/7
F 10/9
M 10/12
W 10/14
F 10/16
See next page for important footnotes
Reading*
Ch. 1
163-170; 183200
170-181; 225226; 233-236;
Appendices E
&F
Hulbert &
Else (1990)**
Ch. 22 & 23
pp. 616-638
pp. 638-645
Powell &
Watts
(2006)**
pp. 699-704;
Ch. 28
Laboratory
Introduction to Power
Lab data collection
system
&
Experiment 1
* The Influence of
Temperature on
Crayfish Heart rate
(option for research
paper 1)
No Lab
Experiments 2 & 3
* The influence of
temperature on mouse
oxygen consumption
-OR* The influence of
temperature on
goldfish oxygen
consumption
(both are options for
research paper 1)
Experiments 2 & 3
* The influence of
temperature on mouse
oxygen consumption
-OR* The influence of
temperature on
goldfish oxygen
consumption
(both are options for
research paper 1)
Experiment 4
* Oxygen binding by
hemocyanin
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pp. 705-712;
737-751
Experiment 5
* Crustacean
osmoregulation
pp. 523-530;
542-543
Experiment 6
* Contraction of
isolated earthworm
smooth muscle
&
Project Proposals
Due by 10/16;
consultations
531-535
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Wk
8
9
Date
M 10/19
W 10/21
F 10/23
Topic
FALL BREAK – no class
Muscle fiber types & plasticity
Muscle fiber types continued
M 10/26
Animals & temperature: The ectothermic
response
* Final Submission of Research Paper 1
uploaded to Moodle by 9am
Temperature acclimation and adaptation in
ectotherms
continued
Being endothermic
continued
continued
W 10/28
10
11
12
F 10/30
M 11/2
W 11/4
F 11/6
M 11/9
W 11/11
F 11/13
M 11/16
W 11/18
F 11/20
13
M 11/23
14
W 11/25
F 11/27
M 11/30
W 12/2
F 12/4
15
M 12/7
W 12/9
F 12/14
Winter energetics
EXAM II^
General features of sensory receptors
(Complete the Review of Cellular
Neurobiology worksheet before coming to
class)
Organization of the vertebrate nervous system
– focus on the autonomic nervous system
Neural control of body temperature
* First draft of Introduction & Methods for
your independent project paper uploaded to
Moodle by 9am
Neural control of blood pressure
(Review Principles of Circulatory Systems
assignment that you completed earlier in the
term)
Introduction to endocrinology, organization of
the vertebrate endocrine system, and control
of hormone secretion
* Peer Review of Intro & Methods uploaded
to Moodle by 9am
THANKSGIVING BREAK
THANKSGIVING BREAK
Endocrine system, continued
Endocrine control of stress
Endocrine control of water and salt balance
continued
Endocrine control of fuel homeostasis (time
permitting)
* Final Independent Project Papers
uploaded to Moodle by 9am
FINAL EXAM: Monday 12/14, 8-11 am
Reading*
Laboratory
pp. 536-539
Ch. 21 &
Waters et al.
(2004)**
pp. 233-246
Project consultations
& complete animal
use forms
Projects Week 1
* Set up & begin data
collection
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pp. 250-268
TBA
pp. 316-317;
332-333; 359362
pp. 397-409
Projects Week 2
* Data collection
* Summary of 2
relevant primary
sources
Projects Week 3
* Data collection
* Summary of 2
relevant primary
sources
Projects Week 4
* Data collection
Box 10.2
review pp.
655-658
pp. 419-432
Projects Week 5
* Wrap up data
collection
* Begin data analysis
pp. 419-432
pp. 432-436
pp. 439-444
Projects Week 6
Results section plan
and consultations
about data analysis &
interpretation
Projects Week 7
Oral Presentations
pp. 436-439
* All readings are from your text, Animal Physiology 3rd ed (Hill et al. 2012). To get the most out of the
reading, skim the assigned pages before lecture and then read thoroughly after lecture.
** On Moodle
^ To alleviate some exam stress, exams will be given during a 2 hour period, 5:30pm-7:30pm on the day the
exam is scheduled. We can move this earlier if the entire class agrees on a time.