The Biology of Organisms
Bio 207
Spring 2015
Prof. Jonathan Levitt, Course Director
Office MR731, Phone: 212.650.8539
Office hours: Mon 9-11am or by appointment
[email protected]
Department of Biology, City College of New York, CUNY
About Bio 207
Bio 207 is a core Biology major’s course that meets graduation requirements. It is designed to
build critical understanding about how organisms, both plant and animal, solve some of the
fundamental challenges to sustaining themselves in their environments. Organisms have adapted
to ever-changing environments by the process of evolution. Adaptation at all levels of
organismic organization from molecular processes to interacting organ systems is the result of
this process. In addition to covering the theme of organisms in the environment, the course is
also designed to build skills in experimental design, modern methods of measurement, data
analysis and communicating about experiments. All of these aspects of the course are important
for success in subsequent biology core and elective courses as well as being highly useful for a
variety of future careers. Most of this course addresses “how” and “why” questions and the
solutions to them, thus it is not about memorizing facts.
Key Course Information
• The text for the course is Animal Physiology, Third Edition, by Hill, Wyse and Anderson.
• iClicker2™ is required; available at CCNY Bookstore. Note comments below about
iClicker use and its grading component.
• BlackBoard™ is the central communication site and resource repository. To help you prepare
there will be course resources available online via BlackBoard, so it is important that you
use it extensively, beginning the first week of the term.
• Presentations and exams are in NAC 1-202. All of the course meetings will be interactive and
you will be expected to be ready to contribute to the discussion at any time.
• Labs and tutorials are held in either MR507 or MR511
Course Faculty and Staff
Laboratory Management
Vitaly Zyhadlo, Technician, Room MR514, 212.650.5908, [email protected]
Lab Instructors:
Please ask your lab instructors about how and when they can be contacted.
Roma Rajwani: [email protected]
Yijing Shan: [email protected]
Contributors to the course design are:
Profs. Rochelle Buffenstein, Daniel Lemons, Jonathan Levitt, Jay Edelman, Adrian RodriguezContreras, Hysell Oviedo and Shlomo Simchon
Original lab design and development by: Profs. Rochelle Buffenstein, Jess Hanks, Daniel
Lemons, and Jonathan Levitt.
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Bio 207 Weekly Topics
Week
Topic
Readings
1
2/2
Introduction to course goals and organization; overview of topics; staff;
resources; the organism in the environment: temperature-oxygen-water;
biomes: abiotic and biotic factors; evolution; regulation and homeostasis: the
internal environment vs. the external environment
Ch1: 3-29
2
2/9
Water and solute transport; barriers to water and solute movements; organisms
in the aquatic environment
Ch5: 99-124
3
2/18
Water and solute balance in aquatic environments: osmoconformers,
osmoregulators; water and solute balance in terrestrial environments; marine
and fresh water organisms and those that do it all
N.B. College closed Mon 2/16, Wed 2/18 is Mon schedule
Ch27: 699-715
Ch28: 717-752
4
2/23
Water and solute balance in terrestrial environments: Kidneys; humans and
kangaroo rats in moderate and extreme environments
Ch29: 753-786
Ch30: 787-800
5
3/2
Midterm 1: covers weeks 1-4 (incl Labs 1-2 and Tutorials 1-2)
6
3/9
Internal communication: neurons, resting membrane potentials in excitable
tissues, action potentials; voltage-gated channels;
Ch12: 295-325
7
3/16
The synapse; neurotransmitters; G-protein coupled receptors and 2nd
messenger systems; EPSPs, NMJ
Ch13: 327-358
8
3/23
Muscle and movement; sliding filaments; E-C coupling; length-tension
relationships; biomechanics
Ch.20: 523-540
9
3/30
Animal energy acquisition; energy balance and temperature regulation;
Ch7: 161-182;
Ch10: 225-275
4/6
No class, spring recess
10
4/13
Midterm 2: covers weeks 6-9 (incl Lab 4 and Tutorials 3-4)
11
4/20
Energy utilization by organisms; metabolism and the use of oxygen
Ch9: 207-223
12
4/27
Gases, ventilation in water and air: oxygen for metabolism, gas transfer organs
and processes, transporting gases to and from the body tissues
Ch22: 569-581
Ch23: 583-608
13
5/4
O2 and CO2 transport
Ch24: 617-643
14
5/11
Circulatory systems; flow dynamics, flow regulation in response to
environmental and internal conditions
Ch25: 647-670
Mon
5/18
Final exam: comprehensive, Weeks 1-14 including all benchmarks (6815pm – NAC 1-202)
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(review Ch2: 31-37)
Weekly Laboratory Schedule for Bio 207 Spring 2015
Lab Day
LABORATORY ACTIVITIES
T
2PS
W
3EG
3GW
Th
4PS
1
2/3
1/28
1/29
Laboratory Exercise 1: Introduction to
the Laboratory; collecting field data
2
2/10
2/4
2/5
Tutorial 1: Solutes, solutions and
osmolality. Aquatic environments.
 How to write an Introduction to a paper
3
2/17
2/11
4
2/24
2/25*.
QUIZ WRITING ASSIGNMENTS
**
Laboratory Exercise 2: Environmental
no class salinity and osmolality; osmotic
2/12
regulation of cell volume
2/19
LQ1
TQ1
2/26
Tutorial 2: Organismic responses to
fluctuation in water salinity
 Peer-edit Introduction
 Writing about Methods
LQ2
Introduction to Cell Volume
experiment – Lab 2 (Draft due:
not graded)
W2/18
Mon
sched
5
3/3
3/4
3/5
Laboratory Exercise 3: Digestive and
vascular system of rats
TQ2
Re-written Introduction
(graded)
6
3/10
3/11
3/12
Tutorial 3: Transport systems and
kidney function
 Peer-edit Methods
 Writing about Results
LQ3
Methods section for Cell Volume
– Lab 2 (Draft due: not graded)
7
3/17
3/18
3/19
Laboratory Exercise 4: Muscle and
biomechanics
TQ3
Re-written Methods section
(graded)
8
3/24
3/25
3/26
Tutorial 4: Energy balance and
temperature regulation
 Peer-edit Results
 Writing a Discussion
LQ4
Results for Cell Volume
experiment – Lab 2 (Draft due:
not graded)
9
3/31
4/1
4/2
Laboratory Exercise 5: Field trip to salt
marsh at the Marshlands Conservancy
(Group 3GW Sat 3/28 9am)
TQ4
Web-based articles on Salt
marshes Re-written Results
section (graded)
10
4/14
4/15
4/16
Tutorial 5: Gases in water and air
 Peer-edit Discussion
 Assembling the Reference section
Lab 5a: Analysis of field trip data
LQ5
Discussion for Cell volume
experiment - Lab 2 (Draft due:
not graded)
11
4/21
4/22
4/23
Laboratory Exercise 6: Metabolic rate
in ectotherms and endotherms: RQ
TQ5
Re-written Discussion and
Reference section (graded)
Discuss group-designed
experimental protocol
4
12
4/28
4/29
4/30
Laboratory Exercise 7: Carry out groupexperiments
13
5/5
5/6
5/7
Tutorial 6: Case studies of organisms in
the environment: thermal, fluid, osmotic,
energy balance
 Analyze data from group experiments
 The links between the sections of a
research paper; writing a full paper
14
5/12
5/13
5/14
 Laboratory skills examination
LQ6
Complete paper on group
experiment (graded)
*Monday schedule on Wednesday ** LQ = lab quiz; TQ = tutorial quiz
Assessment
Grades will be comprised of the following:
Assignment
Points
No.
Total
Lab quizzes
20
6
120
Tutorial presentation/writeup
50
1
50
Tutorial quizzes
20
5
100
Writing sections
20
4
80
Final full research paper/presentation
100
1
100
iClicker participation
10
12
120
Lab skills exam
55
1
55
Progress quizzes
25
3
75
Midterm exams
100
2
200
Final exam
100
1
100
Total points for course:
1000
Grades will be determined approximately according to these guidelines: A- to A+, ≥ 90%; B- to
B+, 80-89%; C- to C+, 70-79%; D, 55-69%; F, ≤ 54%.
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Course Learning Outcomes: by successfully completing this course you will be able to:
 compare and contrast the different strategies organisms use to deal with a range of
environmental challenges.
 explain the role and regulation of water and solutes in a number of different organisms found
in a range of environments.
 explain the function of excitable tissues such as nerves and muscles and the way they produce
signaling, coordination and movement.
 explain the way energy acquisition and utilization are regulated to maintain balance.
 mechanistically describe several regulatory processes and predict their responses under a
range of environmental conditions.
 carry out a scientific experiment, analyzing and reporting its results orally and in writing.
 use techniques for computerized data collection, analysis and presentation.
 read and write a scientific research paper according to standard conventions.
 work collaboratively in groups.
 solve problems related to organismic function.
Components of the course
This fourteen-week course includes presentations in the lecture hall and online,
laboratory/tutorial sessions, online materials and quizzes and out-of-class work. All of the
components are designed to complement each other in a thematically-based course. The course
activities have been carefully chosen to support your learning about how organisms function in
their environments. Success depends upon active participation in all the course settings. Despite
the lecture hall’s large size, individual students will be called upon to respond to what is being
presented, and every class session will collect iClicker responses.
IClickers
iClickers are an integral part of each class sessions and are required, beginning with the first
class. If 80% of all questions are answered in a session, six (6) participation points will be
earned. Up to an additional four (4) points may be earned by answering the questions correctly.
Laboratory and Tutorial Sessions
There are fourteen laboratory/tutorial sessions. Tutorials are problem-solving sessions that
are prepared for before class and presented by small student groups. They cover topics that are
included in lecture, reading and laboratories. Tutorials give you an opportunity to learn the
material in greater depth, practice quantitative problems and review. Each student will make one
tutorial presentation. Tutorial presenters receive up to 50 points for their presentations and writeups. Tutorial write-ups of presenters are due the day before the presentation in class and must be
emailed to the class instructor by the end of the day. Tutorial questions can be downloaded from
BlackBoard. A quiz covering the material from the preceding session will be given at the
beginning of each laboratory and tutorial session. It will also cover background material for the
current week’s session. Each quiz will contribute up to 20 points towards the final course grade.
There will be no make-up quizzes. If you miss more than one laboratory and/or one tutorial
session you will be dropped from the course (see attendance policy below).
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Reading
The text is available at the bookstore. Check the publisher website, http://www.sinauer.com/
for deals. The course has also used the text Animal Physiology, by Eckert, which may also be
useful. Some students like the book Animal Physiology: Adaptation and Environment, by K.
Schmidt-Nielsen. Students are encouraged to look through these or other physiology texts. The
publisher of the text also has a website with study aids and other material for each chapter. There
will also be additional reading material posted on Blackboard throughout the term, and some
students may need to consult an introductory level biology text occasionally. Reading
assignments are in the course schedule above. Reading the assigned text sections ahead is good
preparation for getting the most out of class sessions. Because the weekly lab and tutorial quizzes
cover both the previous lab and the current lab, you are expected to come to lab having reviewed
the background material of the current day’s lab and having read the laboratory write-up
carefully.
Written assignments
Writing in a format typical of scientific papers is significant component of the course. There
will be five writing assignments in the term. Four of these assignments cover the major sections
of a published research report according to the current scientific writing style. A significant
amount of class time will be devoted to preparing for, discussing and analyzing this writing. All
assignments must be submitted via email or Blackboard, depending on lab instructor
preference. Papers in their first version will be emailed two days prior to their due date to an
assigned peer-editing partner as well as to the lab instructor. There will be an automatic
deduction for late papers either when the first, ungraded, version is due or when the final,
graded version is due. Revised papers will be submitted via the web and are due by 11:59PM on
their due date. Instructors use a service that identifies plagiarized material. (See the “fine print” at
the end of the syllabus.)
Tests and Exams
There will be two mid-term exams and one final exam. The final exam is comprehensive and
integrates material from the entire term. These exams will consist of multiple choice, matching
and true/false questions. Prior to each exam there will be one online progress quiz. These quizzes
will cover the same material as the exam that follows. A laboratory skills exam will be given in
the lab at the end of the term; it will cover all aspects of the lab, including use of the computer
and various sensors to make measurements and making calculations like the ones performed in
the laboratory. It is important that every member of the class become competent in all of the
skills required for carrying out experiments, and therefore, the tasks performed within lab groups
will be rotated among group members from week to week.
Course Resources – Making it Work
How do you know what you are really supposed to learn?
Since material is learned through reading, presentations, labs/tutorials, online activities and
through out-of-class problem sets, it is reasonable to wonder what is expected. To assist in
knowing that, a guide will be provided for every part of the course that helps define how to
demonstrate learning. Learning Benchmarks will be posted on Blackboard for each unit. They
help indicate what level of detail is expected and how to demonstrate mastery of each topic. The
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assigned reading contains a great deal of detail, and the Benchmarks can serve as a useful guide
in deciding which of those details deserve attention when preparing for quizzes and exams. The
laboratory exercises also have Benchmarks which will be covered in laboratory quizzes.
What are the most important study strategies?
A number of studies show that the most important factors in succeeding as a student are: 1)
allocating enough out-of-class study time; 2) studying and reviewing effectively with fellow
students; and, 3) preparing before class sessions.
Staying up-to-date
Almost all of the materials for the course will be posted on BlackBoard on a weekly basis. It
is advisable to check Blackboard frequently and also to look for updates to materials that are
posted.
Biology Resource Center and Campus Resources (Room MR502 and NAC Tech Center)
A resource center in MR502 is maintained by the Biology department. It holds some useful
tools for self-study including books, tutorial services and internet access. The new NAC cITy
Tech Center has many state-of-the-art group study rooms with full technology available,
including multiple laptop plug-in and display ports per room. These rooms can be scheduled
ahead of time. Students are urged to avail themselves of these resources.
Office hours
Students are encouraged to take advantage of office hours. Phone or email to make an
appointment if the regular office hours conflict with classes or other obligations.
Policies (the fine print)
Grades obtained are final and not negotiable
There will be sufficient graded work to assess class standing before the 2/17/2015 deadline
for withdrawal. Students with an average below 55% at that time may want to seriously consider
withdrawing from the course. There will be no extra-credit options. It is important to remember
that a ‘C’ or better is required for advancement as a biology major.
Attendance Policy (from the College Bulletin)
Students are expected to attend every class session of each course in which they are enrolled
and to be on time. An instructor has the right to drop a student from a course for excessive
absence. Students are advised to determine the instructor’s policy at the first class session. They
should note that an instructor may treat lateness as equivalent to absence. (No distinction is made
between excused and unexcused absences.) Each instructor retains the right to establish his or
her own policy, but students should be guided by the following general College policy: In
courses designated as clinical, performance, laboratory or field work courses, the limit on
absences is established by the individual instructor. For all other courses, the number of hours
absent may not exceed twice the number of contact hours the course meets per week. When a
student is dropped for excessive absence, the Registrar will enter the grade of WU.
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Absences from tests and exams
Unless the instructor is provided with a medically certified reason or official notification of
death in the family, and/or police report of a car accident, there will be no opportunities to
reschedule tests, nor will there be any retakes of missed quizzes, tests or exams. It may be
possible to make arrangements to attend a different lab section to catch up, provided there is one
with available space, and prior permission from the lab instructor is obtained.
Incompletes and other contingencies
Incomplete grades (INC) will not be given for any reason except the documented inability to
finish one major part of the course such as an exam. This is the college’s policy. If
documentation of illness or other serious situation is presented, an Incomplete may be given, and
when the missing material is completed a final grade will be assigned. An Incomplete does not
allow retaking the entire course; and there is only make up of the part missed. An incomplete
should not be requested unless there is a very good reason; it will not be given as an alternative
to a failing grade or a withdrawal.
Laboratory maintenance
The laboratory is managed by Vitaly Zyhadlo. He will ensure that all the materials for the
laboratory exercises are available and that the lab is clean and ready for each session. On
completion of laboratory exercises, students are expected to wash all glassware that was used,
and put any equipment away, leaving the laboratory clean and tidy. No food or drink is
allowed in the lab.
Academic Integrity and Plagiarism
The academic world, like the scientific and medical communities, has no tolerance for
presenting the words of others as your own. This could be simply lifting sections from texts;
copying work off the internet, copying answers from previous years’ classes or copying your
fellow classmate’s work. We maintain the following standard: It is plagiarism if you copy
more than a phrase or a sentence without having it in quotation marks with the original
source indicated, or if you paraphrase a paragraph or more without indicating what the
source is. Please do not plagiarize work, for we will be forced to report you to the College
disciplinary authorities which could lead to your failing the course and/or other disciplinary
consequences.
CUNY Academic Integrity Policy
The CUNY Policy on plagiarism says the following about plagiarism (it can be found at:
http://www.ccny.cuny.edu/about/upload/academic_integrity.pdf
“Plagiarism is the act of presenting another person’s ideas, research or writings as your own. The
following are some examples of plagiarism, but by no means is it an exhaustive list:
1. Copying another person’s actual words without the use of quotation marks and footnotes
attributing the words to their source.
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2. Presenting another person’s ideas or theories in your own words without acknowledging the
source.
3. Using information that is not common knowledge without acknowledging the source.
4. Failing to acknowledge collaborators on homework and laboratory assignments.
5. Internet plagiarism includes submitting downloaded term papers or parts of term papers,
paraphrasing or copying information from the internet without citing the source, and “cutting
and pasting” from various sources without proper attribution.
The procedures in cases of suspected breaches of academic integrity are delineated in the
CUNY document referenced above. Where necessary we will follow these procedures without
exception, working with the CCNY Academic Integrity Office.
Additional information on what constitutes plagiarism can be found at:
http://www.plagiarism.org
iClickers: responding with another student’s iClicker is cheating. At a minimum doing so will
result in point deductions for both students, and it may also result in disciplinary action.
Disability Statement
In compliance with CCNY policy and equal access laws, appropriate academic
accommodations are offered for students with disabilities. Students must register with The
AccessAbility Center for reasonable academic accommodations. The AccessAbility Center is
located in the North Academic Center (NAC), Rm. 1-218. Tel: (212) 650-5913. Under The
Americans with Disability Act, an individual with a disability is a person who has a physical or
mental impairment that substantially limits one or more major life activities. If you have any
such issues, I encourage you to visit the AccessAbility Center to determine which services may
be appropriate for you. If extra time or a special location are needed for examination, a
request should be made by email or letter at least five days in advance of the exam.
Courtesy Policy
Eating, drinking, or use of unauthorized hand held electronic equipment is not allowed in the
classroom.
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