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BIO 111, Spring 2015

PRINCIPLES OF BIOLOGY II
Hubbell Auditorium, Hutchison 141
MWF 9:00-9:50

Bob Minckley
446 Hutchison Hall
robert.minckley@rochester.edu
office hours: 10:30-12:00 W
10:30-11:30 F

LECTURE
BIO 111, Principles of Biology II, is one half of a two-semester lecture biology course required of all
majors and minors in the biological sciences. An understanding of the material covered in the first half
of the sequence (Bio 110) probably helps, but is not essential to do well in Bio 111.
RECITATIONS
These are 50 minutes long, enough time to review material from the lecture, gain insights on how to
prepare for exams, and discuss readings in classic and recent scientific literature.
LABORATORY
BIO 111P, Introductory Biology Lab, is the lab course that accompanies the lecture course Bio 111. The
content of the lab course supports the lecture material, although the same material in lab and lecture
material may not be presented in the same week. Labs meet 1 day/week for 3 hours. The lab is a
completely different course with its own grade. The lab does not have to be taken if you are in the
lecture, but is required for some majors.
For those enrolled in lab, material will be available each week on the Bio 111P Blackboard. See the Bio
111P syllabus on Blackboard.
LECTURE TEXT
Principles of Life, 2nd edition, 2014. Hillis, D., et al. Reading assignments are on the syllabus, but may
change under rare circumstances. Copies of the textbook are on 2-hour reserve at Carlson Library and
at Rush Rhees Library.
This course (lecture) is supported by a web page on blackboard. The slides that have data/ graphs will
be posted as a pdf on Blackboard for download. Grades may be checked through your Blackboard
account.
ATTENDANCE
Lecture attendance is required in as much as it is your responsibility to note any information presented
in lecture including course content, changes in the syllabus, or course requirements. Part of your final
score (approx. 3%) is attendance. For this part, full credit is given if you are in class for 75% of the
lectures. Attendance is taken by clickers that are available either at the Campus bookstore or by
downloading an app to your phone from https://www1.iclicker.com.
GRADING
Most of the points for the grade in the course come from exams and attendance in the lecture.
However, a full 10% is earned in recitation. Grades for the lab are not part of the lecture grade.
Lecture
Lecture exams (4)
Cumulative portion of final exam
Attendance
Recitation
Participation in projects/Pop quizzes

350 pts
50 pts
15 pts
45 pts
460 pts

Grading (based on total points)


A 93-100%
C 73-76.9%
A- 90-92.9%
C- 70-72.9%
B+ 87-89.9%
D+ 67-69.9%
B 83-86.9%%
D 60-66.9%
B- 80-82.9%
D- 55-59.9%
C+ 77-79.9%
E < 55%
Because some exams may be unexpectedly difficult, exam grades may be adjusted relative to the
highest scores in the class.
Final grade breaks will be rounded to the nearest 0.5 points. Cut offs for grades are firm. If you are
below the grade break by a fraction of a point, you have missed the cut off.
Exam schedule
Exam I
Exam II
Exam III
Exam IV

Wed, 11 Feb
Tues, 3 Mar
Wed, 8 Apr
Tues, 5 May

8:30-9:50 am
8-9:30 am
8:30-9:50 am
12:30 -3:30 pm

100 points
100 points
100 points
150 points

All exams will be in Hubbell Auditorium.


The four exams will generally cover one each for the main sections of the course (evolution, diversity,
functional biology, ecology). Questions will be based on material presented in the lecture, in the
textbook, at recitations, and in the scientific papers you will read in recitation. Most questions on the
exam will be short answer. To do well, attend class, think about the material, keep a dictionary of new
terms and concepts, and stay engaged. Hint: Many students who do best make a detailed study guide
(and do not borrow one made by someone else). Tests from some previous years are available on
Blackboard.
The regular exam with the lowest score you receive over the semester will be down-weighted 50% less
than the other three exams. This will mean that if you have a bad day or do poorly for some other
reason this score will not affect your final grade as much. Note, however, that even your worst score
counts, so it is in your best interest to strive to do well on all the exams.
Exams must be written in blue or black non-erasable ink (not pencil).
No pencil or white out will be allowed on questions submitted for regrades.
Missed exams
1. The exam schedule is published. As such, no make up will be given in the case of a previously
scheduled appointment unless notice is given at least one day prior to the exam. One-week notice to
Ms. Baylark should be given for valid reasons for missing an exam, such as religious holidays and
athletic events.
2. Should you miss an exam, you are required to contact Ms. Baylark (jennifer.baylark@rochester.edu)
within 48 hours by email to explain the absence. Oversleeping, forgetting an exam was scheduled, or
having to study for multiple exams are not considered valid excuses for missing an exam.
3. Exam make-ups are NOT graded on a pass/fail basis. Do not assume that skipping your exam and
taking a make up is advantageous. Make-ups must be scheduled and completed within one week of
the date the originally scheduled.
4. Missed exams that are not taken within a week will be entered into the record as a zero.

Exam regrades
Always check that the points on your exam are totaled correctly and the answers are graded properly.
This is a large class so some mistakes will inevitably occur.
If you believe a mistake was made in your grade, submit your explanation in writing. Re-grade forms
will be available on Blackboard. The requests for regrades must be submitted to Ms. Baylark during a
three-day regrade period (dates TBA after each exam) in hard copy and accompanied by the original
examination. If your appeal is determined to be frivolous, you will lose least at least 2 additional
points.
It is your responsibility to show your exam if there is a grade dispute. As such, it is in your best interest
to keep any returned exam until your final course grade has been determined.
Quizzes
Pop quizzes will be given in recitations and consist of simple questions about assigned scientific papers
for that day or lectures in the last week. The quizzes will take no more than 5 minutes. The purpose of
the quizzes is to encourage you to carefully read the assigned readings and attend lectures. We will
drop the lowest pop quiz score. No regrades or opportunities to make up a quiz will be granted.
OTHER MATTERS
Disability: Any one with a disability that might require special arrangements should contact CETL for
assistance.
Extra credit? Grading must be the same for all students, so no extra credit is granted in this course.
Academic honesty: There are extensive guidelines for the boundaries of academic honesty at the
University of Rochester (http://www.rochester.edu/college/honesty/), and this was a point of
emphasis during your orientation. In this class, you are held to this mutual agreement. If you have not
done so previously, be sure to read the entire document. The section on cheating is most relevant to
this course. Exams in this course are closed book, so you are not allowed to consult the text, your
notes, your cell phone, the internet, neighboring students, or any other outside source in answering
exam questions.
The following practices constitute CHEATING and are not allowed: 1) looking at other students work
during an exam 2) using notes or other study aids during an exam (including bathroom breaks) 3)
using unauthorized technology (such as cell phones) during an exam 4) improper storage of prohibited
notes, course materials and study aids during an exam such that they are accessible or possible to view
5) attempting to communicate with other students in order to get help during an exam 5) obtaining an
exam prior to its administration 7) altering graded work and submitting it for regrading 8) allowing
another person to do ones work and submitting it as ones own and 9) undertaking any activity
intended to obtain an unfair advantage over other students.
FACILITATING ACADEMIC DISHONESTY is also prohibited. Examples include: 1) aiding another
person in an act that violates the standards of academic honesty 2) allowing other students to look at
ones own work during an exam 3) providing information, material, or assistance to another person
knowing that it may be used in violation of course, departmental, or college academic honesty policies
and 4) providing false information in connection with any academic honesty inquiry.
If at any time you are experiencing difficulty with the course material, the course organization or
format, please speak with your recitation TA or Dr. Minckley.

Lecture and Examination Schedule


Principles of Biology II (BIO 111)



Spring 2015

nd
The readings listed are for Principles of Life, 2 Edition, 2014. Hillis, D., et al. We do not recommend you purchase or use
any supplemental material provided by the publisher. Dates are estimates of when the material will be covered, and will
surely change. Check Blackboard and attend class for updates.

Lec Date

Topic

Readings Chp. Pgs.

Recitation
No recitations


W Jan 14

Week of 14 Jan
Course overview, What is science?


1:all

F Jan 16

Why study evolution?



3
4

5


M Jan 19
W Jan 21
F Jan 23

M Jan 26

Week of 9 Jan
No classes
Natural selection
Sexual selection
Week of 26 Jan
Kin selection & grandmothers

W Jan 28

Variation in populations: Locus and alleles


Sex/ Recombination

7

8
9
10

11

12

F Jan 30

M Feb 2
W Feb 4
F Feb 6

M Feb 9
W Feb 11
F Feb 13

Population genetics and adaptation


Week of 2 Feb
Species concepts and speciation
Molecular evolution
Homology & Phylogeny
Week of 9 Feb
Catch up day
Exam 1 (8:30 9:50 am)
Genome architecture


13
14


M Feb 16
W Feb 18

Week of 16 Feb
Biogeography & deep earth history
History of life

15

F Feb 20

Three Domains


16


M Feb 23

Week of 23 Feb
Microbial diversity

17

W Feb 25

Porifera to Deuterostomes

18

F Feb 27


19


M Mar 2
T Mar 3

The evolution of sex: Bugs rule:


Arthropods
Week of 2 Mar
Mollusca, Annelida, Echinodermata
Exam 2 (8:00 9:30 am)

1:10-11, 16: 338-339,


15:298-302
Bowler 2009


15:302-304, 310-312
15:306-307, Judson Chp. 1

Lahdenpera et al 2004,
Brembs 2001, 41:839-841
7:140-146, 8:158-170, 9:all,
10:195-197, 15:302-306, 318-
320
8:all, 15:302-323

17:all
10:204-206, 15:313-323
16:all



10: 197-204, 11: 222-224,
12:235-237

41:857-861, 18:all
1:2, 2:34-35, 4:80; Service
2013;
genetics.mgh.harvard.edu/sz
ostakweb/
4:63-68, 19:378-396
Fuhrman & Campbell 1998

8:167-169, 19:378-396,
20:401-406
14:274-278, 23:all
38:788-802
23:476-482, Judson Chp 13

23:all

Watson & Crick


1953; Suarez-
Rodriguez et al.
2013
Hawkes 2004,
McGraw 2002

Review

No recitations

Questions
Anderson &
Klofstad 2012

Review session
for exam

No recitations

20
21


23
24

W Mar 4
F Mar 6


M Mar 16
W Mar 18

25

26

F Mar 20

M Mar 23

The Chordates / vertebrates


No class
Week of 10 Mar is SPRING BREAK!
Week of 16 Mar
Vertebrate evolution & development
Primate evolution, including Homo
sapiens
The decomposers: fungi
Week of 23 Mar
Circulation-animals to plants

27
28

29
30

W Mar 25
F Mar 27

M Mar 30
W Apr 1

Plant adaptations to land


Physiology-terrestrial
Week of 30 Mar
Physiology-aquatic
Immune response-innate & humoral

31

32

33

34
35
36

F Apr 3

M Apr 6
W Apr 8
F Apr 10

M Apr 13
W Apr 15
F Apr 17

Sensory systems
Week of 6 Apr
Behavior
Exam 3 (8:30 9:50 am)
Behavior
Week of 13 Apr
Species interactions
Genomic interactions & evolution
Physical environment

23:all, 33:663-670



23:505-514, 38:802-806
23:514-517
22: all

24:521-532
25:545-551, 31:643-655,
32:661-669
7:130-132, 21:all, 28:597-599
29:605-618

36: 755-759
28:589-597, 39:809-815, 824-
825
34:all

40:all

40:all

43: all
12:237-248
41:845-858


Shehan &
Nachman 2014

Questions

Review

No recitations

Questions
Skelhorn et al
2010

en.wikipedia.org/wiki/Atmospheric_circ
ulation


37
38
39

40
41


M Apr 20
W Apr 22
F Apr 24

M Apr 27
W Apr 29
T May 5

Week of 20 Apr
Population growth & regulation
Communities
Ecosystems
Week of 27 Apr
Biodiversity
Conservation biology
Final Exam 12:30-3:30 pm


42:all
44:all
42:all, 44:906-909

41:861-863, 45:all
45:all

Roemer et al
2002

Review