Biology 220B
Biological Diversity of Plants
I believe a leaf of grass is no less than the journeywork of the stars,
And the pismire is equally perfect, and a grain of sand, and the egg of the wren,
And the tree-toad is a chef-d'oeuvre for the highest,
And the running blackberry would adorn the parlors of heaven,
And the narrowest hinge in my hand puts to scorn all machinery,
And the cow crunching with depress'd head surpasses any statue,
And a mouse is miracle enough to stagger sextillions of infidels.
-- Walt Whitman
Plant Diversity: BIO 220B
Fall 2012
Instructor
Dr. Clinton Whipple
Email:whipple@byu.edu
Phone: 2-9293 Office: 679 WIDB
Office hours: M and W 9-10AM
M W F 8:00 – 8:50 A.M.
231 MARB
Teaching Assistants/Lab Instructors
Zack Golden
McKenzie Macdonald
zgolden@mac.com
kenziekehrer@gmail.com
Required Text
Biology of Plants, Raven, P. H., Ray, F. E., and Eichhorn, S. E., 8th edition, W. H. Freeman and
Company, 2013
Course objectives
This course provides an introduction to plants and other organisms traditionally included in botanical
studies. It is my hope that you will develop a robust affection for this captivating group of organisms.
Plants are truly amazing, and while there are numerous practical reasons to study botany, at the end of
the day plants are more than adequate as an object of careful investigation, independent of any
pragmatic considerations. If you engage this course with curiosity and persistence, you will find that
knowledge of plants is its own reward. The quote on the cover of this syllabus is from Leaves of
Grass, where the poet invites us to loaf with him on the grass a while and observe the world around
us. When we look carefully, even the quotidian species that Whitman mentions reveal universes of
wonder. In this class we will explore worlds of diversity and biological processes that you most
likely have never encountered. We will march through the information at a brisk pace -- so fast, that
it may seem bewildering or tedious. Scientists give names, organize and classify (and we will spend
most of our time doing this) but I encourage you to slow down and loaf with Whitman on occasion.
Indulge yourselves in the manifold beauty of plant diversity, and in the creative ramifications of the
evolutionary process. It is OK to stand back in awe every once in a while and simply consider the
miracle that is life. These normative objectives will have no bearing on your grade, but will have a
bearing on how you much fun you have. They can provide a foundation for lifelong learning about
plants that will, if you give it space to grow, cultivate your soul regardless of your final career,
vocation, or life’s work. Of course there are more tangible learning objectives that will have an affect
on your grade, and these fall under two principle objectives:
1. Gain a broad familiarity with the diversity of plants, algae and fungi -- including morphology, life
cycles, and phylogenetic relationships.
2. Understand, and develop the skills to critically apply evolutionary logic (tree-thinking) to
formulate and test hypotheses that explain biological diversity.
These are intended not as isolated but iterative objectives. Gaining the basic facts and knowledge in
Objective 1 provides the raw material for practicing the critical thinking skills in Objective 2. As you
gain more skill and confidence in tree-thinking you will create the mental paradigm necessary to
order and make sense of the facts, and develop questions (or hypotheses) that require gathering more
facts to answer. Thus it goes round. If you find yourself successfully making this circuit, you will
know you are on the right track.
Practical advice for doing well in this course
•
You will have questions. This is good, ask questions, but do not expect others to do your
thinking for you. As you struggle and work to master the material, you will own it confidently
and your grades will follow.
•
Pay careful attention to lectures. Material and concepts that are not covered in the text will be
introduced, and these will be critical for understanding later material. Students who have a
mastery of all the material in class will be prepared for all the exams.
•
Read the text before the lecture. The lectures are designed to help you put into context the
material you are reading. You will not gain the full benefit of the lectures if you haven’t read,
as lectures will assume a basic familiarity with the text. Lectures will cover some, but not
necessarily all the material in the assigned reading. Consequently, you are responsible for all
the assigned text, not just that covered in class. In general, the reading assignments are short,
so focus your time on really understanding the text. Be sure to look at the quiz preparation
schedule to know which of the “Checkpoints” questions from that day’s reading will be
considered for the next quiz.
•
Participate in class. I enjoy discussion, so when I ask questions I really want to hear what you
think. The feedback helps me evaluate where you are in your understanding and adjust the
material and my approach accordingly.
•
Spread out your study for the exams. Like many biology courses, this one includes a lot of
memorization. You will learn a whole new botanical vocabulary requiring many hours of
study. You will have more success retaining information with daily reading and frequent
reviewing of the material, rather than a last minute, marathon cram session for the exam.
Grading
There will be a total of 700 pts
3 exams x 100 = 300 pts, 10 quizzes x 10 (- lowest score) = 90 pts, Lab = 110 pts, Final = 200 pts
Final letter grades will be calculated as follows:
95-100% = A, 90-95.9% = A-, 87-89.9% = B+, 83-86.9% = B, 80-82.9% = B-, 77-79.9% = C+, 7376.9% = C, 70-72.9% = C-, <70% = D, <60% = E
Quiz policy and scheduling
The quizzes are intended to help you keep current with the reading, and there will be a quiz every
week that there is no exam. As you will see, these are not meant to be difficult. Rather, you will have
ample opportunity to prepare, and if you keep current they should provide an easy 90 points (15% of
your final grade). If you have to miss a day for any reason, plan ahead -- you can drop one quiz, but
there will be no make-ups. The first page of each chapter contains “Checkpoints” questions in order
to focus your attention on key concepts that you should understand, while the chapter ends with
“Questions” intended to assess your comprehension. Listed below are the possible questions from the
Checkpoints or Questions of each day’s reading that could be included in the next quiz. You should
be prepared to answer any of the questions that are listed from the period between the previous quiz
and the current day’s reading. In general, one or two questions will be on the quiz, and answers
should address all the major points from the reading. Be complete, yet concise, i.e. include only the
information relevant to question.
Quiz Preparation Schedule
Week
Monday
Wednesday
1
Aug 27
pg. 2: # 1,2,3
Aug 29
2
Sep 3
Holiday
Sep 5
Tree-thinking handouts
Sep 7
pg. 317: #1 Quiz 1
3
Sep 10
pg 317: #2
Sep 12
pg. 255: #6
Sep 14
pg. 365: #9 Quiz 2
4
Sep 17
pg. 317: #5
Sep 19
pg. 365: #12
Sep 21
pg. 365: #13 Quiz 3
5
Sep 24
(EXAM I)
Sep 26
pg. 366: #1,3
Sep 28
pg. 366: #4
6
Oct 1
pg. 390: #4
Oct 3
pg. 38:#5, 538:#5, 556:#6
Oct 5
pg. 391: #1,2 pg. 429: #1 Quiz 4
7
Oct 8
Oct 10
pg. 391 #5
Oct 12
pg. 391: #6 Quiz 5
8
Oct 15
pg. 430: #1,2
Oct 17 (EXAM II)
Oct 19
pg. 456: #2
9
Oct 22
pg. 430: #3
Oct 24
pg. 456: #3
Oct 26
pg. 456: #5 Quiz 6
10
Oct 29
pg. 457: #1 pg. 477: #2
Oct 31
pg. 500: #6
Nov 2
pg. 538: #4 Quiz 7
11
Nov 5
pg. 579: #1,2
Nov 7 pg. 613: #8
Nov 9
12
Nov 12 pg. 558: #3,5
Nov 14 (EXAM III)
Nov 16
13
Nov 19 pg. 316: #5
Nov 20 pg. 278: #3 Quiz 9
Thanksgiving Holiday
14
Nov 26 pg. 316: #6
Nov 28
Nov 30
pg. 429: #2
pg. 209: #4,5
Friday
pg. 316: #3
Aug 31
pg. 219: #2,3
pg. 614: # 2,4,5 Quiz 8
pg. 278: #1,2
pg. 278: #4 Quiz 10
University policies
Academic Honesty
The first injunction of the BYU Honor Code is the call to be honest. Students come to the university
not only to improve their minds, gain knowledge, and develop skills that will assist them in their life’s
work, but also to build character. President David O. McKay taught that “character is the highest aim
of education” (The Aims of a BYU Education, p. 6). It is the purpose of the BYU Academic Honesty
Policy to assist in fulfilling that aim. BYU students should seek to be totally honest in their dealings
with others. They should complete their own work and be evaluated based upon that work. They
should avoid academic dishonesty and misconduct in all its forms, including but not limited to
plagiarism, fabrication or falsification, cheating, and other academic misconduct.
Honor Code
In keeping with the principles of the BYU Honor Code, students are expected to be honest in all of
their academic work. Academic honesty means, most fundamentally, that any work you present as
your own must in fact be your own work and not that of another. Violations of this principle may
result in a failing grade in the course and additional disciplinary action by the university. Students are
also expected to adhere to the Dress and Grooming Standards. Adherence demonstrates respect for
yourself and others and ensures an effective learning and working environment. It is the university’s
expectation, and my own expectation in class, that each student will abide by all Honor Code
standards. Please call the Honor Code Office at 422-2847 if you have questions about those standards.
Preventing Sexual Harassment
Title IX of the Education Amendments of 1972 prohibits sex discrimination against any participant in
an educational program or activity that receives federal funds. The act is intended to eliminate sex
discrimination in education. Title IX covers discrimination in programs, admissions, activities, and
student-to-student sexual harassment. BYU’s policy against sexual harassment extends not only to
employees of the university, but to students as well. If you encounter unlawful sexual harassment or
gender-based discrimination, please talk to your professor; contact the Equal Employment Office at
422-5895 or 367-5689 (24-hours); or contact the Honor Code Office at 422-2847.
Students with Disabilities
Brigham Young University is committed to providing a working and learning atmosphere that
reasonably accommodates qualified persons with disabilities. If you have any disability which may
impair your ability to complete this course successfully, please contact the Services for Students with
Disabilities Office (422-2767). Reasonable academic accommodations are reviewed for all students
who have qualified, documented disabilities. Services are coordinated with the student and instructor
by the SSD Office. If you need assistance or if you feel you have been unlawfully discriminated
against on the basis of disability, you may seek resolution through established grievance policy and
procedures by contacting the Equal Employment Office at 422-5895, D-285 ASB.
Bio 220B Plant Diversity
Date
•
Lecture/Lab Schedule
Lecture topic
•
Fall Semester 2012
Reading Assignment
Cyanobacteria and algae
Aug
M
27
W
29
F
31
Introduction; Scientific Method and Theory
Evolution, History of Life, Geologic eras
Systematics and Tree-thinking
LAB #1 Aug 30 th Microscopy/Tree thinking
Sep
M
3
5
F
7
No Class: Labor Day
Tree-Thinking
Cyanobacteria, productivity, and the carbon cycle
LAB #2 Sept. 6 Photosynthesis I
M
Euglenoids, Cryptophyta, Dinoflagellates, Haptophyta
Rhodophyta and complex life histories; alternation of generations
Heterokonts/Stramenopiles
W
10
12
F
14
W
(Quiz 1)
Ch. 1
Ch. 11
Pg. 234-245, Handout “The
Tree-Thinking Challenge
“The Tree-Thinking Challenge”
Pg. 263-267, 317-323, 140-141
Pg. 324-330
Pg. 340-344, 250-254
(Quiz 2)
Pg. 330-340
LAB #3 Sept. 13 Photosynthesis II
M
17
19
F
21
W
Chlorophyta
Chlorophyta
Charophyceae & the origin of land plants
(Quiz 3)
Pg. 345-353
Pg. 345-353
Pg. 353- 358
LAB #4 Sept. 20 Chlamydomonas and Algal Diversity
Charophyceae, bryophytes, & early vascular plants
M
24
W
26
F
28
EXAM 1 (100 points)
Bryophytes and the invasion of land
Bryophytes: Liverworts
Pg. 366-373
Pg. 373-377
LAB #5 Sept. 27 C-fern I
Oct
M
1
3
F
5
W
Bryophytes: hornworts and mosses
Vascular systems: life on land
Early land plants
(Quiz 4)
Pg. 378-389
Pg. 56-62, 544-553
Pg. 391-403
LAB #6 Oct. 4 C-Fern II and Plant Anatomy
M
8
10
F
12
W
Lycopodiophyta, heterospory, advantages and consequences
Monilophyta
Monilophyta
(Quiz 5)
Pg. 403-409, 397-398
Pg. 409-429
Pg. 409-429
LAB #7 Oct. 11 Fern and Bryophyte diversity
Seed plants: gymnosperms & angiosperms
M
15
W
17
F
19
Seed evolution, progymnosperms and introduction to gymnosperms
EXAM 2 (100 points) Sept. 26 – Oct. 12
Cycadophyta, Ginkgophyta
LAB #8 Oct. 18 Medicago-Rhizobium Symbiosis I
Pg. 430-437
Pg. 448-453
M
22
24
F
26
W
Coniferophyta
Coniferophyta
Gnetophyta, introduction to angiosperms
Pg. 437-448
Pg. 437-448
Pg. 453-456, 477-481
(Quiz 6)
LAB #9 Oct. 25 Angiosperms: Flowers, Fruits, Seeds, Cells & Tissues
M
29
31
F
2
W
Nov
Angiosperm flowers
Angiosperm fruits and seeds
Plant cells and tissues
Pg. 460-465, 482-492, 605-608
Pg. 465-476, 492-496, 426-532
Ch. 23, (review Ch.3 as needed)
(Quiz 7)
LAB #10 Nov. 1 Leaf Development and Evolution
M
5
7
F
9
W
Shoot development
Leaf development
Secondary growth
Pg. 579-592
Pg. 592-604
Ch. 26
(Quiz 8)
LAB #11 Nov. 8 Medicago-Rhizobium Symbiosis II
M
12
Roots
Ch. 24
Fungi and fungal-like protists
Nov
W
F
14
16
EXAM 3 (100 points) Oct. 19 – Nov. 13
Introduction to Fungi
LAB #12 Nov. 15
Pg. 278-286
Fungi I
Fungi part I
M
19
Microsporidia, Zygomycota and Chytridiomycota
20
Ascomycota
W
21,F23 No Class: Thanksgiving
Tu
Pg. 286-291
Pg. 291-295
(Quiz 9)
NO LABS THIS W EEK – HAPPY THANKSGIVING!
M
26
28
F
30
W
Basidiomycota
Basidiomycetes continued: feast and famine
Yeasts and Lichens
LAB #13 Nov. 29
Dec
M
3
5
W
Th
15
(Quiz 10)
Pg. 295-306
Pg. 295-306
Pg. 306-312
Fungi II
Mycorrhizae
Review
FINAL EXAM, Tuesday Dec. 11th from 7 – 10 a.m.
Pg. 312-316
NO EXCEPTIONS
Bio 220B Lab Syllabus
Location: 480 WIDB
Instructor: Dr. Clinton Whipple 679 WIDB
Materials
We will not use a specific text or published lab manual, rather each lab will be provided at least one
week prior to the beginning of that lab activity. You will be required to bring a lab notebook. Any
bound notebook (i.e. not loose-leaf or spiral bound) will be sufficient, no need to purchase an
expensive version from the bookstore. All other necessary materials will be provided in lab.
Sections
001 Thursday 10AM – 1PM
003 Thursday 1PM – 4PM
Section TA: McKenzie Macdonald
Section TA: Zack Golden
Overview
The purpose of a lab for Plant Diversity, is for you to 1. experience plant diversity first hand and 2.
learn the hypothetico-deductive approach to scientific discovery. The lab topics largely follow the
lectures and are of two basic kinds. In hypothesis driven labs you will perform experiments that test
explicit hypotheses. Some of these labs will be carried out over multiple weeks and may require you
to come in to lab outside of the scheduled time to make observations. In diversity focused labs you
will explore algal, plant and fungal diversity by observing live and prepared specimens. The diversity
labs generally occur before an exam and should allow you to review, synthesize and apply what has
been covered in class.
Lab Groups
Each lab section will be divided into groups of 3 to 4 students. You will work closely with your lab
group to complete each of the activities, then discuss with them the results and their meaning. In order
to make lab time more efficient, it is OK to divide subtasks from the lab activities to different lab
members. However, each lab member must understand what is going on in all parts of the lab, and be
able to discuss the results. Thus while the labs will be performed as groups and the data can and
should be shared, lab reports will be submitted individually and must represent your own work and
synthesis of the data. Your TA will quickly recognize duplicated lab reports.
Quizzes
The reading material and lab activity will be distributed at least one week prior to each lab. You are
required to read this carefully in preparation for the day’s activities. You should be familiar with the
background information as well as the procedures. In order to incentivize preparation for lab, each day
will begin with a quiz. The quizzes are intended only to ensure that you have prepared, not to be a
source of stress. If you have read and thought about the lab you should have no problems. The first
quiz will be for practice, all the following quizzes will be scored and contribute 20% to your overall
lab score. Quizzes will begin promptly at the beginning of lab, so come on time.
Participation
The learning that will happen in lab is a direct function of your engagement and participation. Since
you are required to attend the labs, try to make that time as productive as possible. This means
completing all the activities with an understanding of both what you are doing and why you are doing
it. If you don’t know what you are doing or why ask others from your lab group, the TA or instructor.
Since participation is critical, it will form a part of your grade. These should be easy points if you
make an effort. However, those with unapproved absences or those who chose to spend lab time
socializing will not receive the full participation points.
Lab Notebook
You are required to record all of your lab activities and observations in a lab notebook. Making
careful observations and detailed records of experimental results is critical in science. Your lab
notebook should be detailed enough that you could repeat everything you did that day. It should
contain careful observations as you performed your experiments. If something goes wrong, that should
be noted. All data that is collected should be entered into the notebook. If you analyze that data later
using spreadsheet software for example, the results of that analysis and how the analysis was
performed should also be entered into the notebook. The lab activity for that day will indicate things
that you should include in your lab notebook, but you should include many more observations than
that.
Often you will need to draw what you are seeing. Not everyone is an artist, and this is not an art class,
so no need to make accurate or beautiful representations. The purpose of drawing, is that it forces you
to look carefully at what you are observing. Often important details are missed with a brief glance.
Taking the time to draw the object can reveal such details. Again, they need not be works of art, but
the drawings should be good enough that you are able to interpret them. Lab notebooks will be turned
in for grading at the end of each unit.
Lab Reports
Some of the labs will also involve a formal lab report. This is not intended as transcription of your lab
notebook. Rather, this is your chance to think about what you did, why you did it, and what it means.
Formal written reports are an important part of the scientific process and provide an opportunity to put
diverse experiments in context and develop a narrative that explains the results. These reports need not
be long, 2-4 pages should be sufficient. However, they should be the product of careful thought and
revision. A first draft is not likely to receive full credit. Lab reports will be due at the beginning of
your lab section two weeks after completing the associated lab. The reports should follow the basic
format of a scientific research paper:
Introduction Provide the background necessary to set the stage for the experiments you will report.
Why is the topic of interest? What is known already? What experiments did you perform and why?
Briefly summarize your findings and conclusions.
Materials and Methods Describe the experimental setup and reagents used. Provide enough detail that
others could repeat the experiments.
Results In this section you discuss the experiments you performed and what you observed.
Discussion In this section you will interpret your results. Do they confirm your expectations? If not,
why not? What other hypotheses could be consistent with the data? What follow-up experiments
would be most productive?
References Cited In the body of your report, you will likely make claims that depend on results of
previous studies. If you do, you should cite an original paper that you use as the basis of the statement.
All references should be properly cited using the format as detailed below.
In the text:
Pinnate and palmate compound leaves develop by the activity of genes that regulate adaxial and
abaxial cell identities such as PHANTASTICA (Kim et al., 2003).
Note that the sentence makes a claim about how compound leaves develop, followed by a citation
(Kim et al., 2003) that supports that claim.
In the references cited:
Kim, M., McCormick, S., Timmermans, M., and Sinha, N. (2003). The Expression domain of
PHANTASTCA determines leaflet placement in compound leaves. Nature 424:438-443.
The citation takes this basic format:
Author1 last name, Initial., Author2 last name, Initial., Author 3… (Year of publication). Title of
article. Journal Title. Volume : start page - end page.
Grading
The lab portion of Plant Diversity will contribute 110 points (approximately 25%) to your overall
220B class grade. These points will be distributed accordingly:
Quizzes:
Participation:
Lab Reports:
Lab Notebook:
15%
20%
50%
15%
Lab Topics and Tentative Schedule
The topics and schedule presented here are tentative and subject to revision as the semester proceeds.
Labs that will involve a lab report are indicated.
UNIT ONE
Lab #1 Experience the Microscope/Tree thinking
Lab #2 Photosynthesis (Parts I and II) Lab report
Lab #3 Chlamydomonas mating
Lab #4 Algal diversity
UNIT TWO
Lab #5 C-Fern/Alternation of generations/Sex determination (Parts I and II) Lab report
Lab #6 Bryophyte and Fern Diversity
UNIT THREE
Lab #7 Medicago/Rhizobium symbiosis (Parts I and II) Lab report
Lab #8 Compound leaf development and evolution
Lab #9 Angiosperm diversity: Flowers, Fruits and Leaves
UNIT FOUR
Lab #11 Fungi (Part I and II)