Concepts and Methods of Biology

Biology 104........ Spring 2009........ Dr. G.R. Davis

Office 203E Milliken, Biology Suite
Campus phone 597- 4621 Home 948-9025

Class Meetings TTh 9:30-10:20 am MSH 212 or 206, Lab W 2-5 MSH 212 or 206
Reference book: Life: The Science of Biology 8th Edition 2007
by Sadava, Heller, Orians, Purves, & Hillis

last updated 18 May 2009 at 10:35 am





Final Versions of 6 Posters based on Arabidopsis Research

Posters were displayed on May 8th at the
Wofford Research Symposium in the Olin Building



We will investigate these topics:

Evolution and natural selection
Homeostatis and Energy
Cell metabolism (respiraton and photosynthesis)
The balance of nature (ecology)
How science gets done and by whom
Relevance of Biology to everyday life

As we answer these questions, students will develop skills in

Finding reliable information
Evaluating the credibility of a source
Deciding who and what can be trusted
Designing, conducting, analyzing, interpreting an experiment and communicating the results

During the process, students will

Learn how the peer-review process works.
Learn how research gets funded.
Become conversant in our current understanding of the mechanisms that govern how cells, organisms, and and groups of organisms.
Be able to describe the usefulness and limitations of experimental models.

In the laboratory, students will design and conduct an experiments using
models and several plants and animals.

Gain experience working with laboratory plants and animals.
Grasp the complexities and limitations of laboratory experimentation.
See how our results fit with what is already known and what we have produced that is new!



Class Meeting Topics

Lab Topics

T Feb 3

Who needs Biology and Biologists? The special nature of this course! Deciding what matters to us in this prototype course.

Assignment # 1 Read two papers (links below) and prepare for discussion during lab.

W Feb 4 lab

1st lab Part 1: Comparing Scientific Literature (2-4 pm)

Paper by Kipp on Arabidopsis

Paper by Tuberville et al. on herpetofauna (follow the link on the top of the page.)
Teamwork activities for Evaluating Scientific Papers

1st Lab Part 2 (4-5 pm): Identification of Eight Live Amphibians and Reptiles from South Carolina using Field Guides with Dr. Ab Abercrombie

Th Feb 5

Loose ends from yesterday's lab:
a) The link between herp identification with field guides and the papers we read.
b) The relevance of the Arabidopisis paper to this course: students will design experiments to test hypothesis using this little plant.
c) Teams edit instructions from yesterday's lab.
b) Two Options for Titling a Paper: What They Did ..or.. What They Found. (group practice converting from one category to the other.)
c) Class photos

How Biology Gets Done:
Part 1-- Getting the Money to Do Science: Sources of Funding, The Format of a Grant Proposal, and Review of Grants by "Study Sections."
.............Questions students should be able to answer on "Getting the Money!"
Part 2-- Getting the Training to be a Biologist: Educational sequence and a personal example.

Assignment # 2: Scan this Grant Proposal. Does this proposal have all the components that we expect?

Supplemental information: The timeline for a grant application to the National Institutes of Health and the various types of grants available from NIH.

T Feb 10

Follow-up from Thursday: The comparitive career paths of lawyers, doctors, and scientists (degrees, major accomplishments: bar exam, medical boards, dissertation defense. Various careers in biology with emphasis on academic careers.

How Biology Gets Done:

Part 3-- Getting the Work Done: The Organization of a Research Lab (members of the lab and their roles.)
Part 4-- Getting Published!: The Peer Review Process for Scientific Literature (compared to getting a newpaper or magazine article published.)
..............Choosing a journal, steps in the process, timecourse, roles of editor, peer reviewers, importance of anonymity, potential outcomes, and risk of scooping!
..............Science Direct: an on-line database for searching the scientific literature

Assignment # 3 (due Thursday morning by email): Using your notes and any supplemental information, create a Powerpoint to be shared with the class via our website for each of the following topics. The powerpoint should be a complete concise summary that will serve as a study guide for members of the class.Opening slide must be the topic and the names of contributors. First authors must earn the honor of first authorship. At the end of each powerpoint, include a list of potential test questions. Some questions may be "memorization" type but please include questions that will reveal the level of understanding possessed by a test-taker. Email the finished powerpoint to Dr. Davis at

Table 1) Looking at Research Papers: The Format of Scientific Literature
Table 2) Getting the Money to Do Science: Grants
Table 3) Getting the Training to be a Biologist
Table 4) Getting the Work Done: The Organization of a Research Lab (James' version)
Table 5) Getting Published!: The Peer Review Process

Getting familiar with Arabidopsis Ecotypes.

Looking into ecotypes for Tuesday Lab: With your teammates, be ready to report for your ecotype information on where it originated, the condition under which grows naturally (photoperiod, moisture, soil, etc.) and any additional relevant information. Start with The Arabidopis Information Resource website.

Assignment # 4: due Wednesday at start of lab: Groups 1-6 report on the characteristics of your Arabidopsis ecotype:
Ecotype 1 = Zloc-1; Bulgaria; Ecotype 2 = Bur-0; Burren Ireland; Ecotype 3 = Can-0; Canary Islands, Spain;
Ecotype 4 = Nzl; Hamilton, New Zealand; Ecotype 5 = Sapporo-0, Sapporo, Japan; Ecotype 6 = Tanz-1; Ketumbeine Forest Reserve, Tanzania

Just for fun: Giant Ant colony

W Feb 11 lab

Working with Arabidopsis

Timelapse videos of Arabidopsis growth:
Video 1
view from above, 38 seconds
Video 2
lateral view, 1:38

20-30 Minutes to work with teammates on Assignment #4 , making posters for Arabidopsis Ecotypes

Six groups report on Six Ecotypes.

Review procedures for growing Arabidopsis from seeds. Arabidopis: A laboratory Manual, by Detlef Weigel and Jane Glazebrook pages 1-18

Pouring Agar and Planting Seeds.

Classifying Organisms: Using and Creating Binomial Keys

We'll get some hands-on practice using and creating binomial keys and develop a special appreciation for keys that reveal phylogenetic relationships.

Here's the Lab Exercise on Binomial Keys from Dr. Abercrombie


Th Feb 12

These Questions about Arabidopsis (MS Word doc. or webpage) will guide our investigations over the next several sessions.

~1 hour: Using internet resources, biology textbooks, and Arabidopsis lab manual, teams of 4-5 students try to find the answers, keeping track of references so that information can be traced back to sources.

Group 1- Terminology I: The Parts of a Plant and Revised Terminology I: The Parts of a Plant

Group 2 - Germination and Revised Germination Powerpoint

Group 3 - Terminology II: Ecotypes and Species and Revised Terminology II: Ecotypes and Species

Group 4 - Distribution and Revised Distribution (Caution: The authors of this file did not revise it to include all of the information presented during class on their topic. Therefore, this file will not suffice as the only study guide for this topic. Authors will be provided one final opportunity to revise their file before Tuesday, February 24th.) 3rd version of Distribution

Group 5 - Arabidopsis as a Model Organism and Revised Model Organism

Last 20 minutes of classperiod: Table 1 provides answers to their questions and we begin to build a vocabulary.

Assignment # 5: Each group is to create a powerpoint file containing the answers to the questions and the sources from which answers were obtained. In most cases, devote on slide to each question. Be sure to defined any unfamiliar terms. Email the file to Dr. Davis no later than 5 pm Friday, February 13.

T Feb 17

Continue with Answers to Arabidopsis Questions, reviewing powerpoints from Groups 1-3 and supplementing with notes on whiteboard.

Assignment # 6: Groups 1-3 (Parts of a Plant, Germination,and Ecotypes and Species) are to submit revised powerpoints
via email to Dr. Davis by Thursday at 9:00 am.

How a Pine Grows; excerpted from Pines Above the Snow essay in A Sand County Almanac by Aldo Leopold.

W Feb 18

Measuring Root Length of Arabidopsis Seedlings

Measuring root length with calipers under dissecting microscopes on seedlings 1-7 days in the agar plates.
Sources of measurement error, variability, and the difficulties of consistent data collection.

A lesson on p values and an introduction to hypothesis testing by Dr. Abercrombie.


Th Feb 19

Preparing to test a hypothesis using Arabidopsis. The variables we can manipulate, the characteristics that we can measure, and the questions we can ask.

Continue with Answers to Arabidopsis Questions, reviewing powerpoints from Groups 4 (Distribution) and 5 (Model Organism)

Assignment # 7: Groups 4-5 (Distribution and Model Organism) are to submit revised powerpoints
via email to Dr. Davis by Monday, Feb 23 at 9:00 am.

Class notes

Teams for Grant Proposals using Arabidopsis

Team 1 = Matt Steelman, Joshua Fester, Tinus Van Wyk, & Nicole Sower
Team 2 = Kevin O'Quinn, Mesha Arant, TJ White, Jordan Ball
Team 3 = Morgan Hiler, Carrie Martin, Hannah Liermore
Team 4 = Allison Poole, Hunter Soltis, Victor Makali, plus Lucy Monigle
Team 5 = Aaron Seigler, Matt Boggs, James Skinner
Team 6 = Leah Odum, Gordon Gulledge, & Becky Gardner plus Becka Dunbar

Assignment # 8: Each of the six teams is to prepare a unique Grant Proposal (instructions) that outlines the hypothesis your team intends to test. This Grant Proposal must be submitted as an email attachment to Dr. Davis before 7:00 pm Monday, February 23rd.

T Feb 24

Peer Review "Grant Proposals" for Arabidopsis Experiments

Each of the six Research Team anonymously peer reviews the 5 grant proposals of their classmates, using the Grant Proposal Evaluation Checklist and adding notes and constructive comments to each grant. By reviewing other grants and receiving feedback on their own grant proposals, research teams can make drastic improvements in their own revised grant proposal which will be discussed during Wednesday lab.

Assignment # 9: Each of the six teams is to revise their grant proposal based on feedback from anonymous peer reviewers and send the revised proposal to Dr. Davis as an MS Word.document ASAP but no later than 1:00 on Wednesday.


W Feb 25

Anonymous survey on student perceptions of a) the 104 course so far, and b) the grant writing and reviewing process.

A lesson on strategies for hypothesis testing by Dr. Abercrombie. (~1hr.)

Demonstration of ImageJ software for measuring Arabidopsis root length by Thomas Player (~20 minutes)

Remainder of lab period:Davis & Abercrombie consultation with each of the 6 research teams on their Revised Grant Proposals

Th Feb 26

Test # 1. Expect questions based on the factual information covered thus far in the course as well as procedural skills that we've been developing (such as critical reading of research papers and grant proposals, evaluating the credibility of information, etc.

Study Guide for Test 1.

Assignment # 10: Send final revision of Grant Proposal via email attachment to Dr. Davis by Monday at 5:00 pm.

Six Arabidopsis Grant Proposals by Student Research Teams

T Mar 3

Return Test # 1. Students can review their tests in Dr. Davis's office and ask for individualized advice on how to improve for Test #2

Lecture Topics from Chapter 23 Species and Their Formation and Chapter 1 Studying Life

Forms of Reproductive Isolation
Examples of Behavioral Isolation: Bird of Paradise Mating Display (YouTube # 1) Blue Footed Boobie Mating Display (YouTube #2)
Sympatric Speciation in Progress: Ragholetis pomonella flies in New York State (Sadava p. 513)
Speciation on the Galapagos Islands: Marine iguanas of Galapagos Islands (Blowing Salt video)

W Mar 4

Begin Six Arabidopis Experiments: Updated Grant Proposals

Each of the 6 Research Teams sets up their experiment.

Design data collection sheets and to bring to lab for approval by professors.

Template for Scientific Poster (a single "slide" in Powerpoint format.)

Fluorescent Light: All photoperiods are 16 hr light/ 8 hr dark

LED Light


Drought Test
3 Ecotypes
2 big trays of soil

Measure stem length 1x per week for 2 wk.

Hunter, Victor, Allision,Lucy

Wk1 Data


Planting Depth Test
6 plates horizontal

Measure shoot and root length at
end of 2 wk.
Monitor germination.

Morgan, Carrie, Hannah

Wk 1 Plate Scan

Wk 1 Data


Agar vs Soil Test
6 cups agar,
6 cups soil

Measure shoot length and germination daily for 2 wk

Leah, Gordon,
Becky, Becka

Wk 1 Data


Oil Pollution Test
8 plates vertical

Measure shoot and root length 1x per week
for 2wk

Matt, Tinus,
Joshua, Nicole

Wk 1 Part 1 Scan
Wk 1 Part 2 Scan

Wk 1 Data


Agar Concentration Test
6 plates vertical

Measure root length 1x per week for 2 wk.

Aaron, Matt, James

Wk 1 Plates Scan

Wk 1 Data



Light Type Test
3 plates vertical

Measure root length 1x per week for 2 wk.

Kevin, Mesha,
Jordan, TJ

Wk 1 Plates Scan
LED left side, FLO right side

Wk 1 Data



Light Type Test
3 plates vertical

Measure root length 1x per week for 2 wk.

Kevin, Mesha,
Jordan, TJ


Th Mar 5

Lecture Topic: Chapter 23 Speciation, Adaptive Radiation and Lessons from the Galapagos Islands

Homer Simpson Evolution Video What's incorrect about this depiction of evolution?

T Mar 10

Lecture Topics: Chapter 1 (portions), Chapter 2, and mostly Chapter 3 Macromolecules

W Mar 11

Data collection for Week 1 of Arabidopsis Experiments
Measuring germination and growth
Germination rates for Week 1

Practice using ImageJ by measure the dimensions of this scan of a calculator or classring

Test image file

Agar concentration image 10 March 2009

Th Mar 12

Chapter 3 Molecules of Life

T Mar 17

Guest Lecturer: Dr. Moeller: Origins of Life, Part 1, Sadava Chapter 26

W Mar 18

Data collection for Week 2 of Arabidopis Experiments
Making Graphs of Results

Th Mar 19

Guest Lecturer: Dr. Moeller: Origins of Life, Part 2, Sadava Chapter 27

T Mar 24

No class meeting today

W Mar 25

Data Analysis and preparation of scientific communication

Th Mar 26

Guest Lecturer: Dr. Moeller: Evolution of Body Plans, Sadava Chapter 31

Spring Break


T Apr 7

Five minute progress report in Powerpoint format (links below) on Arabidopis experiments from each research team:
Instructions for informal progress report

Team presenters: 1 = Victor, 2 = Carrie, 3 = Becky, 4 = Tinus, 5 = Matt, 6 = Jordan.

Drought Test

Oil Pollution

Deep vs Surface Seeds

Effect of Agar Concentration

LED vs Fluorescent Light

Soil vs Agar

Assignment # 11: Each student should generate twenty questions with answers based on the lectures by Dr. Moeller and his
powerpoint presentation. These questions and answers are due at the beginning of the class period and should be in the form of a printout with the authors name and honor pledge on the back side of the last page (so that each students work can be graded anonymously.) Students must work individually on their questions and each will receive a grade based on the quality of the questions and the answers provided. Questions and answers that earn higher grades will be those that demonstrate more than simple recall of information or facts. Student should avoid questions that have simple "yes-no" or "true-false" answers. Questions and answers that reveal a grasp of concepts and relationships will earn higher grades. Grammar and spelling counts so be sure to write carefully and use complete sentences with proper punctuation.

W Apr 8

Non-invasive indices of metabolism: Human electrocardiograms and surface temperature. Our website for EKG lab.

Making scientific posters for Arabidopsis research (Rubric for evaluating research posters.)

Introduction to a crocodile and a turtle.

Th Apr 9

Thermoregulation and Heat Exchange, Components of Reflexes and Negative Feedback Loops Lecture Powerpoint

T Apr 14

Thermoregulation and Negative Feedback Loops Lecture Powerpoint

W Apr 15

Heat Exchange and Thermoregulation: 1) Conduction and Radiation in clay models and 2) Correlations of ECGs and body temperature in reptiles

Reference paper: R.M. Holtz and P. Holtz (1995) Electrocardiography in anesthetized red eared sliders (Pseudomys scripta elegans) Research in Veterinary Science 58(1):67-69

Th Apr 16

Thermoregulation part 3

T Apr 21

Test # 2 Study Questions for Test # 2

W Apr 22

Create, peer review, and final print Arabidopsis Research Posters (What to do before lab)

Revised Graphs for Arabidopsis Posters Each research team should copy their revised graph into their research poster.

Rubric for evaluating research posters Use this as a checklist for your poster.

Steps for Editing and Printing Posters

SPSS data files for each research team:

Oil Concentration, LED vs FL light, Surface vs Deep, Soil vs Agar, Ecotypes and Watering Conditions, Agar Concentration

Second Drafts of Research Posters (Powerpoint file with all 6 posters!)

Th Apr 23

Thinking about Turtles and Evolution, Part 1: How the Turtle Got its Shell by Dr. Ab Abercrombie (read part 1 of this essay for class)

T Apr 28

Thinking about Turtles and Evolution, Part 1 continued: Genetic control, Transcription, Translation, and Gene Switches Powerpoint Lecture

W Apr 29

Organisms in natural habitats: Thermal regimes and macroinvertebrates at the Glendale Environmental Center

Driving Directions to Glendale Environmental Center

Background for Glendale Shoals

Identifying the Critters in the Water at the Glendale Shoals: A Brief Key with Drawings

Th Apr 30

Biogeochemical cycles and the role of organisms:
Cycling of carbon in nature.

Friday May 1 at 2 pm: Absolute final deadline for Final Version of Research Poster in powerpoint format.

Final revised versions of all 6 research posters in one powerpoint file

T May 5

Topic: Global Warming and The Tragedy of the Commons , an essay by Garret Hardin

Assignment: Watch An Inconvenient Truth. Al Gore's Documentary on YouTube.

Think about these questions as you view the movie:
How convincing is the evidence he produces?
What is the credibility of his sources?
Does he explain graphs clearly?
Does he interpret graphs appropriately?
What strategies and techniques does he use to appeal to his audience?
In what ways is Gore misleading or deceptive? (provide examples.)
Why does he include personal stories such as the injury of his son and the death of his older sister?
What was his motivation for producing this documentary?
What should he have done to be more effective in making his case?
Based on what you see and hear in this video, are you convinced that global warming is real? Is a problem? Is a serious problem? Is a serious problem that requires action?
How is global warming related to "the tragedy of the commons?"

Assignment # 12: We'll consider these questions and others during class. To encourage you to view the movie and think about it, at the beginning of class, I'll ask you to respond in writing to one of the above questions (so be prepared to have something to write about each of them).

Climate experts warn about short-term trends.

W May 6

Analysing aggressive territorial animal behaviors with crayfish in the laboratory with Dr. John Moeller

Background information to prepare for lab by Dr. John Moeller

Focus Group: Anonymous Oral Feedback for Course Improvement.

Th May 7

Lecture: The Biology of Viruses.

Topics covered: What is a virus? Why aren't antibiotics effective treatments for viral infections? What are some well-know viral diseases? Which of these might be considered the worst and why? How can one have a viral infection and yet have no symptoms? How does one get a viral infection? By what means are viruses spread from host to host? What accounts for the host specificity of viruses? How did the "swine flu" become a problem for humans (that is, how can viruses "jump" species?) Which parts of the human body are most susceptible to viral infections and why? Describe the way in which viruses can be manipulated for good purposes. How can one be protected from a viral infection? Once a person has become infected, how is the infection eliminated by the immune system? Why is Human Immunodeficiency Virus such a diffucult viral disease to battle?

All the above questions were discussed during class. Information about viruses can be found in Sadava Chapter 13 p 282-288 and selected passages in Chapter 18 related to Figure 18.15.

Friday, May 8 at 1:30-2:00 : Selected Posters printed in large format displayed in Olin Lobby as part of Wofford's Research Symposium

T May 12

Exam 9-noon

The questions from Test # 1

The questions from Test # 2

Exam covers all material from Test 1 and Test 2 plus the topics covered from test 2 to the end of the course:

Thinking about Turtles and Evolution: Part 1.
Photosynthesis and the formation of fossil fuels and the cycling of carbon and water
Global warming and the Tragedy of the Commons
Studying animal behavior with crayfish in the laboratory

The biology of Viruses

Expect the exam to consist of some multiple choice questions (especially covering the topics of Test # 2) and short answer questions. You may also be provided a research paper to evaluate using the skills we developed early in the course.



MEASURING PROGRESS TOWARD OBJECTIVE:  The quality and quantity of contributions to class discussions will be graded.

TECHNOLOGY SKLLS:  Students will develop skills in using electronic resources to locate reliable reference materials. Student will create powerpoint presentation to be shared with the class.

INSTRUCTIONAL FORMAT:  Primarily class discussions in journal club format supplemented with lectures as necessary.

ATTENDANCE POLICY:  Attendance at all class meetings is mandatory. Absences will excused only when proper documentation is provided (doctors note, etc.) Students will be given up to 2 personal absences from lecture; these require no explanation. Upon a third unexcused absence, students will be reported to the Dean. Students are responsible for all assignments, announcements and materials covered in class whether presented orally or in any assigned readings or handouts. No exceptions are made for non-attending students. Excuse for absence does not relieve a student from responsibility for materials from the class meeting missed. It is the student's responsibility to notify the instructor of the reason for their absence, preferably in advance, and provide written documentation. Absence from lab should be avoided if at all possible. Inform Dr. Davis PRIOR to lab if you must absent. Unexcused absences from lab will result in a deduction of 5 participation points from your grade. No lab make-ups will be allowed.

GRADING: 10 point scale:  A = 90-100, B = 80-89, etc.  60 = lowest passing grade. Grades of + and - are determined once all grades have been obtained.

Course grade components: 5% Homework, 15% Class Participation, 20% Research Poster, 60% Test 1, Test 2, and Exam (drop lowest).

I reserve the privilege to alter the content and/or requirements of this course should I find this plan unsuitable at a future date.

Statement for Academic Integrity:  Cheating occurs in many forms. Copying homework, lab work, sharing information regarding material on a quiz or exam, or signing another person's name to an attendance sheet are but a few. All acts of academic dishonesty will be addressed to the fullest extent allowed by the guidelines set forth by the College (See Student Handbook). Honor Code

Dr. Davis's home page

Other Links

Advice for preparing powerpoint presentations

Do's and Don'ts for Effective Presentations

Presentation Evaluation Form