Biology 304 - Evolution
Spring 2014
Instructor: Jim Dooley

Update: 4/21/2014

Office: 428 Boyd Science Center                                                          
E-Mail: jdooley                                                                                                                  
Phone: 826-8227
       
                                                                                      

Lecture: BSC 437, MWF  11:00 a.m.
Laboratory: BSC 437, Tues - 12:30 - 3:20.

____________________________________________________________________________

Course Description:

My goal with this course is to advance and deepen your appreciation for the intellectual framework that provides the underpinning for all of the life sciences.   You were exposed to the general principles of evolution in your introductory biology course (Biol 111).  In this course we will work to solidify your command of basic principles and advance your understanding of some of evolution's most important implications.

You will probably find that this course challenges you in ways that differ from other biology courses.   Along with factual material, you will also need to work through and learn some quantitative theory.  That's nothing new, but there is a challenging array of important conceptual information - some of it highly nuanced - that you will need to reflect on before you can come to a robust understanding of evolutionary theory and its implications.   Finally, I believe you'll find that the reading load may well be higher than what you may have encountered before.  

Understand that I see the reading (of the text, lecture notes that I provide, and other materials) to be the primary source of learning - listening to lectures should only reinforce what primarily occurs through your own, self-directed efforts at learning by reading and reflection.  In that context then, understand that I teach this course at a very high level.  


The bottom line: I see Biology 304 as a demanding educational experience that will require
a l
arge time commitment from all of us
.

 
Course Learning Objectives:  Course Leaning Objectives extend directly from the Biology Department's Learning Goals.   In particular, the learning objectives for this course emphasize Biology Department Learning Goals 1, 3 & 4.   As a result of demonstrated clear commitment to the course's learning vehicles - that is readings, lecture presentations, laboratory experiences, and videos students should anticipate signficant advancement in the knowledge-base & skill sets within the domain of Ecological Science.  More specifically students should demonstrate:


Course Resources:


Textbook: 
Evolution (3rd edition) by Douglas J. Futuyma (ISBN = 978-1-60535-115-5)

Companion Website: http://www.sinauer.com/evolution3e

Other Online Materials:

 
 

Course Policies:

Attendance: Laboratory attendance is mandatory - as a practical matter, please understand that your laboratory grade will be lowered for each absence.   Attendance to lectures is optional.  You're upper level students now so the choice of coming to lecture or not is yours.  I may be a bit biased, but my sense is that attending lectures aids in the learning process but hey, ... it's yours to call.
 

Grading:    The course will consist of both lecture and laboratory. Grades from the two parts will be combined with a participation mark in computing the final course grade. The final course grad will be determined based on the following breakdown: 70% lecture, 25% laboratory and 5% active participation.

Lecture and laboratory grades will be based on the following:

1) Lecture (70%):


2) Laboratory (25%):
3) Active Participation (5%):  I'm looking here for engagement in our learning process.  Showing up to lab is a very basic element, but vigorous & thoughtful participation in our discussions is another.  One new and very important way to amass participation points is to be a strong contributor to our Wednesday Discussion Posts.  You'll see a discussion post session for each Wednesday of the term.   The idea is for you to post your thoughts and questions about the material we are covering that week.  If you get your posts in by midnight on Wednesday, you'll get participation credit for that week.   In addition, if you identify issues or ideas that you are finding challenging, I'll do my best to address them in Friday's class.   Posts can come in the form of your own ideas or reacting to the ideas of others (but posts like "yeah, I agree" aren't going to earn you much credit). 

Important: Much of the material in the lecture notes is derived from the text, but I have also included some information from addition sources and updated textual information where appropriate.  Importantly, several years ago I made the decision to change from using Futuyma’s graduate level text to his new book designed for undergraduates.   Though this new book does a pretty good job on the whole, there are some key points of information (or in some cases, pieces of contextual information), that are left out and really valuable.  That material will now only be found in the lecture notes.  By the same token, there is material in the text that I do not include in the notes.  In some cases, the text material is so straightforward that I feel it would be redundant to repeat the same ideas in the lecture notes.  In some other cases, the ideas are more complex and ideally should be covered in the lecture notes, but I haven't had time to add them in.  

Therefore, expect that tests will have questions drawn broadly from the lecture, text reading, and other materials I've assigned - don't limit your preparation to material directly discussed in class!

Strategies for Success:
    1. Prior to class: read the chapter and take notes on the material.  Doing so will help you identify points or concepts that are unclear. 

    2. Take smart notes on class - focus on what I'm saying rather than copying everything you see on the PowerPoint slides - you'll have full access to that material.   Try to let yourself listen more so you can quickly identify points that are not clear.

    3. After class: review your notes and the posted PowerPoint slides.  Then spend some time reflecting on what makes sense and what doesn't.   Make written notes about what is not clear and bring those questions to class - then be sure to ask me about them.   Next - back to step 1.
In the end, you are going to teach yourself this material through reading and reflection!  

 In structuring the course in this fashion, I'm trying to prepare you for the fact that you are coming to the end of the stage in your life when you should associate learning with teaching.   Before long the learning you will need to do (and there will be plenty up the road) will have to be self-designed.   Mainly, you'll find that reading and reflection will be your tools.   In that spirit, I want to emphasize once again that you should see text and other material reading as critical components to your learning in this course.


Classroom Schedule


Week
Dates
Topic/Activity/Assignment

1
1/13


1/15

1/17

Course Introduction: Overview of Syllabus
Lecture
: Evolutionary Biology  Reading: Chapter 1


Lecture: Evolutionary Biology Reading: Chapter 1

Lecture:  Tree of Life: Classification and Phylogeny Reading: Chapter 2

2
1/20

1/22

1/24

MLK Day - No Class

Lecture:  Tree of Life: Classification and Phylogeny Reading: Chapter 2

Lecture:  Tree of Life: Classification and Phylogeny Reading: Chapter 2

3
1/27

1/29

1/31

Lecture:  Patterns of Evolution  Reading: Chapter 3

Lecture:  Patterns of Evolution  Reading: Chapter 3

Lecture:  Patterns of Evolution  Reading: Chapter 3


2/3

2/5

2/7

Lecture:  Evolution in the Fossil Record  Reading: Chapter 4

Lecture:  Evolution in the Fossil Record  Reading: Chapter 4

Lecture:  Evolution in the Fossil Record  Reading: Chapter 4

5
2/10

2/12

2/14

LectureHistory of Life on Earth  Reading: Chapter 5

LectureHistory of Life on Earth  Reading: Chapter 5

LectureHistory of Life on Earth  Reading: Chapter 5

6
2/17

2/19

2/21

Lost week due to disease, frozen pipes and severe cold (Next year move chap 6 here and add in 7)

Lost week due to disease, frozen pipes and severe cold

Lost week due to disease, frozen pipes and severe cold

7
2/24

2/26

2/28

LectureThe Geography of Evolution  Reading: Chapter 6

LectureThe Geography of Evolution  Reading: Chapter 6

LectureThe Geography of Evolution  Reading: Chapter 6

8
3/3

3/5

3/7
Lost week

9
3/10-14 Spring Break
10
3/17

3/19

3/21

Lecture: The Origin of Genetic Variation   Reading: Chapter 8

Lecture: The Origin of Genetic Variation   Reading: Chapter 8

Lecture: The Origin of Genetic Variation   Reading: Chapter 8

11
3/24

3/26

3/28

LectureVariation   Reading: Chapter 9

LectureVariation   Reading: Chapter 9

LectureVariation   Reading: Chapter 9

12
3/31

4/2

4/4

Lecture:  Genetic Drift: Evolution at Random Reading: Chapter 10

Lecture:  Genetic Drift: Evolution at Random Reading: Chapter 10

Lecture:  Genetic Drift: Evolution at Random Reading: Chapter 10

13
4/7

4/9

4/11

Lecture:   Natural Selection and Adaptation  Reading: Chapter 11

Lecture:   Natural Selection and Adaptation  Reading: Chapter 11

Lecture:   Natural Selection and Adaptation  Reading: Chapter 11

14
4/14

4/16

4/18

TBA

TBA (Next year add chapter 18 here)

No Class: Easter Break

15
4/21

4/23

4/25

TBA and The Evidence for Evolution Video

Lecture:  Evolutionary Science, Creationism and Society Reading Chapter 23 & TBA

Lecture:  Evolutionary Science, Creationism and Society Reading Chapter 23 & TBA

16
4/28

4/30
 
TBA: Perhaps Example Lecture: Some thoughts on how to present Evolution in a public arena  Discussion: TBA

Course Evaluations:

   5/?? Final Exam:    









 
 
 

 
Laboratory Schedule:
 
 

Week
Dates
Topic/Activity/Assignment
1 1/14 Video: Evolution: Darwin's Dangerous Idea [4332"] - part I
Check out Book's Companion Web Site: http://sites.sinauer.com/evolution3e
Literature Discussion:  Chance Riches by SJ Gould 1980 [3202"]
TBA

Comment on journal entry protocol & bringing laptops.
2 1/21 Journal Post Due 1/20 by 5 pm on Blair & Stowasser 2009
Video:
Evolution: Darwin's Dangerous Idea [4332"] - part II
Individual Meeting with Students
Exercise: Undirected Networks
Exercise:
Morphological Observation, Variation, & Comparison
Literature Group Work & Discussion:  Blair & Stowasser [5093"] - Fundamentals of data paper in science. Groups review paper using Journal Paper Review Form
3 1/28 Exercise: Observation and Variation
Demonstration: Cladistics: A Practical Primer on CD ROM (Chapters 1 & 2) [4734"]

4 2/4
Literature Discussion & Exercise: Fitzgerald 2006 [6165"]
Exercise: Fossil morphometrics - assessing evolutionary change with Dr. David Rodland

5 2/11 Video: Great Transformations
Literature Discussion& Exercise: Fitzgerald 2006 [6165"] (from wk 3)
Exercise: Observation and Variation (from wk 3)
Exercise: Futuyma Supplemental Materials: Bird Brains and Genome Size.
6
2/18 Journal Post Due on Gould & Lewontin 

7 2/25 Turn in: Bird Brains and Genome Size Exercise
Literature Discussion: Gould and Lewontin 1979 (complete journal entry before lab)
Literature Discussion: Bring Chance Riches by SJ Gould 1980 [3202"]
back to lab.
Exercise: Unique, derived features of Mammalian Skulls & Teeth.
Exercise: Genetics, Basic Probability, and Simulations
8
3/4
Turn In: Genetics, Basic Probability and Simulations

Test I 12:30-2:30
9
3/11
Spring Break!
10 3/18 DVD: Why Sex?
Post Test Meetings:
Exercise: Additional Probability & Simulation
TBA:
11 3/25 Bring laptop if you like
DVD: Origins Battle for the Planet
or
Literature Discussion: Grant & Grant 1992 Demography and genetically effective population sizes of two populations of Darwin's finches [2088"] - Group Work using Journal Paper Review Form.
Exercise
: Genetic Variation and Hardy-Weinberg
12 4/1
DVD: The Evolutionary Arms Race
Literature Discussion: Grant & Grant 2002
Literature Discussion: Galis et al. 2001 [4364]
Exercise: Gene flow and Population Structure
13 4/8 Test II 12:30-2:30
14 4/15 Literature Discussion: - Must a Darwinian Be Skeptical About Religion? 1990 [4876"}
Video: The Evidence for Evolution
TBA - Maybe some lecture
15 4/22 Literature Discussion: Milner & Maestro 2002 [4493"] - "Intelligent Design," 
Video: PBS Evolution Series: "What About God?"
Preparation Laboratory Final

4/29
Turn in Laboratory Final by 5 pm




Additional Modules
Appreciating the Burges Shale

DVD: Origins Battle for the Planet
Exercise: Fossils - diversity in form

Exercise:  Additional Work with Probability and Simulation
Literature Discussion:  Balter 2000 [3693"] & Gould 1980 [3202"]
  Literature Discussion: Gould 1994 - "The persistently Flat Earth: Irrationality
in science and religion " [2299"]
  Literature Discussion:  Galis et al.  [4364"]
Literature Discussion:  Mace et al. 2003 [4760"] - Preserving the tree of life and/or
Benton & Ayala 2003 [4758"] - Dating the tree of life
Exercise
Literature Discussion: Gould & Lewontin 1979 "The spandrels of San Marco paradigm: a critique of the adaptionist programme." [0502"]
  Literature Discussion: Balter 2000 - "Was Lamark Just a Little Bit Right?" [3693"]

Literature Discussion: Gould 1994 - The Persistently Flat Earth

Literature Discussion: Culotta & Pennisi 2005 - [4950"] - article on Blackboard site ;  Discussion of posts about Gould 1980; explanation about Raup 1979 from Gould - why simulations are important.
Turn in: Genetics, Basic Probability, and Simulations  worksheet

Literature Discussion: Judson 2008: Evolution: Darwin's Dangerous Idea [4332"] - part II
Literature Discussion:  Galis et al. 2001 [4364] - Why five fingers? ...
Literature Discussion: Cowley 1996 - The Biology of Beauty