Evolutionary Biology

BIOL 6223

Fall, 2008 Dr. Aldemaro Romero Arkansas State University     1. Course Objectives   1.1. Introduction:  This is a seminar-type course aimed at discussing some of the most controversial and/or intriguing hypotheses, facts, and speculations in evolutionary biology in the broader sense.   1.2. Methodology: The discussions will be based on papers and ideas proposed by both, the instructor and the students.  The approach by the instructor will be that of thought-provoking, challenging questions about the topics discussed.   1.3. Expected outcome:  By the end of the semester, you should have a very broad and comprehensive vision of some major evolutionary questions but, more importantly, you should have sharpened your critical thinking abilities as a scientist.     1.4. Prerequisites: Permission of the instructor.

2. Instructor   Dr. Aldemaro Romero, Chair and Professor of Biological Sciences at the Department of Biological Sciences, Arkansas State University.  I have been working and publishing on evolutionary questions since my times as undergraduate student.   Some relevant papers I have published on evolutionary biology are:   Romero, A. & . L. Vía. 1977. Tarracolimulus rieki, nov. gen., nov. sp., nuevo     limúlido del Triásico de Montreal - Alcover (Tarragona). Cuadernos de Geología     Ibérica 4:239-246. Romero, A. & L. Vía. 1978. Paleocyphonautidae: nuevos fósiles del triásico español,     probablemente relacionados con las actuales larvas cifonautas. Estudios Geológicos     34:497-504. Romero, A. 1983. Introgressive hybridization in a population of Astyanax fasciatus     (Pisces: Characidae) at La Cueva Chica. National Speleological Society Bulletin     45:81-85. Romero, A. 1984. Behavior in an "intermediate" population of the subterranean-     dwelling characid Astyanax fasciatus. Environmental Biology of Fishes 10:     203-207. Romero, A. 1985a. Cave colonization by fish: role of bat predation.  American     Midland Naturalist 113:7-12. Romero, A. 1985b. La evolución de la conducta en peces cavernícolas. Natura     (77):13-17. Romero, A. 1985c. Can evolution regress? National Speleological Society Bulletin     47(1):86-88. Romero, A. 1985d. Ontogenetic change in phototactic responses of surface and     cave populations of Astyanax fasciatus (Pisces: Characidae) Copeia 1985(4):     1004-1011. Romero, A. 1985e. Specialized petiole feeding behavior in Cichlasoma tuba.     Brenesia (24):385-389. Green, S. & A. Romero. 1997. Responses to light in two blind cave fishes     (Amblyopsis spelaea and Typhlichthys subterraneus) (Pisces: Amblyopsidae).     Environmental Biology of Fishes 50(2):167-174. Romero, A. 1999. Useless abilities. New Scientist 162(2190):54-55. Romero, A. 2001a. Evolution is opportunistic, not directional. BioScience 51(1):     2-3. Romero, A., A. Singh, A. McKie, M. Manna, R. Baker, K. M. Paulson, & J. E.     Creswell. 2002. Replacement of the Troglomorphic population of Rhamdia     quelen (Pisces: Pimelodidae) by an epigean population of the same species in the     Cumaca Cave, Trinidad, W.I. Copeia 2002(4):938-942. Romero, A., S. M. Green, Andrea Romero, M. M. Lelonek & K. C. Stropnick. 2003.     One eye but no vision: troglomorphic Astyanax fasciatus (Pisces: Characidae)     with induced eyes do not respond to light. Journal of Experimental Zoology     (Molecular and Developmental Evolution 300B(1):72-79. Romero, A.  2004. Adaptation: Behavioural.  pp. 3-4, In: J. Gunn, Ed.  Encyclopedia     of Cave and Karst Science. New York: Fitzroy Dearborn. Romero, A.  2004. Biospeleologists. pp. 151-154, In: J. Gunn, Ed. Encyclopedia of     Cave and Karst Science. New York: Fitzroy Dearborn. Romero, A.  2004. Evolution of hypogean fauna. pp. 347-349, In: J. Gunn, Ed.     Encyclopedia of Cave and Karst Science. New York: Fitzroy Dearborn. Romero, A. & S. M. Green. 2005. The end of regressive evolution: examining and     interpreting the evidence from cave fishes. Journal of Fish Biology 67(1):3-32. Romero, A., R. R. Rogers & J. Seguí. 2006. On the evolutionary significance of the     Paleocyphonautidae: How fossils and larvae impact evolutionary reconstructions.     Batalleria 12:149-154. Submitted Manuscripts 2006. Romero, A., R. R. Rogers & J. Segui. Cnidarians from the Montral-Alcover     Lagerstatten (Ladinian, Middle Triassic), Northeastern Spain. To: Batalleria.     Manuscripts in Preparation Romero, A. The Evolutionary Significance of Prions. Romero, A. The Red Queen Hypothesis 30 years later. Regal, P. & A. Romero. Predestination as an idea in evolutionary biology. Romero, A. The Ecology of Cave Fauna. Cambridge University Press.

3. Academic Approach   I give the best of myself in each one of my classes in order to offer you the opportunity to maximize your chances of learning lasting lessons in science.  I consider myself motivational, challenging, and enthusiastic.  I encourage questions.  I greatly appreciate students who come to me for further discussion and inquiring.  Please do not hesitate to see me during my office hours or by appointment to discuss the subject as well any problem that may arise regarding class schedule and grading.  I expect the finest from you.  I will do my best to ensure that you learn the maximum and that your effort is rewarded with good grades.  I take a great deal of pride on how much my students learn and on the well-earned grades they receive.

4. Office Hours   My policy regarding office hours is that if I am in my office or my lab, I am available.  If you need to discuss something that requites a lot of time, please make an appointment. Office: Biology Office; Lab: LSW 443 Phone Number: (870) 972-3082 Email address:  aromero@astate.edu

5. Evaluation Criteria   You will be evaluated based on your participation in class (50%) and the writing of a research paper (25%) and its oral presentation (25%).  That means, be very very proactive in all the discussions!   Class participation (50%): Students are expected to attend class, and to have read any assigned readings prior to class.  For each article to be discussed, students should prepare a brief outline of the major premise(s) presented in each article and the basis in support for any ideas advanced by the author(s).  In addition, students should come to class with at least 3 questions or comments relating to the content or topic of each article.  Students should be prepared to lead a discussion of an article if called upon. I also ask that we all do our best to be intellectually honest, while also being tolerant of personal differences.  Everyone in the class should feel safe to express an idea, even if that idea is not a popular one.  I welcome and encourage intellectual controversy‑‑ it is how we learn best, I believe.  I demand, however, that we respect one another's right to believe differently, even as we challenge the ideas supporting those beliefs.  I promise to value each of you as individuals independently of how well you do in your assignments.   Research paper: (25% of your total grade) After discussing the topic with me, you may have the opportunity to write an original research paper on a particular topic.  Grading will be based on originality, clarity of ideas, and quality of the substance and presentation.  The paper must be type-written and double-spaced and submitted electronically. The paper must be a review article about a topic in evolutionary biology, that is an in‑depth summary and discussion about your topic.  This assignment is in two parts. First, a literature search plus a 2‑page summary of two of the articles from the primary literature is due at the beginning of class on September 23, 2008.  You must include your summary of the two articles.  This summary must be at least 2 full pages, but not more than 3.  The summary must be typed exactly in the style of a term paper, i.e., the statements that you make in the summary must be supported with appropriate citations that are then listed in the "literature cited" section at the end of the paper.  The two articles must address the same topic and your summary must indicate the relationships between the two papers.  For example, one paper builds on the work of a previous paper, or the two papers present opposite views of the same topic, or the two papers reach the same conclusions but use different methods.  The summary should include why the authors performed the research, how they did the research, what they found, and a discussion of the results.  Also include a paragraph discussing why you chose your particular topic.  This summary is worth 25% of this assignment.  The summary will be graded upon your ability to summarize the findings and its grammatical correctness. The second part is the paper itself, which is worth 75%.  There is no upper limit to the number of citations that would be appropriate.  You should use as many as is possible concerning your  topic, however, minimally the literature cited section must contain at least 10 citations, with at least 7 of these from the primary scientific literature.  Your paper should be typed and double‑spaced and at least six pages of text, exclusive of the literature cited.  PAPERS THAT DO NOT MEET THESE VERY MINIMUM REQUIREMENTS CAN EXPECT NO MORE THAN 70%.  Your paper will be graded on its scientific content and the coverage of the topic, in addition, the paper will be graded on grammar, clarity, and freedom from typographical and spelling errors.  Papers are due on December 9, 2008.  Plagiarizing your paper from some other source or collaborative efforts with other students will be considered cheating and your behavior will be reported to the appropriate ASU office for punishment that may include expulsion from the university.  In addition, if you turn in essentially this same paper for a different class, I will consider it cheating and you will also be prosecuted for violation of academic integrity.  I will always be available to discuss with you the progress of your research paper at any stage prior being handled to me.  However, you must know that I will measure it to the highest scientific standards.  Any work submitted by an individual student is expected to represent his/her individual, personal work.  Passages of text, images, diagrams, pictures, or original ideas drawn from other sources must be clearly identified, both by separating the passage from the neighboring student‑written narrative (using quotation marks or block indents) and with citations and reference to the original work or individual.  Any student submitting in their name the work of another student, individual, or author is committing plagiarism and will be referred for disciplinary action.  Read the academic integrity section of the Student Handbook. Details of all suspected violations of academic integrity will be reported to the appropriate authorities. Paper presentation: (25% of your total grade) I expect you give a 20-30 min. presentation of your paper meeting the highest standards of clarity, depth, and quality. I will be available to help you with your presentation, something I recommend very strongly.   All deadlines must be met.  No flimsy excuses will be accepted. In other words, if you miss a deadline because your grandmother died, I will require a death certificate; if it is because you were hospitalized, I will require copy of the hospital's bill; if you could not do it because you were abducted by space aliens, I will require a copy of the complaint you filed with the FBI for kidnapping, and so on. The grading scale will observe the following perceptions A: Integrates theory and examples; evidence of original thinking and knowledge of  the literature.  Strong in theory or examples and integration, knowledge of the literature, application to new problems.  B: Weak in theory or examples; poor in integration, knowledge of the literature, application to new problems.  C: Problems with accuracy; weak in both theory and knowledge of examples.  Show severe signs of lack of critical thinking D: Very inaccurate; very vague knowledge of major concepts; completed the assigned work. F: Did not complete the assigned work.  I: Incomplete; granted only in response to written explanation and request and under extraordinary and strongly justifiable circumstances.

6. Letters of Recommendations   Those students that have excelled in my class can always count with strong letters of recommendation upon request.

7. Withdrawals   You are the sole responsible for fulfilling all necessary steps to formally withdraw from this course.

8. Students with Special Instructional Needs   If you have any special needs related to learning or testing in this course, please let me know as soon as possible so I can address those needs.

9. Readings August 31: September 7: September 14: September 21: September 28: October 6: October 12: October 19: October 26: November 2: November 9: November 16: November 30: December 7:

Disclaimer:  The information contained in this syllabus is as accurate as possible, but may be subject to change with reasonable advance notice.  Changes may involve additions, deletions, substitutions, or changes in sequence or due dates.   FAILURE TO FOLLOW THE DIRECTIONS CONTAINED IN THIS SYLLABUS COULD CAUSE YOU TO GET A POOR GRADE IN EVOLUTIONARY BIOLOGY

2004 students' evaluations:   "Liked the format of the course.  Engaged the wide variety of topics.  Much better than memorize and spit back out." "I enjoyed this class tremendously.  The only suggestion that I could give is less papers on a given topic so that we can cover more evolutionary topics.  The participation in class helped to understand and think through topics presented." "This course was well instructed and gave me insight in many topics / fields that I am unfamiliar with.  I would recommend this course to any graduate student.  This course requires the students to think critically." "This has been the best course I’ve take at ASU.  The topics and conversation were always stimulating.  Dr. Romero knows how to ask questions that require critical as well conceptual thinking." "Thanks for the class.  It helped me withstand others that were less than engaging and opened my eyes to new ideas.  I’ll be chewing on this stuff for quite a while." "This was a very beneficial course.  It promoted critical thinking and novel ways of looking at biological ideas.  Dr. Romero possess a wealth of biological information as well as interesting trivia.  History of Biological Ideas was my favorite course, but this one would be in my top 3 of graduate school." "This course challenged in a variety of positive ways.  Dr. Romero was a great professor!  His knowledge of the subject matter was incredible and he expressed/taught the course in the way that you truly learned and understood the material.  Great course!" Statistical responses (n=8): Totally agree = 5 ... Totally disagree = 0 1. I am very interested in this course                               4.9 2. Instructor was knowledgeable                                     4.9 3. Instructor was always available                                   4.8 4. Instructor gave assistance outside the class                   4.8 5. Instructor effectively presented the material                  4.9 6. Instructor explained the assignments clearly                  4.8 7. Instructor returned assignments timely                         4.9 8. Instructor provided adequate feedback                         4.9 9. Instructor made students feel comfortable                     4.9 10. Instructor was well prepared and organized                 4.9 11. Instructor encouraged students to ask questions           5.0 12. Instructor encouraged respect among students             5.0 13. Instructional aids were appropriate                              4.9 14. Instructor evaluated my work fairly                             4.9 15. Instructor gave sufficient number of tests                     5.0 16. Instructor was concerned about the students' learning   5.0 17. Instructor responded respectfully to students' questions 4.9 18. Instructor motivated students to do their best                4.9 19. Instructor increased my interest in the course                4.9 20. Helped me to become more of a critical thinker             4.9 21. Instructor fulfilled stated objectives and goals                4.9 22. This course was intellectually challenging                      4.9 23. This course expanded my understanding of the subject   4.9 24. The required reading material helped me                       4.8 25. The text required for this course is appropriate               n/a 26. Overall this was a great course                                      4.9

2006 Students' Evaluations "I loved this course. The only thing I would change is to have lit in 2 weeks early so you could read it and ok it before before we do. You shouldn't have to do this but the semester suggested otherwise." "This course was the definitive grad seminar style course. Students were able to choose topics and interpret/discuss topics pretty much on our own. Dr Romero's anecdotes and knowledge gave great perspective and historical relevance to topics and discussion as well as to correct misconceptions in ore discussion. The only draw backs include the very loose structure of the course, although this was good for most students who knew what their topic of choice was. Some students needed more guidance in their topic - this may not have been Dr Romero's fault as students may not have consulted him. The TBA schedule might not have have the desired effect. It was difficult to schedule in the late evening. This may have been a side effect of the class size, which could have reduced by a fixed class time and scheduling conflicts. I feel that this course should be offered more often to ensure all students get to take it. so class size restrictions don't restrict students being able to take it @ some point in their time here." Statistical responses (n=2): Totally agree = 5 ... Totally disagree = 0 1. I am very interested in this course                               5.0 2. Instructor was knowledgeable                                     5.0 3. Instructor was always available                                   5.0 4. Instructor gave assistance outside the class                   4.5 5. Instructor effectively presented the material                  4.5 6. Instructor explained the assignments clearly                  4.5 7. Instructor returned assignments timely                         5.0 8. Instructor provided adequate feedback                         5.0 9. Instructor made students feel comfortable                     5.0 10. Instructor was well prepared and organized                 5.0 11. Instructor encouraged students to ask questions           5.0 12. Instructor encouraged respect among students             5.0 13. Instructional aids were appropriate                              5.0 14. Instructor evaluated my work fairly                             5.0 15. Instructor gave sufficient number of tests                     5.0 16. Instructor was concerned about the students' learning   5.0 17. Instructor responded respectfully to students' questions 5.0 18. Instructor motivated students to do their best                5.0 19. Instructor increased my interest in the course                5.0 20. Helped me to become more of a critical thinker             5.0 21. Instructor fulfilled stated objectives and goals                4.5 22. This course was intellectually challenging                      5.0 23. This course expanded my understanding of the subject   5.0 24. The required reading material helped me                       5.0 25. The text required for this course is appropriate               5.0 26. Overall this was a great course                                      5.0