Biospeleology: Life in Darkness

	Biospeleology: Life in Darkness (BIOL 4313, BIOL 5313)

	Spring 2008 Dr. Aldemaro Romero Arkansas State University
	1. Course Objectives 1.1. Introduction: This course is aimed at studying hypogean (underground) organisms, particularly in cave and artesian environments. This will be done by analyzing and discussing the current knowledge in this area including the historical development of biospeleology as a science, a survey of hypogean biodiversity, past and current hypotheses on cave biology evolution, physiology, behavior, ecology, and conservation. 1.2. Methodology: You will be trained in how to recognize the most interesting species of hypogean organisms and to further develop the knowledge and skills required of the research scientist, skills which are also required in many other professions. Whether you enter (and/or pursue further) into graduate school, pursue a teaching or research career, or follow some other career path, you will be compelled to understand and integrate a large body of knowledge, to think analytically, identify and critically evaluate pertinent literature, to communicate effectively, and to work with others. This is how this course aims to develop those abilities. A. Solid foundation in the knowledge of Biospeleology. You will be introduced to the content of the course in the classroom and in the field. B. Application of scientific methods of inquiry, search and, critically read the scientific literature. We will examine the diverse approaches used by researchers to uncover the basic concepts of the study of biospeleology. C. Development of analytical thinking skills. Hypogean organisms are mostly unfamiliar to most humans. To make your approach as scientific as possible you will need to rely heavily on critical thinking. The true test of understanding comes when you use your knowledge in different situations. 1.3. Expected Outcome: By the end of the semester, you should have a general knowledge of the diversity of hypogean life as well as on the major topics relating to their biology such a evolution, physiology, behavior, ecology and conservation. Additionally, you should have further developed your skills in planning a biospeleological research program, conducting field and laboratory studies, analyzing information, and critically reviewing the scientific efforts of others.
	2. Instructor Dr. Aldemaro Romero, (B.S.- Master: University of Barcelona, Spain, 1977; Ph.D.: University of Miami, 1984). I am Professor and Chair of the Department of Biological Sciences at Arkansas State University. I have published numerous papers and books related to biospeleology. Here are some of the most recent: 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. & L. Bennis. 1998. Threatened fishes of the world: Amblyopsis spelaea De Kay, 1842 (Amblyopsidae). Environmental Biology of Fishes 51(4) :420-420. Romero, A. 1998. Threatened fishes of the world: Amblyopsis rosae Eigenmann, 1842 (Amblyopsidae). Environmental Biology of Fishes 52(4):434-434. Romero, A. 1998. Threatened fishes of the world: Typhlichthys subterraneus Girard, 1860 (Amblyopsidae). Environmental Biology of Fishes 53(1):74-74. Romero, A. 1998. Threatened fishes of the world: Speoplatyrhinus poulsoni Cooper and Kuehne, 1974 (Amblyopsidae). Environmental Biology of Fishes 53(3):293-294. Romero, A. 1999. The blind cave fish that never was. National Speleological Society News 57(6):180-181. Romero, A. 1999. Useless abilities. New Scientist 162(2190):54-55. Romero, A. 1999. Myth and reality of the alleged blind cave fish from Pennsylvania. Journal of Spelean History 33(4):67-75. Romero, A. & Andrea Romero. 1999. Cope, caves, and skeletons in the closet. National Speleological Society News 57(11):341-343. Romero, A. 2000. The speleologist who wrote too much. National Speleological Society News 58(1):4-5. Romero, A. & P. B. S. Vanselow. 2000. Threatened fishes of the world: Milyeringa veritas Whitley, 1945 (Eleotridae). Environmental Biology of Fishes 57(1):36-36. Romero, A. & A. McLeran. 2000. Threatened fishes of the world: Stygichthys typhlops Brittan & Böhlke 1965 (Characidae). Environmental Biology of Fishes 57(3):270-270. Romero, A. & K. Benz. 2000. The unsung heroes of Speleology. National Speleological Society News 58(4):106, 126. Romero, A. & P. B. S. Vanselow. 2000. Threatened fishes of the world: Ophisternon candidum (Mees 1962) (Synbranchidae). Environmental Biology of Fishes 58(2):214-214. Romero, A. & J. Creswell. 2000. In search of the elusive "eyeless" cave fish of Trinidad, W.I. National Speleological Society News 58(10):282-283. Romero, A. & Z. Lomax. 2000. Jacques Besson, Cave eels and other alleged European fishes. Journal of Spelean History 34(2):72-77. Romero, A. 2001. Evolution is opportunistic, not directional. BioScience 51(1):2- 3. Romero A. & K. M. Paulson. 2001. Humboldt's alleged subterranean fish from Ecuador. Journal of Spelean History 36(2):56-59. Romero, A., A. Singh, A. McKie, M. Manna, R. Baker & K. M. Paulson. 2001. Return to the Cumaca cave, Trinidad, W.I. National Speleological Society News 59(8):220-221. Romero, A. 2001c (Ed.). The Biology of Hypogean Fishes. Developments Environmental Biology of Fishes, Volume 21. Kluwer, The Netherlands: Dortrech. Romero, A. 2001. An introduction to the special volume on the biology of hypogean fishes. Environmental Biology of Fishes, 62(1-3):7-12. Romero, A. & K. M. Paulson 2001. It’s a wonderful hypogean life: a guide to the troglomorphic fishes of the world. Environmental Biology of Fishes 62(1-3):13- 41. Romero, A. 2001. Scientists prefer them blind: the history of hypogean fish research. Environmental Biology of Fishes, 62(1-3):43-71. Proudlove, G. S. & A. Romero 2001. Threatened fishes of the world: Caecobarbus geertsi Boulenger, 1921 (Cyprinidae). Environmental Biology of Fishes 62(1-3):238-238. Romero, A. 2002. Between the first blind cave fish and the last of the Mohicans: the scientific romanticism of James E. DeKay. Journal of Spelean History 36 (1):19-29. Romero, A. 2002. The life and work of a little known biospeleologist: Theodor Tellkampf. Journal of Spelean History 36(2):68-76. 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. 2003. Cypriniformes II (Loaches and relatives), pp. 321-334, In: Grzimek’s Animal Life Encyclopedia, 2nd. Edition, Vol. 4, Fishes I., (M. Hutchins, D.A. Thoney, P.V. Loiselle, and N. Schlager, eds.). Farmington Hills, MI: Gale Group. Romero, A. 2003. Percopsiformes (troutperchers and relatives), pp. 5-13, In: Grzimek’s Animal Life Encyclopedia, 2nd. Edition, Vol. 5, Fishes II., (M. Hutchins, D.A. Thoney, P.V. Loiselle, and N. Schlager, eds.). Farmington Hills, MI: Gale Group. Romero, A. 2003. Synbranchiformes (swamp and spiny eels), pp. 151-156, In: Grzimek’s Animal Life Encyclopedia, 2nd. Edition, Vol. 5, Fishes II., (M. Hutchins, D.A. Thoney, P.V. Loiselle, and N. Schlager, eds.). Farmington Hills, MI: Gale Group. Romero, A., S. M. Green, Andrea Romero, M. M. Lelonek & K. C. Stropnicky. One eye but no vision: troglomorphic Astyanax fasciatus (Pisces: Characidae) with induced eyes do not respond to light. Journal of Experimental Zoology 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. 2004. Pisces: Amblyopsidae. pp. 595-597, In: Encyclopedia of Cave and Karst Science (J. Gunn, ed.). London: Fitzroy Dearborn. Romero, A. & J. S. Woodward. 2005. On white fish and black men: did Stephen Bishop really discover the blind cave fish of Mammoth Cave? Journal of Spelean History 39(1):23-32. 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.
	3. Textbook and Supplies 3.1. The Textbook Believe it or not there is not any recent textbook on biospeleology that satisfies the requirements of this course. I am finishing one titled “The Ecology and Conservation of Caves” to be published by Cambridge University Press, which covers most of the material dealt with in this class. I will provide you with portions of the books as well as some additional material. 3.2. Other Supplies I recommend that you obtain CD disks to download the electronic material I will be e-mailing you
	4. Other Resources 4.1. Library Resources: ASU’s Library has various scientific periodicals and books and I also have a private library with numerous books, journals, and reprints on the subject; you are welcome to use those resources in my lab. 4.2. Computer Resources: All officially enrolled students have access to the E-mail system. I heavily use the system to communicate with you (up to several times a week). Please check your email regularly for class announcements. You can also send me email to ask me questions or to engage in discussions with your colleagues. Please avail yourself of this opportunity.
	5. 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 during lectures and will stop lecture until you are satisfied that your question has been answered. I greatly appreciate students who come to me for further discussion and inquiring. Please do not hesitate to see me to discuss the subject as well any problem that may arise regarding class schedule and grading. At the same time, I have high expectations for your personal growth and success as a student in this semester. If you cannot figure something, I expect you to see me so we can seek a solution to the problem. 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. Your total effort per week should average 9 hours. This will include approximately 3 hours of lecture and at least 6 hours of outside work
	6. Recording and Duplication of Course Materials Lecture presentations, lecturer's notes and outlines, handouts, and exam materials are the property of the instructor and may not be recorded or duplicated for commercial use or sale without the permission of the instructor. Students are permitted to record lectures for individual use only. Commercial note-taking services are expressly prohibited.
	7. 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 requires extra time, please make an appointment. Office: Biology Office; Lab: LSW 443 Phone Number: (870) 972-3082 Email address: aromero@astate.edu
	8. Evaluation Criteria Exams: The course will have four sources of evaluation totaling 500 points broken up as follows: a) Two 100-point exams will be given. They will consist of critical thinking questions about the material covered in the lectures. These exams will be take-home exams. Also, these exams may be oral. POINTS 200 b) Class participation POINTS 100 c) Paper POINTS 200 TOTAL = 500 No make-up exams will be given under any circumstances. If a student misses a scheduled examination s/he will receive a grade of zero. All deadlines must be met. No excuses will be accepted. The grading scale is as follows: % Grade 450-500 A 400-449 B 350-399 C 300-349 D 299 or below F Incomplete grades will be given only in rare cases where the student suffers from some type of physical disability or illness that prevents the completion of the second half (that is after the first exam) of the semester. Medical documentation will be required. Also, if you feel I have erred in grading, please let me know, and I will regrade your entire exam. You might get points back, but then again, I might see something I missed before...
	9. Letters of Recommendations Those students that have excelled in my class can always count on strong letters of recommendation upon request.
	10. Attendance Attendance is expected at all lecture sessions. Attendance will be taken at the beginning of each class. I can be flexible if in a very occasional fashion you are late and I will give you an "attended" mark for that day. However, regular tardiness will not be excused. Since there is not textbook, students are expected to come to all sessions. I reserve the right to penalize those who do not attend by not granting favors. Class attendance is one of the major characteristics that employers are interested in when hiring new employees because it tells a lot about one's commitment to assigned tasks and the ability to deal with varying life situations. For example, there is an increasing tendency for some students to miss a class in one course in order to study for a test scheduled later in the day. Although there might be times when such decisions are necessary, studies suggest this is usually not a valid decision. Not only does it seldom result in a significant increase in the test score, it is considered an indication of lack of confidence and/or poor time management. The problem is usually magnified when one is later tested without adequate notes (or no notes) from the missed class. If you must miss class for any reason, you should get notes from two classmates, review the notes, and then see me to clear up any questions about the missed class. It is best to do this by the next class period since the importance of the missed notes often quickly diminishes with time only to resurface the day before an exam or perhaps during the exam.
	11. Academic Honesty To ensure the highest standards of academic honesty and ethical behavior, the Honor Code will be strictly enforced. In other words, do not even think about any behavior that may be construed as academic dishonesty, plagiarism, misrepresentation, or cheating. Academic dishonesty includes, but is not limited to the following: A. Cheating on an examination, taking information or allowing information to be taken from tests. B. Receiving help from others in work to be submitted, if contrary to the stated rules of the course. C. Plagiarizing, i.e., taking and passing off as one's own the ideas, writings or work of another, without citing the source. This is true whether the material used is only a brief excerpt or an entire paper or article and whether the original source is the work of another student or some publication. D. Submitting work from another course. E. Stealing examinations or course material. F. Falsifying data and/or records. G. Assisting anyone to do any of the above. The honor code protects the honest student, the reputation of ASU, and the value of degrees earned here. We should all support it both by personal honesty in all things and by refusing to tolerate dishonesty in others. Any graded work must be performed completely unaided. Students must report to me any suspected cheating. If you have any questions about your assignment, plagiarism, or the Honor Code, please contact me.
	12. Withdrawals You are the sole responsible for fulfilling all necessary steps to formally withdraw from this course.
	13. 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.
	COURSE OUTLINE Week 1: Introduction to life in darkness. Lexicon Week 2: A brief history of biospeleology. Week 3: What is a cave organism? Week 4: Cave colonization: between chance and necessity. . Week 5: Is there such as thing as “preadaptation”? Week 7: Why phenotypes change? Week 8: The physiological picture. Week 9: Why cave animals behave and why they behave the way they do? Week 10: The ecological structure of hypogean environments. Visit to Mammoth Cave: Week 11: Conservation of hypogean organisms and their habitats. Week 12: Students presentations: Hypogean biodiversity: from microbes to mammals.
	HOW TO SUCCEED IN MY CLASS Every professor has his/her own values on how to judge students. This ranges from knowledge to attendance, from attitude to hard work. Each one of us is different in his/her methods and approaches, but all of us want our students to succeed by learning and getting good grades. What follows are a series of recommendations that, if pursued, would put you pretty much on the path to success: 1. Show up. My lectures and discussion sessions contain the information you should know. Attending class and taking notes will help you focus on what is really important, in what I consider to be essential. I use a lot of visuals in my presentations. I also like to challenge my students, to engage in discussions, to make the class a truly participative experience. You cannot get this information from another student's notes. You need to observe my delivery: you need to know not only what was said but also how it was said. Besides, when you study without having been in class, you are learning the material for the first time. When you study after you have been to class, you are reviewing. 2. Attendance record. Make no mistake about it: in the subjective realm of grading, attendance always counts. I respond positively towards students who come to class regularly. Repeated absences will lose you the benefit of the doubt when it comes to grading, and you might very well need that benefit. For this class, learning is accumulative, with each class building on the previous one. If you fall behind, it becomes increasingly difficult to catch up. 3. Prepare for class. The schedule included in this syllabus tells you exactly what topics will be covered and I will email you notices on the reading material before hand. I will ask questions during the class; your class performance will be evaluated. Know the scientific vocabulary and terminology and practice critical thinking. 4. Choosing the right seat. I use a lot of visuals for this class. Thus, try to seat in the very first rows. That will allow you to read the visuals without difficulty, it would let me notice you (leading me to believe that you are involved and conscientious), and will ensure your participation 5. Take notes. Unless you have a photographic memory you should take notes, but do not confuse taking notes with stenography. I try to make you think during the class and you cannot listen, think, and respond if you are busy playing secretary. Most of the things that are written on the board and/or shown in transparencies tend to be very important. Many of my past students have told me that they have found that the best way to follow my classes is by tape-recording my lectures and just taking notes on the information written on the board or the transparencies. Since it is not practical to have 40 tape recorders on my desk while I am lecturing, I strongly suggest that you form study groups where one student per group is responsible for recording and sharing the tape (see "Recording and Duplication of Course Materials policies," above). Do not hesitate to come to me with questions or concerns about past lecture material. Try to understand why we know what we know in science. Establish connections and links between concepts and ideas covered throughout the course. Know how the information presented is used, and why it is useful in the real world. Extend and relate your knowledge and understanding into new contexts and situations. 6. Class participation. I seek, need, and appreciate student involvement in my class. Many of my ideas in biospeleology are controversial and are not shared by many of my colleagues. Animated discussions are one of the best rewards I can receive as an instructor. Some class sessions will be specifically aimed at discussion of reading material. I know that speaking before a group is a scary experience for many. Survey after survey, it has been shown that what people fear most (even more than death, accident, or even losing their job) is to speak in public. Do not think that by participating you are annoying others, that you have nothing to contribute, or that by asking a fundamental question people will judge you negatively. They will not judge you: they are too busy thinking about their own comments. However, as much as I encourage participation, there is one and only one question I do not like to hear, and that is: "Do we need to know that?" Make no mistake about it: you are not paying tuition (and the University is certainly not paying me) in order to use the class time to engage myself into idle talk and/or irrelevant material. Everything I say, everything I point out to, is because I feel is important for you to know, and in consequence it can be asked in a test. I will use the review sessions, however, to point out to those aspects that I consider really relevant for you to prepare for the exam. 7. Form study groups. My most successful students form study groups. Talking about the material, quizzing each other, and sharing time exploring the material builds your interest and comprehension, and makes learning fun. Disclaimer: The information contained in this syllabus is as accurate as possible, but may be subject to change with reasonable advance notice. The schedule and content of lectures and assignments may be changed at the discretion of the instructor upon oral notification in class. Changes may involve additions, deletions, substitutions, or changes in sequence or due date.
	Results of Past Course Evaluations Spring 2006 "Was well spoken and always instigated discussions, controversal or otherwise" "I took the class because of subject but also b/c instructor’s great reputation. He lived up to it. Thank you." "Good discussions" "The class discussions were interesting and enthusiastic. Romero is very excited about the subject and that translated to the class well." "Refreshing course made me think Hooray for critical thinking w/o memorization." "Very interesting class. Enjoyed the subject matter and the critical thinking in discussions. One of the best classes so far." "My only real complaint was that there was no difference between graduate and undergraduate requirements and that the assignments could be a little unclear. Otherwise the class was great very interesting." "I was a little discouraged in the first several classes b/c I was not as versed in the subject matter as others in the class were, but in got better. I highly enjoyed the class." "Very educational and interesting course would take it again if I could." Undergraduate Students' Evaluations Statistical responses (n=4): Totally agree = 5 ... Totally disagree = 0 1. I am very interested in this course 4.8 2. Instructor was knowledgeable 5.0 3. Instructor was always available 3.8 4. Instructor gave assistance outside the class 3.8 5. Instructor effectively presented the material 4.0 6. Instructor explained the assignments clearly 3.0 7. Instructor returned assignments timely 4.3 8. Instructor provided adequate feedback 4.0 9. Instructor made students feel comfortable 4.5 10. Instructor was well prepared and organized 5.0 11. Instructor encouraged students to ask questions 4.8 12. Instructor encouraged respect among students 4.8 13. Instructional aids were appropriate 4.8 14. Instructor evaluated my work fairly 4.5 15. Instructor gave sufficient number of tests 3.8 16. Instructor seemed concerned about the students' learning 4.5 17. Instructor responded respectfully to students' questions 4.8 18. Instructor motivated students to do their best 4.0 19. Instructor increased my interest in the course 4.5 20. Helped me to become more of a critical thinker 4.5 21. Instructor fulfilled stated objectives and goals 4.5 22. This course was intellectually challenging 4.8 23. This course expanded my understanding of the subject 5.0 24. The required reading material helped me 4.3 25. The text required for this course is appropriate 4.3 26. Overall this was a great course 4.5 Graduate Students' Evaluations 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 5.0 4. Instructor gave assistance outside the class 4.9 5. Instructor effectively presented the material 4.9 6. Instructor explained the assignments clearly 4.9 7. Instructor returned assignments timely 4.6 8. Instructor provided adequate feedback 5.0 9. Instructor made students feel comfortable 4.9 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 4.9 14. Instructor evaluated my work fairly 5.0 15. Instructor gave sufficient number of tests 4.9 16. Instructor was concerned about the students' learning 4.9 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 4.9 20. Helped me to become more of a critical thinker 4.9 21. Instructor fulfilled stated objectives and goals 5.0 22. This course was intellectually challenging 5.0 23. This course expanded my understanding of the subject 4.9 24. The required reading material helped me 4.9 25. The text required for this course is appropriate 4.6 26. Overall this was a great course 5.0
	Spring 2008 (n=8) "This was one of the only evaluations that got all 5's! Very good job Dr. Romero!! I really enjoyed it! "Dr. Romero is by far the best instructor I have had. He is knowledgeable and shares his knowledge. Through critical thinking then spelling out facts." "Dr. Romero was great. I really enjoyed the class." "Dr. Romero is the best professor I've ever had. Thoroughly enjoyed my time spent in lecture." "I loved the class! I learned so much and I never felt intimidated to ask questions. I loved being in class. I can't say that for many classes. I wanted to be in class and learn!!" "One of the best courses I've taken. Dr. Romero's teaching style challenges students to think about the subject." "This was a great class. Really opens your mind to different kinds of thinking." "Dr. Romero has done an awesome job presenting this course! I appreciate his candor during each and every lecture. I would suggest this course to any student interested in any fact of the Biological sciences."
	FAILURE TO FOLLOW THE DIRECTIONS CONTAINED IN THIS SYLLABUS COULD CAUSE YOU TO GET A POOR GRADE IN BIOSPELEOLOGY Drawings of all extant species of fishes of the family Amblyopsidae. All these species are found in North America (two of them in Arkansas). One is a surface species, another is a facultative cavernicole, and the others are obligatory cave species. Can you tell which is which? What does that tell you? Can your observations be generalized? What can you learn from it? Cover Drawing by John Ellis; from Romero, 2003, The Amblyopsidae...
	Cave form of the Astyanax fasciatus species complex.	Individual from a cave population of the species Rhamdia quelen from Trinidad, W.I.