Paleobiology T, R 3:00‐5:30 Spring 2011 Birck Hall 236 Instructor: Dr

Biology 322: Selected Topics: Paleobiology T, R 3:00‐5:30 Spring 2011 Birck Hall 236 Instructor: Dr. Phil Novack‐Gottshall Office: Birck 332 E‐mail: Blackboard mail preferred Office hours: T 11–1:30, W 11‐1, R 11–12:30 (or pnovack‐[email protected]) or by appointment

Course description Paleobiology is the science that uses fossils to understand the evolutionary and ecological history of life. It includes such topics as mass extinctions, evolutionary diversifications, quantification of evolutionary rates, microevolution and speciation in the fossil record, evolutionary development, evolutionary transitions, fossilization, climate change, competition, functional morphology, conservation biology, and long‐term trends in evolution and ecology,. During this combined lab and lecture course, you will also practice many of the analytical methods used in the discipline, including statistics, modeling, computer databases, phylogenetics, theoretical morphology and biomechanics. Learning objectives 1) Summarize basic geological processes and the importance of fossils as geological materials, and practice using the geological timescale. 2) Identify major lineages of organismal life and their place in geological history. 3) List and describe the major events (extinctions, diversifications, and environmental transitions) and long‐term trends in the history of life. 4) Understand critical issues in evolutionary and ecological theory, including evolutionary radiations, competition, escalation, evolutionary mechanisms (especially natural and species selection), and extinction. 5) Summarize the historical development of the field of paleobiology, especially in terms of its increasing reliance on analytical (hypothesis‐testing) methods. 6) Appreciate the important roles of artifacts and biases when evaluating historical patterns, critique the strengths and weaknesses of available analytical methods, and defend which methods are most suited for addressing scientific questions. 7) Understand and practice the analytical methods of paleontologists, including the Paleobiology Database, statistics, simulation models, calculation of evolutionary rates and diversity curves, rarefaction and sampling standardization, morphometrics, functional morphology, morphospaces phylogenetics, and molecular dating. Required textbooks 1) Foote, M. and A.I. Miller. 2006. Principles of Paleontology. 3rd ed. W.H. Freeman, NYC. 2) Shubin, N. 2009. Your Inner Fish. Vintage, NY. Supplementary textbooks available in Novack‐Gottshall research lab (Birck 107) Boardman, R.S., A.H. Cheetham, and A.J. Rowell, eds. 1987. Fossil Invertebrates. Blackwell Scientific, Boston. Clarkson, E.N.K. 1998. Invertebrate Palaeontology and Evolution. 4th ed. Blackwell, NYC. Feldmann, R.M., ed. 1996. Fossils of Ohio. Ohio Division of Geological Survey Bulletin 70. Moore, R.C., ed. 1953‐2008. Treatise on Invertebrate Paleontology. Geological Society of America, New York, and University of Kansas, Lawrence. Thompson, I. and T.P. Dickinson. 1982. National Audubon Society Field Guide to Fossils. Knopf, NY. Prerequisites: At least one 200‐level organismal biology course (e.g., Invertebrate Zoology, Botany, Vertebrate Embryology) or BIO229 (Biostatistics) is a prerequisite for this course because of the courseʹs application of basic organismal, evolutionary, ecological, and quantitative methods. IDEA Objectives: 1. Gaining factual knowledge (terminology, classifications, methods, trends). 2. Learning fundamental principles, generalizations, or theories. 4. Developing specific skills, competencies, and points of view needed by professionals in the field most closely related to this course. Blackboard and technology requirement Although regular attendance is vital to success in this course, it’s not sufficient. The Blackboard site will also have important information for you, such as course assignments and important announcements. You can get to the course site using http://www.ben.edu/blackboard. Once there, log‐in and click on the course site. If you have problems logging in or locating the site, just follow the links. A note on my office hours The best science teachers also practice scientific research. Although I do research throughout the week, I reserve Mondays for uninterrupted research. I will not regularly be available to meet with you on this day except for exceptional circumstances. You are still welcome to e‐mail me with questions and concerns during this time, and I will make every effort to respond in a timely manner. However, an e‐mail response cannot be guaranteed until the next work day. On other days, you’re welcome to call me on campus (678‐839‐4061), stop by my office or lab, or e‐mail me (pnovack‐[email protected]). I don’t accept phone calls at my home.

Grading Policies Your grades will be assigned on a percentage scale, as follows: ≥90% = A; 80‐89% = B; 70‐79% = C; 60‐69% = D; <60% = F Exam #1 (Feb. 22)* 15% Exam #2 (April 7)* 15% Cumulative Final Exam (May 12)* 15% Your Inner Fish Chapter Summaries 10% Timescale Quiz (Feb. 3) 5% Lab assignments 10% IRP Portfolio* (May 3) 10% Lab exam #1 (Mar. 10)* 5% Lab exam #2 (May 5)* 5% Field Trip Report* 5% Attendance and participation 5% * ‐ Asterisks denote major assignments; see Academic Honesty Policy below.

2 Lecture and lab exams (and policy on attendance on test dates) There will have three lecture‐based exams (including a cumulative final exam) and two (non‐cumulative) lab exams. Attendance is required on all exam dates. Make‐ups will only be allowed for exceptional circumstances. The professor will make the determination of whether or not the documentation justifies a make‐up exam. In those rare cases where a make‐up is allowed, the exam will be scheduled for final exam week. Make‐up exams will be essay‐based and substantially more demanding than regular exams. Do not leave campus until your scheduled final exams are over. If you have a plane ticket requiring you to leave before your scheduled exam, you will either receive a zero on the exam or be out the price of a plane ticket. The format of lecture‐based exams will include multiple choice, matching, fill‐in‐the‐ blank, short answer, and essay questions, and may include conceptual knowledge learned during lab. Exams will have you apply concepts learned in class instead of asking you to repeat facts and definitions (although you will still be expected to use relevant terms correctly). Memorization, last minute studying, and over‐dependence on lecture notes are not useful strategies. Reading the textbook throughout the semester will help support and enrich your knowledge. Lab exams will involve application of analytical methods learned during labs. The final exam is cumulative, although it will emphasize material since the second exam. Although longer than previous exams, it will have the same general format. It will occur in our regular classroom on Thursday, May 12 at 3:15‐5:15 pm. The Individual Research Project (IRP): Thinking like a paleobiologist To expose you to the excitement of studying fossils, you’ll become an expert on some major taxonomic group. This semester‐long project will help you “Think like a paleobiologist” and a historical scientist in general. You will choose your group during the first week of class, and then use this group to apply course concepts and conduct your own analyses of your groupʹs fossil record and evolutionary and ecological history. These applications will occur both in class and as homework throughout the semester (approximately weekly). At the end of the semester, you will submit a portfolio of all this research on your group, plus a culminating essay that synthesizes your overall knowledge of the history of your group. The due date for the portfolio will be Tuesday, May 3. Additional class assignments, timescale quiz, and Your Inner Fish summaries There will be additional assignments and activities throughout the semester. Among others, these include on‐line activities, a geological timescale quiz (start of class on Feb. 3), and weekly written summaries (~500 words) of chapter readings in Shubin’s (2008) Your Inner Fish (due the start of each Tuesday class). Field trip: There will one mandatory field trip to visit a local quarry to collect fossils. We will choose the date for this field trip early in the semester. The field trip will most likely occur on a Friday, and your attendance will be required so that you can prepare a graded field trip report. Lateness A late portfolio will be penalized 10% per 24‐hour period from the time it was due. All other assignments will be penalized 10% per lecture. The timescale quiz cannot be made up and will receive a grade of 0%. . See above for the lateness policy on exams.

3 Attendance and participation Because this class is relatively small and thrives on discussion and hands‐on analyses, it is critical that you come to, and participate in, every class. Regular participation will give you full credit; regular indifference will not. Appropriate participation includes attentiveness, participation in class discussions, respectful behavior, and courteousness to your peers. I will record your attendance throughout the semester. You can miss up to two classes without penalty. You will be penalized ½% from your final class grade for missing each additional class, regardless of excuse. Withdrawing from class The last day to withdrawal from class is Sunday, April 17. If you are considering withdrawing, please come speak with me first. I want to help you do the best you can in this class. You may be doing better than you fear! Extra credit Extra credit is unlikely, will be made at the discretion of your professor, and only when made available to the entire class. Your grade will be based solely on your performance on items in the syllabus Grading Policy. Make the most of every opportunity this semester.

Academic honesty policy The university faculty and student representatives have agreed to the following uniform statement of academic honesty. The search for truth and the dissemination of knowledge are the central missions of a university. Benedictine University pursues these missions in an environment guided by our Roman Catholic tradition and our Benedictine heritage. Integrity and honesty are therefore expected of all members of the university community including students, faculty members, administration and staff. Actions such as cheating, plagiarism, collusion, fabrication, forgery, falsification, destruction, multiple submission, solicitation, and misrepresentation are violations of these expectations and constitute unacceptable behavior in the university community. The penalties for such actions can range from a private verbal warning, all the way to expulsion from the university. The universityʹs Academic Honesty policy is available at http://www.ben.edu/AHP and students are expected to read it. Giving information to another student about the contents of a test or receiving such information is considered cheating, regardless of whether the action was intentional or consequential. Using cheat notes on a test is cheating. Copying from or looking at another student’s test or allowing someone to see or copy from your test is also cheating. In‐class cheating is a very serious offense. In the Biology department, the first infraction on an assignment/paper/quiz will result in a zero for that task. The second infraction will result in an F in the course. Dishonesty on major assignments (those items above noted with an asterisk) will result in an F for the course. According to university policy, the Provost will be notified of all incidents of cheating and you will be subject to the penalties imposed by that office which may include expulsion from the university. (See Student Handbook for details on academic honesty policies.)

4 Cell phones, calculators, and laptops Please turn off your cell phones, ipods, Blackberries, and other electronic devices before coming to class. Calculators will be supplied if they are required during exams. Laptops and classroom computers can only be used during lecture to take notes or do assignments; you cannot use them to catch up on Facebook, e‐mail, or to surf the internet. Policy on academic accommodations for religious obligations A student whose religious obligation conflicts with a course requirement may request an academic accommodation from the instructor. Students must make such requests in writing by the end of the first week of the class. Upon receiving such a request, the instructor will offer reasonable accommodations whenever feasible, and communicate this to the student. However, the course requirements listed in the syllabus remain in effect if accommodations cannot be offered. Disability support If you have a documented learning, psychological, or physical disability, you may be eligible for reasonable academic accommodations or services. To request accommodations or services contact the Student Success Center, Room Krasa 012A (630‐829‐6512). All students are expected to fulfill essential course requirements. The university will not waive any essential skill or requirement for a course or degree program. What if I miss a class? It is your responsibility to come to class regularly and to take notes. If you miss a class, you should contact at least two other classmates to learn what happened in class on the day you were absent, to get updated on announcements, and to photocopy any materials distributed that day. Do not ask your professor what you missed; it is not his responsibility to catch you up! What if I come late to a class? Students who arrive to class late not only miss important information, but also disrupt other students’ learning. For this reason, I expect that you will be on time and ready to begin work. A final caveat Your professor is not capricious, but he does reserve the right to alter this syllabus, class policies, or the class schedule to best accommodate the needs of the class. If such a change is needed, you will be given sufficient and timely notice, as well as the ability to contest or contribute to the alterations thereof.

5 Lecture Schedule As a new course format, it is difficult to predict the timing of course material. Instead, this lists the order of topics covered, with readings from Miller & Foote (2006). Topic Readings* Introduction to the Paleobiology Database Pp. 236‐237 How to name fossils Ch. 4 (pp. 85‐96) A geological context to the history of life (Rocks & depositional Reading on blackboard environments) Telling time: Stratigraphy, index fossils, & radiometric dating Pp. 149‐152, inside front cover, and reading on blackboard Fossilization: Skeletons, taphonomy, & Lagerstätten Ch. 1 (pp. 1‐17, 20‐30) Measuring diversity & creating diversity curves: Sepkoski & the Pp. 211‐218 Paleobiology Database Rarefaction & sampling biases Pp. 17‐24 Introduction to Sepkoskiʹs three evolutionary faunas & the Pp. 219‐220 & 225‐226 history of life The major lineages of life Inside back cover A brief history of earth: Tectonics, climate, & sea level Introduction to morphometrics, growth, & form Ch. 2 (pp. 31‐44) Morphological species Ch. 3 (Pp. 66‐83) Functional morphology & biomechanics Ch. 5 (pp. 121‐134) Growth & evolution: Ontogeny, allometry, & heterochrony Ch. 2 (pp. 44‐60) Theoretical morphology Pp. 135‐148 Cladistics & phylogenetic relationships Ch. 4 (pp. 96‐120) Comparing morphological & molecular phylogenies to the fossil Pp. 110‐112, 171‐173, 292‐293 record: Molecular dating, stratocladistics & confidence limits Measuring evolutionary rates Ch. 7 Evolutionary originations, key innovations & exponential Pp. 236‐241 diversification Cambrian radiation Pp. 287‐297 Morphological disparity Pp. 243‐247 Competition, biological transitions, &logistic diversification Pp. 220‐225, 242‐243 Background & mass extinctions & the Red Queenʹs hypothesis Pp. 180‐186 & ch. 8 (pp. 226‐236, 241‐242) Late Permian mass extinction Pp. 297‐305 Tempo & mode of evolution: Punctuated equilibrium Pp. 191‐199 Evolutionary trends & species selection Pp. 199‐210 Paleoecology: Communities, coordinated stasis, & climate change Ch. 9 (pp. 249‐264, 276‐282) Evolutionary paleoecology & long‐term trends in the ecological Ch. 9 (pp. 265‐275) history of life Conservation paleobiology, recent extinctions, & astrobiology Pp. 305‐319

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