Denné N. Reed
— Ph.D., Stony Brook University
- E-mail: firstname.lastname@example.org
T C 302 • Relig/Sci In Amer: Evol/Creatn
TTH 330pm-500pm MAI 220B
Starting with the late 17th century inquiries of Nicholas Steno, debate and discussion on the question of evolution raged in biology until the neo-Darwinian synthesis of the 1930’s established evolution by mutation, genetic drift, and natural selection as the consensus paradigm of modern biology and the organizing principle around which the discipline is based. The universal adherence to evolutionary principles in biology stands in stark contrast to popular perceptions, where only about half of the U.S. population accepts the basic tenants of evolution.
The goal of this course is to provide basic scientific and religious literacy in a single course that is team-taught by a physical anthropologist and a specialist in Biblical literature. We will examine the interplay between scientific and popular thought through the lens of the contemporary debate on evolution and human origins in the U.S. The course takes a broad look at how different religious traditions, including Christianity, Islam, Judaism, Buddhism and indigenous religions approach the question of origins, and how they interact with one another and with science. Through critical reading, civil discourse, and concise writing students explore the scientific basis of evolution; different definitions of science, religion and mythology; the debate on intelligent design; scientific and mythic cosmologies; the bases of epistemologies; the role of science and religion in morality and ethics; and contemporary politics surrounding science education.
Adler, M. J. & C. van Doren. 1972. How to Read a Book. New York: Touchstone.
Bagir, Z. A. 2005. Science and Religion in a Post-colonial World: Interfaith Perspectives. Adelaide: ATF.
Bowler, P. 2003. Evolution: The history of an idea. Berkeley: Univ. of California Press
Cunningham, M. K. 2007. God and Evolution: A Reader. New York: Routledge,
Dawkins, R. 2006. The God Delusion. New York: Bantam.
Doniger, W. 1999. The Implied Spider: Politics and Theology in Myth. New York: Columbia Univ. Press
Ferngren, G. 2002. Science and Religion: A historical perspective. Baltimore: Johns Hopkins Univ. Press
Iqbal, M. 2007. Science and Islam. New York: Greenwood Press.
Kurtz, P. 2003. Science and Religion: Are They Compatible? New York: Prometheus.
Lincoln, B.1989. Discourse and the Construction of Society: Comparative studies of myth, ritual and classification. New York: Oxford.
Wallace, B. 2003. Buddhism & Science: Breaking new ground. New York: Columbia Univ. Press.
This course seeks to develop three important skills: 1) critical thinking and the ability to analyze written and spoken arguments, 2) the ability to share ideas through discourse rather than heated argument with the aim of reaching greater understanding for all participants rather than coercive persuasion to a particular point of view, 3) the ability to craft a laconic, well-reasoned essay.
In pursuit of these goals the coarse requires students to annotate assigned readings and to keep a written journal with short entries (ca. 150-200 words) of reading notes and discussion questions for each class session, along with a brief summary of the in-class discussion. Journals are graded and account for 40% of the total grade.
Each class discussion is led and moderated by one student with help from the instructors. In preparation to lead a class discussion students must prepare written summaries of the readings, along with a list of major and minor discussion questions. This critical reading assignment accounts for 10% of the student’s grade.
Drawing on the critical reading assignment and the class discussion, the student is expected to write a well-crafted short essay (ca. 1000-1200 words) on the topic that was discussed. This essay may draw upon points raised during the class discussion but must be more than a mere summary of the discussion. The essay should reflect the student’s position on the topic and also provide evidence and reasoned argument in support of that position. The essay is due one week after the student moderates the class. Critique on the essay is provided by the instructors, a revised version of the essay is submitted and accounts for 25% of the student’s grade.
Students will apply their writing skills to a final exam covering major topics that arise in the course. The final exam will count for the remaining 25% of the students’ grades.
About the Professors:
Denné Reed is Assistant Professor in the Department of Anthropology who studies the influences of ecology and environment on hominin adapations and behavior. Denné conducts field work on human origins in Ethiopia, Tanzania, and Morocco.
Steve Friesen is the Louise Farmer Boyer Chair in Biblical Studies, Department of Religious Studies. His area of research is Christian origins. His special interests include apocalyptic literature, and economic inequality in the early Roman Empire.
Dikika Research Project
Early human evolution in Ethiopia.
In the remote Afar triangle of northeastern Ethiopia a team led by Zeresenay (Zeray) Alemseged has discovered spectacular fossil remains of a young Australopithecus afarensis. My work examines the micromammalian fauna associated with this fossil and the paleoecological context of our early adaptation and evolution. Our study area, called Dikika, is remarkably fossiliferous and every season yields exciting fossil discoveries. Check out Zeray's TED conference presentation!
Micromammal Spatial Ecology
Taphonomy and spatial distribution of rodents and insectivores in a savanna ecosystem.
This research in the Serengeti ecosystem of northern Tanzania examines the spatial abundance patterns of small mammals based on their occurence in owl-pellet assemblages. Owl pellets are an excellent and efficient method for biodiversity survey. Understanding the spatial ecology of small mammals that occur in owl assemblages provides the baseline data needed to improve our interpretation of fossil micromammal assemblages, many of which were created by owls hunting in the ancient past.
The process of fossilization in a savanna ecosystem.
Taphonomy is the study of how bones become fossils. Kay Behrehnsmeyer has been researching taphonomy in savanna landscapes for many years. Working with Kay and others in Amboseli I have been exploring the fate of small mammal remains accumulated by both mammalian and avian predators.
Grotte de Contrebandiers
Archaeozoology on the Atlantic coast of Morocco.
Grotte de Contrebandiers (Smuggler's Cave) preserves Middle Stone Age and Aterian artefacts. The Aterian is a stone tool culture spread throughout the Maghreb but it is poorly understood. Research at Contrebandiers seeks to understand the origin and context of the Aterian. My work focuses on archaezoological analysis of the micromammals from Contrebandiers and their implications for past environments at the site.
Vegetation structure in modern savanna ecosystems.
The study of modern savanna ecosystems plays a critical role in understanding paleoenvironments and the ecological context of human evolution. Using satellite imagery and GIS data, I have been exploring vegetation structure in the Serengeti Ecosystem. pdf. serengeti vegetation map.
In reverse chronological order
Reed DN, and D Geraads. 2012. Evidence for a Late Pliocene faunal transition based on a new rodent assemblage from Oldowan locality Hadar A.L. 894, Afar Region, Ethiopia. Journal of Human Evolution 62(3):328337. doi: 10.1016/j.jhevol.2011.02.013. pdf
Reed DN 2011. New murid (Mammalia, Rodentia) fossils from a late Pliocene (2.4 Ma) locality, Hadar A.L. 894, Afar Region, Ethiopia. Journal of Vertebrate Paleontology 31(6):13261337. doi: 10.1080/02724634.2011.620676. pdf
Reed D, Denys C. (2011) The taphonomy and paleoenvironmental implications of the Laetoli micromammals. In: Harrison T, (Ed.) Paleontology and Geology of Laetoli: Human Evolution in Context. Volume I: Geology, Geochronology, Paleoecology & Paleoenvironment. Springer, Dordrecht, The Netherlands. pdf
Reed D. (2011) Serengeti micromammal communities and the paleoecology of Laetoli, Tanzania. In: Paleontology and Geology of Laetoli: Human Evolution in Context. Volume I: Geology, Geochronology, Paleoecology & Paleoenvironment. Springer, Dordrecht, The Netherlands. pdf
McPherron SP, Alemseged Z, Marean CW, Wynn JG, Reed D, Geraads D, Bobe R, and Bearat, HA. (2010) Evidence for stone-tool-assisted consumption of animal tissues before 3.39 million years ago at Dikika, Ethiopia. Nature 466(7308):857-860. doi: 10.1038/nature09248. pdf
Reed DN, Barr WA. (2010) A preliminary account of the rodents from Pleistocene levels at Grotte des Contrebandiers (Smuggler's Cave), Morocco. Historical Biology. 22:286-294. pdf
Geraads D, Alemseged Z, Bobe R, Reed D. (2010) Nyctereutes lockwoodi n. sp., a new canid (Carnivora: Mammalia) from the middle Pliocene of Dikika, Lower Awash, Ethiopia. Journal of Vertebrate Paleontology. 30(3):981-987. doi:10.1080/02724631003758326. pdf
Reed D, Anderson TM, Dempewolf J, Metzger K, Serneels S. (2009) The spatial distribution of vegetation types in the Serengeti ecosystem: The influence of rainfall and topographic relief on vegetation patch characteristics. Journal of Biogeography.36(4):770-782. pdf
Wynn JG, Roman DC, Alemseged Z, Reed D, Geraads D, Munro S, (2008) Stratigraphy, depositional environments, and basin structure of the Hadar and Busidima Formations at Dikika, Ethiopia. In: Quade J, Wynn J, (Eds.) The Geology of Early Humans in the Horn of Africa. Vol. 446. Geological Society of America, Boulder, Co. pp. 87-118. pdf (large 4.6 MB)
Anderson TM, Dempewolf J, Metzger KL, Reed DN, Serneels S. (2008) Generation and Maintenance of Heterogeneity in the Serengeti Ecosystem. In A. Sinclair (ed). Serengeti III: The Future of an Ecosystem. Chicago: University of Chicago Press. pdf (large 4.4 MB)
Reed DN. (2007) Serengeti micromammals and their implications for Olduvai paleoenvironments. In: R Bobe, Z Alemseged and K Behrensmeyer (eds.) Hominin environments in the East African Pliocene an assessment of the faunal evidence. New York: Kluwer Academic Press. pdf
Wynn JG, Alemseged Z, Bobe R, Geraads D, Reed D, Roman D. (2006) Geology and palaeontological context of a Pliocene juvenile hominin at Dikika, Ethiopia. Nature 443:332-336.
Alemseged Z, Spoor F, Kimbel W, Bobe R, Geraads D, Reed D, Wynn J. (2006) A juvenile hominin skeleton from Dikika, Ethiopia. Nature 443:296-301. pdf
Alemseged Z, Wynn JG, Kimbel WH, Reed DN, Geraads D, Bobe, R. (2005) A new hominin from the Basal Member of the Hadar Formation, Dikika, Ethiopia, and its geological context. Journal of Human Evolution. 49:499-514.
Reed DN. (2005) Taphonomic implications of roosting behavior and trophic habits in two species of African owl. Journal of Archaeological Science. 32:1669-1676. pdf
Geraads D, Alemseged Z, Reed D, Wynn J. (2004) The Pleistocene fauna (other than Primates) from Asbole, lower Awash Valley, Ethiopia, and its environmental and biochronological implications. Geobios. 37:697-718. pdf
Reed D. (2003) Micriomammal Paleoecology: Past and present relationships between African small mammals and their habitats. PhD thesis. Stony Brook University. pdf
This page provides links to helpful web resources.
Guides and HOWTOs
Links to instructional pages.
- SQLite - DBVis MINI HOWTO A short guide on how to connect to SQLite databases using DBVisualizer.
Data, schemas and resources for bioinformatics
- Biodiversity Collections Index a central index of biological collections. Part of GBIF's Global Biodiversity Resources Discovery System (GBRDS).
- Biodiversity Information Standards, also known as the Taxonomic Databases Working Group (TDWG), is a not for profit scientific and educational association that is affiliated with the International Union of Biological Sciences.
- Chronos Geochronology working group.
- Darwin Core data structure and schema for biodiversity developed and maintained by the TDWG.
- DELTA DEscription Language for TAxonomy. One of the first computer implimentations of a taxonomic system.
- DiGIR Distributed Generic Information Retrieval. Biodiversity web services. A client/server protocol for distributing biodiversity data.
- Dryad an online repository for published datasets in the basic and applied biosciences.
- eSkeletons a digital database for comparative morphology.
- ESRF Virtual Database a digitial specimen database for the European Synchrotron Radiation Facility.
- ETE database the Evolution of Terrestrial Ecosystems database at the Smithsonian.
- GBIF the Global Biodiversity Information Facility. Making biodiversity data available on the net.
- Global Mammal Parasite Database a comprehensive collection of host-parasite records from the published scientific literature and supplemented with original data on taxonomy, sampling localities, and parasite characteristics, such as transmission mode. The data can be used to investigate mammalian socioecology, parasite "spillover" to humans, and human evolution.
- MaNIS the Mammal Networked Information System. Data services on mammal biodiversity.
- Morphobank an online workspace for phylogenetic research on phenotypes (e.g., morphology, behavior, development). A web application and database, it has a user-friendly interface for collaboration on phylogenetic matrices in real time in a private workspace, and intuitive media tools.
- Morphobrowser a web tool tool for exploring digital morphological datasets.
- Nomenclator Zoologicus a comprehensive database of taxonomic Genera since Linnaeus.
- NOW the Neogene of the Old World database
- NYCEP Morphometrics Group (NMG) a loose association of researchers who share an interest in analyzing morphological evolution of primates using three-dimensional geometric morphometric (3D GM) methods; GM is an approach to the quantitative interpretation of form utilizing coordinate data, which thus retains the relative placement of structures under study.
- PaleoanthPortal provides links to active databases in paleoanthropology. The plan is for it to serve as a portal through which users may search such databases from a single entry point without visiting their sites directly; this may direct users to those databases which contain information of the type sought and avoid those which don't.
- Paleobiology Datase a comprehensive database of paleontological occurrences, as reported in the paleontological literature.
- Paleontology Portal a web portal for all things paleontological.
- PRIMO the NYCEP PRImate Morphometrics Online database, is an open-access resource for a range of data types. Caliper data on teeth and skulls of cercopithecids (and a few hominoids) are posted now, and 3D Microscribe digitizer landmark data are being prepared for inclusion. Surface scans (as well as digital images) will be available later, as will additional geographical information.
- RHOI specimen database the database for the Revealing Hominid Origins Initiative.
Computer programming languages, IDEs, libraries
- Python An elegant language and perfect for acdademic programming
- R A not-so-elegant but very powerful statistical programming language. Excellent for ecology and paleobiology.
- R Studio An excellent cross platform IDE for R
- Tinn-R A Windows based editor and IDE for R. For you poor souls who don't (yet) have macs.
- ggplot2 Hadley Wickham's grammar of graphics. The best way to make plots in R. See also Andrew Barr's basic introduction to using ggplot2.
- reshape Another great R package from Hadley Wickham for structuring data.
- RPy A simple, yet robust, python interface to the R programming language. Two great tastes that taste great together.
- Julia A high level programming language similar to python, perl and java.
- Eclipse Cross-platform programming IDE for Java, C++, and Python (with PyDev)
- PyDev A plugin to Eclipse that provides functionality for Python and Jython programming.
- Boa Constructor Cross-platform IDE and GUI development for Python.
- Xcode Apple's excellent IDE and GUI development platform. Now supports python via PyObjC.
- Jython A wrapper for Python in Java
- REALBasic If you simply must use basic. Nice GUI development and DB integration.
- Python vs. Java? Comparison between the two languages.
- TeXshop Typsetting for the fierce.
- LyX The only way to LaTeX! A great open source document processor. What you see is what you mean
- Sweave Embed R in your Lyx documents. That's right, dynamic document production with embedded R code!
- Reproducible Research A new approach to scientific publishing.
- JabRef Cross-platform bibtex database management tool.
- LaTeX bibliography database A database of LaTeX bibliographic styles for different journals.
- fink Open source package management tool for mac.
- gentoo Brass knuckles linux distro for those who like to customize...everything! Great documentation and online support.
- ubunto User friendly linux distro for those who don't need an extra headache.
- Red Hat Tried and true enterprise ready linux distro.
HTML editors, Web Application Servers
- Taco A nice, lightweight HTML editor for Mac.
- Django Pythonic web application framework. Fantastic.
- Zope A python based web application server.
Database management systems, DB clients
- SQLite An open-source, light-weight, cross platform database engine
- SpatiaLite A spatially aware open-source database engine.
- PostgreSQL An open source relational database management system (RDBMS) that is geospatially enabled.
- PostGIS PostGIS adds support for geographic objects to the PostgreSQL object-relational database.The stuff that makes PostgreSQL geospatially enabled.
- XMLSpy A windows based XML editor
- oXygen A mac based XML editor
- DBVisualizer Cross-platform database administration and editing tool.
- Database Spy Windows based database administration and editing tool. From the makers of XML Spy.
File servers, web servers and project resources
- University of Texas Laits File Server File server for collaborative projects. Hosted at: file.laits.utexas.edu, ip:126.96.36.199. Accessible via ssh, sftp.
- SSH Free ssh and sftp client for windows. This is the software needed to connect to the UT (and other) project file server.
- FUGU Free sftp client for Mac. Note that you can also use ssh, sftp, rsync from the command line in a mac terminal window. rsync is ... powerful.