12.491 is a seminar focusing on problems of current interest in geology and geochemistry. For Fall 2005, the topic is organic geochemistry. Lectures and readings cover recent research in the development and properties of organic matter.

The homeobox genes that define the basic body plan of mice and fruit flies are illustrated in this graphic from The Human Evolution Coloring Book by Adrienne Zihlman. The accompanying article describes how these genes act as molecular architects in all animal species.

This is an introduction to some of the issues faced when comparing different sets of phylogenetic hypotheses.

This workshop, which is half wet lab and half Internet lab, uses DNA sequences to examine the relatedness of different species. DNA from several insect and/or fish species are compared. This chapter includes instructions for extracting DNA from gels and making PCR products. We prepare PCR products to send to a computerized automated sequencing facility. (No radioisotopes are used in this sequencing!) We recover sequence from the facility over the Web as four-color graphics on a computer screen and as text. We make pair-wise DNA sequence comparisons between species with BLAST2 and multi-species comparisons with MultAlin. We see substitutions, insertions, and deletions. Then we make a distance-based evolutionary tree with GeneBee.

This course will look at the various mechanisms of evolution, how these mechanisms work, and how change is measured. The course will begin by reviewing the evolutionary concepts of selection and speciation. The student will then learn to measure evolutionary change and look at the history of life according to the fossil record and a discussion of the broad range of life forms as they are currently classified. Upon completion of this course, students will be able to: define evolution and describe different types of selection; provide examples of microevolutionary forces and describe how they impact the genetics of populations; describe the Hardy-Weinberg principle and solve problems related to Hardy-Weinberg equilibrium; provide examples of games used in evolutionary game theory; connect biological phenomena to game theory; develop simple phylogenies from molecular or morphological data; identify important evolutionary events that have occurred throughout geologic time; characterize and provide examples of major plant and animal phyla. (Biology 312)

This course describes biological changes that happen on a very large scale, across entire populations of organisms and over the course of millions of years, in the form of evolution and ecology. Upon successful completion of this course, students will be able to: Use their understanding of Mendelian genetics and patterns of inheritance to predict genotypes and phenotypes of offspring or work backwards to identify the genotypes and phenotypes of a parental generation; Distinguish between inheritance patterns that involve autosomal vs. sex-linked traits and identify the respective consequences of each type of inheritance; Identify what distinguishes DarwinŐs theory of evolution from other arguments that attempt to explain diversity across species and/or many generations; Identify which of many types of natural selection is acting on a particular population/species; Identify which of many types of sexual selection is acting on a particular population/species; Identify the factors that alter the frequencies of alleles in populations over time and describe the effects of these factors on populations; Recognize, read, and create phylogenies and cladograms, using them to explain evolutionary relationships; Determine the ecological interactions affecting a particular community and identify the effects of specific relationships (e.g. symbiosis, competition) on species within that community; Distinguish between world biomes in terms of their climate, nutrient cycles, energy flow, and inhabitants; Use their knowledge of nutrient cycles and energy flow to estimate the effect that changes in physical or biological factors would have on a particular ecosystem. (Biology 102; See also: Psychology 204)

In modern systematics, both morphological features and DNA or amino acid sequences are used to determine phylogenetic relationships. This two-week exercise demonstrates two methods used by systematists to create phylogenetic trees. In the first week students score morphological features of fictional and real organisms, create data matrices showing number of synapomorphies, and then use the matrices to draw phylogenetic trees. In the second week they use Bio Workbench, an online bioinformatics software package, to create phylogenetic trees based on nucleotide or amino acid sequences. Students learn how modern systematics helps answer questions about ecology, evolution, and behavior.

This module introduces the student to the concept of cladograms and phylogenetic trees. It explores some online bioinformatics tools that will produce tree diagrams.

This exercise introduces students to analysis of evolutionary relationships both by analysis of molecular similarity and by cladistic techniques. The molecular analysis uses both paper-and-pencil and bioinformatics comparison of the amino acid sequence of the hemoglobin beta chain of eight vertebrates. The cladistic exercises introduce students to cladistic principles, and then allow students to solve hypothetical problems both with and without homoplasy. Students then test their cladistic ability by analyzing published data on the flightless birds. Finally, students solve an entertaining problem using "organisms" made out of nuts and bolts.

This workshop demonstrates on-line use of the national electronic bulletin board, complete with electronic mail started in 1987 by the National Association of Biology Teachers. Once on-line, 14 special interest areas are available, such as AP- Biology, magazine and book reviews, ABT Journal, NABT membership services, question and answer forum, software reviews, and swap/sale of used equipment. Also available for downloading onto your computer are extensive files of labs, graphics, and handouts. Discussions of this and other databases will emphasize the power of these new professional communication tools. Note: This workshop is not included in the published proceedings volume because it was not submitted by the author.