Schedule for Fall 2005

MONTH	DATE (Articles to Read)	CHAPTER PowerPoint links	TOPIC References for Class and Links to Informative Web Sites
Sept	1	Handouts PowerPoint	Discussion of course: syllabus, Overall objectives Writing objectives and procedures Web & e-conference instructions Scientific methods: experiments, theory, surveys; models and assumptions, testing, usefulness vs. correctness, types of variation. Scientific models: descriptive, linear, branched, feedback loops, complex (lag times, nonlinear relations and interactions), etc.
	6 (Seats assigned)	Handouts PowerPoint	Experiments and Demonstrations: Complexities of gene action to produce a phenotype Chromosome Structure and Cell cycle structure and dynamics: How can a chromosome that is several centimeters long coil for movement in mitosis or meiosis spindle that extends only one or two micrometers across? How does the positioning of the centrioles play a central role in differentiation of cells? How do adjacent cells participate in the differentiation of their neighbors? How can cells that are far away affect the differentiation patterns during G1?
	6 (Seats assigned)	Leading question	DNA structure as an active response to the environment in which it resides; how is it different from and the same as a parasite or you?
	8 (attendance taken from today forward)	Read: handouts, assignments as described on supergenes PowerPoint	Analysis of AgBioForum and other ways to establish reliability and credibility; From UT Library Journals, you can search for Primary journals and also in some cases read them directly online: Nature, Nature Biotechnology, Science, Cell, Developmental Biology Review and "News" journals: Science News Media: *New York Times, The Guardian, others (compare US papers with others in Europe for different versions of a story) NOTE: you may need to enter through the UT PCL online journals since these require a subscription fee. You may need to do this from a campus computer. If so, enter from http://www.lib.utexas.edu/journals/fulltext/search.html and select the appropriate service. Cell processes and control systems -- genes to phenotypes, many scales!
	13	Read: handouts, assignments as described on supergenes & in class PowerPoint	Reliability of information sources! More discussion. Systems that translate genetic information into cell processes. Check the index of your textbook for related reading. How do jumping genes jump? What conditions determine if other genes can "jump"? What are some consequences of a gene jumping, and how do we know? Track the multiple scales of gene control and ways genes are expressed in the cell and cell differentiation.
	13		Note the changes over time in the diagrams of interactions!
	15 Science & Business-- Chap. 13 (A Different Universe)	Read: handouts, assignments as described on supergenes & in class PowerPoint	Example of new techniques, new features (yeast vibrating); Why did Mendel use the pea, and how did he choose the things he looked at? What did he assume in order to predict the results (or show how a model could be used to predict them)? What "makes" a phenotype of a particular trait? What are the assumptions to create a Mendelian model for such predictions? Can a phenotype of one species require the presence of other species for it to appear? Explain your perspective with examples or conditions that allow or prevent this extension beyond an individual.
	15 Science & Business-- Chap. 13 (A Different Universe)		What is the Central Dogma, and how has it been modified so that we don't consider it either "central" or a general description of the role of genes in determining complex phenotypes (such as formation of tissues and organs)?
	20 1-Mitotic Spindle, 2- What is Science	Handouts on small RNAs, signal proteins PowerPoint	Gene transcription, formation of mRNA, translation into polypeptides: Role of many other genes for function of transcription at a single locus; Role of timing and movement of molecules and complexes of molecules from cytoplasm to nucleus for transcription; Role of "molecular signals" in transcription, translation, transport of molecules needed in the processes, and molecules resulting from the processes.
	22 Public and Scientific Uncertainty	PowerPoint	Multiple functions of *individual* genes - Developmental control, tissue differentiation, organ formation, "quality control" of the tissue-forming cells, cancer, pleiotropy. Most of DNA is not protein coding (only 1%). What is function of the remaining 99?
	22 Public and Scientific Uncertainty	PowerPoint	Note writing assignment and way to submit it via mailing list.
	27 1- Crossover control 2- ER Chaperones (Protein folding)	PowerPoint	Essays and describing processes, their genetic basis, their regulation of function, and their localization in a cell. Suggestions for writing scientific essays, even when you are expressing your own perspective. How does a blender making a mouse smoothie destroy life? +Where is the "genetics" located in a living organism?
	29 Chap. 12	Chap. 12 PowerPoint	Lac operon and Arg regulon; DNA replication initiation, shape changes; living support system and external conditions for functions.
	29 Chap. 12	Analysis/Focus questions	(Note: electronically turn in revised Analysis/Focus answers by Oct. 7)
Oct	4	Review, see Chaps. 10, 11, 12, 13, 14 PowerPoint	Review of how networks are created in similar ways in both prokaryotes and eukaryotes, and examples of their dynamics; many genes, cell localizations, signals to coordinate, etc. "How the blender changes the mouse." Bring "life" to the cartoons in preparation for Exam 1 essays.
	6 lac operon as a model NatGeograp-Flu Telomeres	Chap. 23 PowerPoint	Eukaryotic gene structure, relation of structure to diversity of gene products from a single "gene" and Immunoglobulin loci as examples. Bringing the concepts into the larger context. Study groups and discussion sections.
	11 1-Biofilm, 2-Bacterial Communication, 3-Symbiosis, 4-Evolution by Vertical Transmission, 5-Gut Bacteria, 6-Symbiosis Doctrine, 7-Cobweb of Life, 8-Comment-Cobweb of life	PowerPoint	Extended Organism: Systems within and among organisms that are integrated symbiotically, and evolutionarily. A "free living" organism is an oversimplification caused by viewing only part of what is required for living, adapting, and surviving.
	13 1-lac operon Dynamics, 2-Re-staging Mitosis Progression 3-Reference for Ques. 3 of exam	PowerPoint	Strategies and expectations for exam essays
		PowerPoint	(Exam 1 questions distributed electronically, but must be written in class on Thursday, Oct. 20. Use references linked from Schedule, class handouts, plus textbook or that you otherwise select, & evaluate reliability and credibility as instructed.)
	18	PowerPoint	Immune loci and introduction to the molecular gynmastics; relationship to systems, somatic mutation, cell selection.
	20		Exam 1-- Essays, written in class, open book, notes, handouts
	25 1- Founder Mutations 2- Steve Jobs 3- Telomerease 4- Retoblastoma	PowerPoint Questions (last slide)	Completion of Ig-loci; Mutation repair systems, practice questions connecting systems in time and scale
	27 1- small DNA mutations and disease	PowerPoint	Asking the right questions and fitting the chromosome dynamics into the cell cycle. (Note the handout link and ponder the ways these DNA variations might be functionally related to the diseases. Be prepared to discuss these in class next Tuesday. How does this discovery modify the concept of inheritance of Mendelian genes?
Nov	1 1- Insights of Cell Division 2-Chaperone-passing thru membrane 3-Sculpting Membranes	PowerPoint Chapter 21	Mutations: DNA to cell systems -- effects on function of information transfer, physical transport in cell space, phenotypes of function. Mutation "repair" or modifying mutation expression in a system. Prospects for genetic engineering in practice - hype or realism.
	3 1 - Cobweb Of Life 2 - Diversity	PowerPoint	Mutations: Transposons as mutagens, as sources of genetic diversity for adaptation and evolution.
	8 1 - Mitosis History 2 - Cytokinesis Contractile Machinery	PowerPoint	Transposons are almost half of the DNA in the human genome, and come in different "kinds." They can move in their location, increase or decrease their number, inactivate other genes, and many other "strange behaviors" normally considered in genetics. They are "normal" in most species and can include DNA copied from RNA viruses. My "body" is 90% bacterial cells, my genome is nearly 50% genes that can create novel properties in my body, and may be acquired after I am born as well as picked up similarly from individual acquisitions in my ancestors. Where do "I come from," and "who am I related to" are profoundly different than "just" philosophical or geneological questions. Discussion of writing essays about processes, their control, and supply lines.
	10 1- Genetic Engineering 2- DNA replication dynamics in the cell 3- Chromosome dynamics in gene activity	PowerPoint	Discussion of exam, learning from the exercise, and ways to plan for remainder of semester; GMO testing, assumptions and critique of testing, potential in science, in economic potential, and detrimental effects of misleading advertising, regulation, and inappropriate timing of economic drivers today. Note the references, the last two have been annotated with comments for you. Open the pdf files, and the yellow highlighting is an area with an associated comment. Hold our "hand" pointer (also used to move the page up or down in the Acrobat Reader) over the highlighted text, and the comment will appear for you to read. These comments will help you learn how to read articles and extract the parts most relevant to this class.
	15 1- Exam 2 2- DNA forms 3- Protein Transfer Pores 4- Mammal X-chromosome inactivation	PowerPoint	Body organization systems of differentiation, genetic systems involved, parallels between insects and mammals.
	17 1- Plague & HIV resistance 2- European HIV SmallPox-Resistance-2003 3- Engineering Biology 4-Contractile-Cell Division	PowerPoint	Discuss Exam 2, forms of DNA and properties, nature of signals to organize a complex system from chemical interactions to differentiation of a body. Writing with metaphors and models. Telling a "story" from cartoons using scientific models as (and with) metaphors.
	18		2nd Exam preparation and review, Burdine 228, 1:00-2:00pm (and longer, as needed)
	22		Exam 2-- Essay, written in class, open book, notes, handouts
	23		Thanksgiving Day
	29 1- Nature-Bias from Money 3- Peer Review 4- DNA replication 5- Nature-siRNA protects mRNA in cell during transport to site of protein syn.		Comments on last exam, discussion of ways to improve your grade on final, and in class. MUST KNOW FOR FINAL: "Signals" in biology, multiple examples, difference between mouse and mouse "smoothie" (cell organization, differentiation, molecular transport, cell recognition of an "environment", cell's response(s) to recognition a particular environment (outside cell, inside cell), "need" for synthesis and transport of DNA, RNA, protein, lipids, localization of cell components in pores, vacuoles, endoplasmic reticulum, "which-when-where-howmuch" control in gene regulation, cell division, fertilization, cell movement, cell's recognition of "self" in space and time, i.e. "its environment" - and more). Examples are to be based on handouts, text and class discussion for "specifics" but presence must be recognized in places we do not know in detail, but can surmise.
Dec	1 return Exam 2	PowerPoint
	6 1- Final Exam Dog References	PowerPoint	Note that there are 4 references (pdf files) linked here on dog evolution that may help you on Question 2 of your Final Exam.
	8 Univ. Closed		Review, course evaluation
	15 9:00-noon	Burdine 130	Final Exam: - written during specified time. Turn in references unless from class handouts or text.

Approximate Lecture Schedule, Fall Session '05 (Incomplete, will evolve with class)

Approximate Lecture Schedule, Fall Session '05
(Incomplete, will evolve with class)