Class resources

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Lecture 2: Scientific method

Lectures 5-6: Scientific method & responsible conduct of research

Lectures 7-8: Scientific writing

Lectures 9-10: Evolutionary genetics

Lecture 11: Directed and random mutation (Cairns et al.)

Lecture 12: Introduction to identification of genetic basis of adaptation


Assignment 1:

Example SURF application

Writing an effective review (Neill (2009))

Assignment 2:


Assigned reading:

Reading for Feb 17/19: de Visser et al (1999) Diminishing returns from mutation supply in asexual populations. Science 283: 404-406

Reading for Feb 26: Cairns et al. (1998) The origin of mutants. Nature 335: 142-145 

Reading for March 3 & 5: Bjedov et al. (2003) Stress-induced mutagenesis in bacteria. Science 300: 1404-1409

Reading for March 10 & 12: Barrick et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247.

Reading for March 31 / April 2: Lieberman et al. (2011) Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nature Genetics 43: 1275-1281. For some background, see also: Lenski R.E. (2011) Chance and necessity in the evolution of bacterial pathogen. Nature Genetics 43: 1174-1176.

Reading for April 7 & 9: Kurenbach et al. (2015) Sublethal exposure to commercial formulations of the herbicides Dicamba, 2,4-dichlorophenoxyacetic acid, and glyphosphate cause changes in antibiotic susceptibility in Escherichia coli and almonella enteric server Typhimurium. mBio 6: e00009-15. Presentation in popular press:

General Reading/Study Materials:

Office for Research Integrity: Introduction to the Responsible Conduct of Research

"On Being a Scientist: Responsible Conduct in Research" Proceedings of the National Academy of Sciences USA (1995)

Almossawi A. An Illustrated Book of Bad Arguments. 

Brownell SE et al. (2014) How students think about experimental design: Novel conceptions revealed by in-class activities. Bioscience 64: 125-137. Discussion of the 'intermediate' experimental design and analysis in-class test.  

Gopen G and Swan J (1990) The science of scientific writing. American Scientist 78: 550-558

Hurlbert SH (1984) Pseudoreplication and the design of ecological experiments. Ecological Monographs 54: 187-211. General argument for the importance of properly accounting for experimental design before drawing conclusions

Marvier M (2002) Improving risk assessment for nontarget safety of transgenic crops. Ecological Applications 12: 1119-1124. Demonstration of the importance of not interpreting an absence of evidence as evidence of absence.

Sutherland WJ, Spiegelhalter D and Burgman M (2013) Twenty tips for interpreting scientific claims. Nature 337: 335-337

Willingham (2007) Critical thinking: why is it so hard to teach? American Educator, Summer: 8-19



Grading rubric (use as is useful for peer-review of other students work)