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Friday 27 Feb 2015:
   No Bio 112 lecture class today.
   No Bio 344 Ecology class today.  The 2nd Ecology exam is postponed until next Monday 2 Mar 2015.

Bio 501, Graduate Seminar, Rapid Evolution

Schedule of paper discussions (discussion leader):
26 Jan   Kawecki et al. 2012.  Experimental evolution.
2 Feb   Yeaman et al. 2010.  No effect of environmental heterogeneity on the maintenance of genetic variation in wing shape in Drosophila melanogaster.   (Thomas)
9 Feb   Sniegowski et al. 1997.  Evolution of high mutation rate in experimental populations of E. coli.  (Karen)
16 Feb  Burch and Chao. 1999.  Evolution by small steps and rugged landscapes in the RNA virus phi 6.  (Danielle)
23 Feb  Lenski and Travisano. 1994.  Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations.  (Kirk)
2 Mar  Grant and Grant. 1993.  Evolution of Darwin's finches caused by a rare climatic event.  (Kirk)
9 Mar  Grant and Grant.  2002.  Unpredictable evolution in a 30-year study of Darwin's finches.  (Kirk)

Bio 471, Senior Seminar

Handouts:  Syllabus,  How to give a talk,  Example diagrams,  Grading rubric.

Schedule of talks (speakers):
21 Jan   Faculty leader talk (Kirk).
28 Jan   Max group (Max and Jered), Kayla group (Kayla and Arianna).
4 Feb    James group (James and Robert), Marena group (Marena and Paige).
11 Feb   Lisa group (Lisa and Shannon).   Faculty leader talk (Kieft). 
18 Feb   Kayla group (Reina and Joseph),  James group (Jolene and Sean).
25 Feb   Marena group (Natasha and Enrique),  Lisa group (Danielle and Steven).
4 Mar    Max group (Ashley and Sabrina).  Faculty leader talk (Voyles). 
11 Mar  2 group talks.
25 Mar  2 group talks.
1 Apr    1 group talk.  Faculty leader talk (Rogelj). 
8 Apr    2 group talks.
15 Apr  2 group talks.
22 Apr  1 group talk.

Bio 344, Ecology (spring 2015)

Required handouts (date assigned):
Syllabus (12 Jan),  First day questions (12 Jan),  Thermal ecology (14 Jan),  Problem set (16 Jan),  How to read a scientific paper (21 Jan),  Discussion of paper #1 (23 Jan),  Photosynthesis (26 Jan),  Problem set (30 Jan),  How to write a research proposal (2 Feb),  Example research proposal (2 Feb),  Problem set (4 Feb),  Demography (9 Feb),  Survival, mortality, fecundity (11 Feb),  Age structure (11 Feb),  Problem set (13 Feb),  How to use gapminder (13 Feb),  1st exam key (16 Feb),  Problem set (16 Feb),  Population growth equations (18 Feb),  Problem set (23 Feb),  Discussion of paper #2 (25 Feb)

Required papers (date of discussion):
#1:  Deutsch et al. 2008. Impacts of climate warming on terrestrial ectotherms across latitude.  Detailed methods.  (23 Jan)
#2:  Zanette et al. 2011.  Perceived predation risk reduces the number of offspring songbirds produce per year.  Detailed methods and video.  (25 Feb)
#3:  Terborgh et al. 2001.  Ecological meltdown in predator-free forest fragments.  (1 Apr)
#4:  Natali et al. 2014.  Permafrost degradation stimulates carbon loss from experimentally warmed tundra.  (29 Apr)

Slides used in lectures:
Thermal ecology (26 Jan)

Sources cited in lectures:
Paladino et al. 1990.  Metabolism of leatherback turtles, gigantothermy, and thermoregulation of dinosaurs.
Casey et al. 2014.  Behavioral and metabolic contributions to thermoregulation in freely swimming leatherback turtles at high latitudes.
Portner and Knust. 2007.  Climate change affects marine fishes through the oxygen limitation of thermal tolerance.  (eelpout study)
Jones et al. 2014. Diversity of ageing across the tree of life.
gapminder.org:  Human demography, population growth rate, and economics.  Gapminder World, the graphical tool.  "200 years that changed the world", an introductory video.

Other resources:
Last year's exam keys.
Hallman et al. 2014.  Declines in insectivorous birds are associated with high neonicotinoid concentrations.  (The example research proposal is based on this paper).
Natural Resources Defense Council:  An effective group of environmental lawyers and biologists.
Three of the best environmental law programs:  Lewis and Clark,  University of Vermont,  UC Berkeley.

Bio 112, General Biology II (spring 2015)

Required video (date assigned):  Control of gene expression (14 Jan).

Required handouts (date assigned):  

Syllabus (12 Jan),  First day questions (12 Jan),  Control of gene expression (14 Jan),  The big picture (16 Jan),  Problem set (21 Jan),  Animal development (23 Jan),  Hormones (28 Jan),  Problem set (2 Feb),  Exam #1 key (4 Feb),  Blood sugar regulation (6 Feb),  Signal transduction (9 Feb),  Problem set (13 Feb),  Female reproductive cycle (16 Feb),  Neurons (18 Feb),  Problem set (23 Feb),  Exam #2 key (25 Feb)

Slides used in class (date first used):

Development (23 Jan),  Hox genes (26 Jan)

Recommended general sources:

An introductory textbook for biology majors.  Two good examples are Campbell et al., and Sadava et al.
Glossaries of biological terms:  1,  2.
Screencasts on muscle structure and function: 1,  2,  3.
Science and creationism (National Academy of Sciences).
Evolution is change in the inherited traits of a population through successive generations (nature.com).
nature:Education:  EvolutionMutationsNatural selection.
TalkOrigins:  Radiometric datingTransitional formsAnatomical vestiges.
Why evolution is true.    Understanding Evolution.    Your Inner Fish.

Teaching and learning

Minerva University: A new 4-year college that teaches skills, not facts.  It may be a glimpse of what will replace typical colleges and universities.
The future of college?  An article in The Atlantic about Minerva.

Oakley (2014).  A mind for numbers: How to excel at math and science (even if you flunked algebra).   An excellent book on the neurobiology of learning, with practical advice.
Rules of good (and bad) studying, by Barbara Oakley.
Richard Felder's research on science and engineering education.

Karpicke and Blunt (2011).  Retrieval practice produces more learning than elaborative studying with concept mapping.    Students: Don't study passively.  Instead, quiz yourself, over and over.  Teachers: Quizzes and exams help students learn.

Belluck (2011).  To really learn, quit studying and take a test.  A New York Times article about the findings of Karpicke and Blunt (2011).

Tufte E. The Cognitive Style of PowerPoint.  
PowerPoint weakens reasoning.  Never read aloud from slides.

Excellent books

Austad SN. Why We Age. Both the physiological why and the evolutionary why.
Brand, S. Whole Earth Discipline: An Ecopragmatist Manifesto.   Only science and engineering can solve environmental problems.
Csikszentmihalyi M. Finding Flow.   Happiness comes from doing difficult things.
Dawkins R. The Selfish Gene.   Evolution is stranger than you thought.
Diamond J. Guns, Germs, and Steel.  Why didn't Native Americans invade Europe?
Kelly, K. What Technology Wants.  Biology and technology are inseparable.
Simpson, GG.  Quantitative Zoology.  A classic, readable introduction to the biological applications of statistical methods.
Vogel S. Life in Moving Fluids.   The interface between physics and biology.
Weiner J. The Beak of the Finch.   A lifetime of field work on the evolution of Galapagos finches.
Weiner J. Time, Love, Memory.   How to be an experimental biologist, and why fruit fly behavior matters.
Wilson EO. The Social Conquest of Earth.  Ants and humans rule because of their social structures.  Group selection can work.