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Fall 2015 Courses

Evolutionary Biology (Bio 444/544):
The required textbook will be the 2nd edition of Zimmer and Emlen, "Evolution: Making sense of life".  The 2nd edition is not yet available, but it is due in July.

General Biology (Bio 111):

There is no textbook for this course.  Instead, there will be many handouts and several video screencasts.  If you are curious, here are last year's handouts and videos.

Bio 344, Ecology (spring 2015)

Graded 3rd proposals are available from the Biology Secretary.

The grading scale:  90-100% A, 80-89% B, 70-79% C, 60-69% D, ≤59% F.  As noted on the syllabus, plus and minus grades were not given. 

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),  Exam #2 key (2 Mar),  How to write a research proposal: The Bold Remix (4 Mar),  SIR model of epidemics (4 Mar),  Climate change (23 Mar),  Global C cycle (23 Mar),  Problem set (25 Mar),  Exam #3 Key (30 Mar),  Discussion of Paper #3 (1 Apr),  Geoengineering using sulfate (10 Apr),  What happens if we burn all the fossil fuel? (13 Apr),  Problem set (15 Apr),  Exam #4 key (20 Apr)

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.  [The methods are more clearly explained in the Appendix.]   (29 Apr)

Slides used in lectures:  
Thermal ecology (26 Jan),  Rainforests (9 Mar),  Cedar Creek LTER (11 Mar),  Ant mutualisms (11 Mar),  Lago Guri (13 Mar),  Trophic downgrading (13 Mar)

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.  Human demography, population growth rate, and economics.
Tilman et al. 1997.  The influence of functional diversity and composition on ecosystem processes.
Estes et al. 2011.  Trophic downgrading of Planet Earth.
Robock et al. 2009.  Benefits, risks and costs of stratospheric geoengineering.
Matthews et al. 2009.  The proportionality of global warming to cumulative carbon emissions.
Greenstone. 2015.  If dig out all our fossil fuels, here's how hot we can expect it to get.
McGlade and Ekins. 2015.  The geographic distribution of fossil fuels unused when limiting global warming to 2 degrees C.
De-extinction?  Beth Shapiro's Paleogenomics Lab.

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)

The graded final exams are available from the Biology Secretary (2nd floor Jones Annex).

You cannot get your graded exam, or your exam score, or your course grade, directly from me.

The grading scale: 90-100% A, 80-89% B, 70-79% C, 60-69% D, ≤59% F. As noted on the syllabus, plus and minus grades were not given. 

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),  Synapses (4 Mar),  Sensory physiology (9 Mar),  Muscles (13 Mar),  Problem set (23 Mar),  Exam #3 Key (27 Feb),  Exercise physiology (30 Mar),  Problem set (1 Apr),  Energy for muscle contraction (6 Apr),  Evidence for evolution (8 Apr),  Exam #4 Key (15 Apr),  Natural selection (22 Apr),  Problem set (27 Apr),   Final Exam Key (7 May).

Slides used in class (date first used):

Development (23 Jan),  Hox genes (26 Jan),  Aplysia and neurons (9 Mar),  Muscles (13 Mar),  Evidence for evolution (10 Apr),  Your inner fish [slides from chapters 1 and 2] (17 Apr).

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.
Tutoring hours, at the NMT Office of Student Learning

Highly recommended specific sources:
Gene expression
Animation of transcription
Hox genes and body patterns
Signal transduction pathways
Menstrual cycle
Action potential videos:  1,  2,  3.
Screencasts on muscle structure and function:  1,  2,  3.
Evolution,  Mutations,  Natural selection.

Other sources:

Review of molecular genetics
Hox genes in development
Neuroscience Online: Chapters 1-3 and  6.
TalkOrigins:  Radiometric datingTransitional formsAnatomical vestiges.
Books: Why evolution is true;  Understanding Evolution;  Your Inner Fish.
Tiktaalik, a transitional fossil between fish and amphians.
MRSA (methicillin-resistant Staphylococcus aureus).
Westendorp and Kirkwood. 1998. Human longevity at the cost of reproductive success.

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.    Don't study passively.  Instead, quiz yourself, over and over.

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.