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Bio 111, General Biology I (fall 2014)

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

Your grade is available from NMT Banner.

From the syllabus:  "Course grades will be based on the average of the six exam grades, using the following scale: 90-100% A, 80-89% B, 70-79% C, 60-69% D, ≤59% F. If necessary, the scale will be shifted down (curved) until the top 10% of students receive an A. Plus and minus grades will not be given."  No curving was needed.

The final exam key is here

You can pick up your graded final exam from the Biology Department secretary from 9 am Friday 12 Dec through the second week of spring semester.

Required videos (date assigned):
Biochemicals (25 Aug),  Membrane transport (15 Sep),  Thermodynamics (29 Sep),  Kinetics (3 Oct),  Aerobic respiration (20 Oct),  Anaerobic fermentation (29 Oct),  Complex inheritance [all except codominance] (14 Nov)

Required handouts (date assigned):
Syllabus (18 Aug),  Chemical bonds (20 Aug),  Problem set (22 Aug),  Biochemical structures (27 Aug),  Biochemical functions (27 Aug),  Problem set (8 Sep),  Exam #1 key (10 Sep),  Cell structure (12 Sep),  Problem set (17 Sep),  Membranes (17 Sep),  Exam #2 key (24 Sep),  The Big Picture (26 Sep),  Thermodynamics and kinetics (29 Sep),  Problem set (1 Oct),  Enzymes and redox reactions (6 Oct),  Problem set (8 Oct),  Problem set (13 Oct),  Exam #3 key (15 Oct),  Aerobic cellular respiration (20 Oct),  Aerobic respiration diagrams (20 Oct),  Catabolic and anabolic (27 Oct),  Problem set (27 Oct),  Reactive oxygen species (29 Oct),  Anaerobic metabolism (31 Oct),  Problem set (31 Oct),  Exam #4 Key (5 Nov),  Mitosis and meiosis (7 Nov),  Classical genetics (12 Nov),  Problem set (14 Nov),  Problem set (17 Nov),  Exam #5 key (19 Nov),  DNA (21 Nov) [all except DNA repair],  Transcription and translation (1 Dec),  Gene expression (1 Dec),  Problem set (3 Dec).

Slides used in class:

27 Aug,  29 Aug,  3 Sep and 3 Sep,  12 Sep,  6 Oct,  21 Nov.

Recommended optional sources:
1.  An introductory textbook for biology majors.  Two good examples are Campbell et al., and Sadava et al.
2.  Online books from Nature Education: GeneticsEssentials of Cell Biology, and Cancer.
3.  MIT OpenCourseWare: Fundamentals of Biology, and Introductory Biology.
4.  Inside the Cell, from NIH. The structure and function of organelles.
5.  Glossaries of biological terms: 123.

Specific recommended readings (with excellent animations) for DNA replication, transcription and translation:  Units 1.2, 1.4, 1.5 and 1.6 from "Essentials of Genetics".
The entire genetic code (showing how mRNA codons are translated into amino acids).
Specific recommended animations for molecular genetics:  DNA replication, transcription, translation.
Specific recommended readings for mitosis, meiosis, and classical genetics:  Units 2.2, 2.3, 2.4 and 3.3 from "Essentials of Genetics".

Other resources:
Metabolic pathways (interactive map of all the pathways).
An owner's guide to the cell.
Protein Data Bank: What is a protein?Molecular machinery.
Searchable books: Molecular Biology of the CellThe Cell, and Biochemistry.
Exams and keys from previous years.
Drop-in tutoring hours, at the Office of Student Learning.


Bio 446, Environmental Toxicology (fall 2014)

Evaluations of the 3rd group talks are available from the Biology secretary (Vanessa Q.).

Course grades have been posted on NMT Banner.  From the Syllabus:  "Course grades will be calculated from the average of all nine graded items, using the following scale: A 94-100, A- 90-93, B+ 87-89, B 83-86, B- 80-82, C+ 77-79, C 73-76, C- 70-72, D+ 67-69, D 60-66, F 0-59%."

Required handouts (date assigned):
Syllabus (18 Aug),  Fate of toxins in individuals (20 Aug),  Toxin metabolism (25 Aug),  How to read a scientific paper (3 Sep),  Discussion of paper #1 (5 Sep),  1st Group project (8 Sep),  Epidemiology (12 Sep),  Exam #1 Key (17 Sep),  Pesticides (19 Sep),  How to give a scientific talk (26 Sep),  How to write a research proposal (26 Sep),  Example research proposal (1 Oct),  Discussion of paper #2 (10 Oct),  2nd Group project (13 Oct),  Exam #2 key (15 Oct),  Organic pollutants (3 Nov),  Possible exam #3 questions (10 Nov),  Exam #3 Key (12 Nov),  3rd Group project (14 Nov).

Required readings (download pdfs using a computer on the NMT network):
1st:  Hallman et. al. 2014. Declines in insectivorous birds are associated with high neonicotinoid concentrations.
2nd:  Hayes et al. 2010. Atrazine induces complete feminization and chemical castration in male African clawed frogs (Xenopus laevis).   [Detailed methods are available here.]
3rd:  Warner et al. 2002. Serum dioxin concentrations and breast cancer risk in the Seveso Women's Health study.
4th:  Acevedo et al. 2013. Perinatally administered bisphenol A as a potential mammary gland carcinogen in rats.

Specialized journals:
Environmental Health Perspectives;  Environmental Pollution;  Environmental Toxicology;  Environmental Toxicology and Chemistry;  Reproductive Toxicology.

Chemical Carcinogenesis Research Information System;  Carcinogenic Potency Project;  Hazardous Substances Databank.

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.