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Bio 111, General Biology (fall 2015)

No Bio 111 lecture on Wednesday 25 Nov.

Final exam:  Tuesday 8 December, 6:00 pm, Jones Annex 101.  For security reasons, students who arrive late will not be allowed to take the final exam.

Required handouts (date assigned):
Syllabus (17 Aug),  First day questions (17 Aug),  Chemical bonds (19 Aug),  Biochemical structures (26 Aug),  Biochemical functions (26 Aug),  Exam #1 Key (2 Sep),  Cell structure (14 Sep),  Problem set (16 Sep),  Problem set (21 Sep),  Exam #2 Key (23 Sep),  Membrane transport (25 Sep),  Problem set (30 Sep),  Thermodynamics (3 Oct),  Problem set (5 Oct),  Enzymes (9 Oct),  Redox reactions (9 Oct),  Problem set (12 Oct),  Exam #3 Key (14 Oct),  Aerobic respiration reactions (19 Oct),  Aerobic respiration diagrams (19 Oct),  Problem set (23 Oct),  Catabolic and anabolic metabolism (26 Oct),  Reactive oxygen species (26 Oct),  Mitosis and meiosis (28 Oct),  Classical genetics (4 Nov),  Problem set and Key (6 Nov),  DNA (9 Nov),  Problem set (11 Nov),  Transcription and translation (13 Nov),  The big picture (13 Nov),  Problem set (16 Nov),  Exam #4 Key (18 Nov),  Gene expression (23 Nov),  Problem set (23 Nov)

Required videos (date assigned):
Biochemicals (26 Aug),  Membrane transport (28 Sep),  Thermodynamics (30 Sep),  Kinetics (5 Oct),  Aerobic respiration (19 Oct),  Anaerobic fermentation (26 Oct),  Complex inheritance [all except "Codominance", 2:30 - 8:10] (4 Nov)

Slides (date first used in lecture):
Protein structure (31 Aug),  PDB 3-D structures: 1ppi, 2ptc (31 Aug),  Biochemistry questions (9 Sep),  Cell structures (14 Sep),  Molecular genetics (9 Nov)

Specific, highly recommended sources:
Molecular genetics:  
   Units 1.2, 1.4, 1.5 and 1.6 from "Essentials of Genetics".
   The genetic code.
   Animations: DNA replication (youtube)transcription (youtube)translation (youtube).

Mitosis, meiosis, and classical genetics:  Units 2.2, 2.3, 2.4 and 3.3 from "Essentials of Genetics".
Aerobic respiration: ATP and respiration
Thermodynamics and Aerobic respiration: Unit 1.3 of Essentials of Cell Biology.
Organelles:  An owner's guide to the cell.  Inner life of a cell.
Proteins:  Protein Data Bank,  What is a protein?,  Molecular machinery.
Chemical bonds:  Khan Academy videos Atoms, molecules and ions;  Types of chemical bonds (1st 3 videos only). 

General recommended  sources:
1.  An introductory textbook for biology majors.  Two good examples are Campbell et al., and Sadava et al.
2.  Online books: GeneticsEssentials of Cell Biology, and Cancer.
3.  Inside the Cell.  The structure and function of organelles.
4.  Glossaries of biological terms: 12.

Other resources:
Exams and keys from previous years.
Drop-in tutoring hours, at the Office of Student Learning.


Biol 444/544, Evolutionary Biology (fall 2015)

No Evolution lecture on Wednesday 25 Nov.

You WILL be allowed one page of notes for the Final Exam; this is a change from the syllabus.

Final exam:  Saturday 5 December, 9:00 am, Jones Annex 101.  For security reasons, students who arrive late will not be allowed to take the final exam.

Required handouts (date assigned):
Syllabus (17 Aug),  Major ideas in evolutionary biology (17 Aug),  Problem set (19 Aug),  Non-graded "exam" (21 Aug),  Problem set key (26 Aug),  Review papers (28 Aug, Bio 544 only),  Exam key (28 Aug),  Phylogeny definitions (31 Aug),  Problem set key (2 Sep),  Exam key (4 Sep),  Genetics questions (9 Sep, non-graded),  Population genetics #1 (14 Sep),  Problem set key (16 Sep),  Exam key (18 Sep),  Population genetics #2 (21 Sep),  Problem set key (23 Sep),  Exam key (25 Sep, revised),  Quantitative genetics (28 Sep),  Problem set key (30 Sep),  Exam key (2 Oct),  Problem set key (7 Oct),  Signatures of selection #1 (7 Oct),  Exam key (9 Oct),  Haplotypes and sequence variation (12 Oct),  Signatures of selection #2 (12 Oct),  Revised schedule (14 Oct),  Problem set (21 Oct),  Exam key (23 Oct),  Exam key (30 Oct),  Aging (9 Nov),  Exam key (13 Nov),  Human evolution (23 Nov)

Slides (date used in class):
Hominin carbon isotopes (24 Aug),  Phylogeny (31 Aug),  Mutations (11 Sep),  Darwin's finches (5 Oct),  Signatures of selection (14 Oct),  Constraints (19 Oct),  Fitness landscape (26 Oct),  Gene regulatory networks (28 Oct),  Naked mole rats (18 Nov),  Human evolution (23 Nov)

References and websites cited in class:

Cerling et al. 2013.  Stable isotope-based reconstructions of Turkana Basin hominins.
Tree of Life Web Project.
Kong et al. 2012.  Rate of de novo mutations and the importance of father's age to disease risk.
Denver et al. 2000.  High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans.
Pickrell et al. 2009.  Signatures of recent positive selection in a worldwide sample of human populations.
Smith et al. 2011.  Effects of BRCA1 and BRCA2 mutations on female fertility.
Rodriguez-Verdugo et al. 2014.  Different tradeoffs results from alternate genetic adaptations to a common environment.
Boddy et al. 2015.  Cancer susceptibility and reproductive trade-offs: a model of the evolution of cancer defenses.
Jimenez et al. 2013.  Comprehensive experimental fitness landscape and evolutionary network for small RNA.
Hulbert et al. 2007.  Life and death: Metabolic rate, membrane composition, and life span of animals.
Westendorp and Kirkwood. 1998.  Human longevity at the cost of reproductive success.
Lahdenpera et al. 2004. Fitness benefits of prolonged post-reproductive lifespan in women.
Li et al. 2008.  Worldwide human relationships inferred from genome-wide patterns of variation.

Other resources:
Annual Review of Ecology, Evolution, and Systematics.  Good examples of review papers, for students taking Bio 544.
Center for Evolution and Cancer, at UCSF.

Teaching and learning

This is not the official NMT logo, but it should be, proudly:

Carey (2014). How we learn.  Practical advice on how, when and where to study, based on current learning science.

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.

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.

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

Excellent books

Each of these books caused a major change in the way that I think about a particular subject.

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.