Annotated bibliography by subject (both books and web sites)

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What is Science?
**********
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Medawar, P.B.
The Limits of Science
Harper & Row, 1984.

SRLib: Q175 .M433 1984
(out of print)

The book contains three related essays:
"An essay on scians", "Can scientific discovery be premeditated?",
and "The limits of science".  The latter seems most likely
to provoke some good discussion; it's about 50 pages long.

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Frank Wolfs, Physics, University of Rochester
Introduction to the Scientific Method
http://teacher.nsrl.rochester.edu/phy_labs/AppendixE/AppendixE.html

see also a course Wolfs taught more recently (Physics by Inquiry)
http://teacher.nsrl.rochester.edu/PhyInq/PhyInqHomePage.html#info

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Fred Senese, Frostburg State University (MD)
The Scientific Method (scroll to bottom of page)
http://antoine.frostburg.edu/chem/senese/101/intro/index.shtml

(there is a "randomized quiz" on the same page which isn't
very random, and with some debatable "correct answers")

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<no byline>
"Rogue Scientist has Own Scientific Method"
The Onion 42(23), June 5, 2006
http://www.theonion.com/content/science
<downloaded to PDF file; URL not stable> 

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(HW? find another description of "the scientific method"
from a book or from the Web)

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John L. Casti
Paradisms Lost (Chapter 1: Faith, Hope, and Asperity; 67 pages)
Wm. Morrow & Co., 1989.

SRLib: Q173 .C35 1989

some paired examples of science and pseudo-science,
detailed discussion of philosophy of science:
Wittgenstein, Popper, Kuhn, et al.
Merton's norms: 
originality, detachment, universality, skepticism, public accessibility
Kuhn: a good scientific theory should be
accurate, consistent, broad, simple, fruitful

See also Overton criteria in Chapter 2, page 124; science:
is guided by natual law, 
has to be explanatory with reference to natural law,
is testable against the empirical world, 
has tentative conclusions (not the final word), 
is falsifiable.

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Thomas Kida
Don't Believe Everything You Think:
The 6 Basic Mistakes We Make in Thinking
Prometheus Books, 2006.

Perhaps it suffices to just use his list as a starting point for discussion.
1. We prefer stories to statistics
2. We seek to confirm (i.e., we filter what we see/remember)
3. We don't appreciate the role of chance and coincidence in life
4. We can misperceive our world
5. We oversimplify
6. We misremember

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Basic Quantitative Issues
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Powers of 10
Eames Office
http://powersof10.com/index.php?mod=poster

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Quizzes and tutorials on measurement, conversion, significant digits
General Chemistry Online
http://antoine.frostburg.edu/chem/senese/101/tutorials/

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Frank Wolfs, Physics, University of Rochester
Appendices on Units, Error Analysis (Significant Figures,...)
ALSO Purpose of the Physics Labs, How to write a lab report,...
http://teacher.pas.rochester.edu/PHY_LABS/Labs_113.html

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Lab: find the cost of an atom of aluminum
(need to find Avogadro's #, atomic wt of Al,
weigh the sample and find its area; given are
the cost of the roll of aluminum foil and the
number of "feet" or square feet from the package)

Taken from the National Center for Case Study Teaching in Science
at Univ of Buffalo
http://ublib.buffalo.edu/libraries/projects/cases/case.html
http://www.sciencecases.org/avogadro/avogadro.asp

The lab description appears to misrepresent the Pace
University court case, which involved a claim that
a computer programming course required more background
than the syllabus suggested.

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Conway's game of Life
http://www.ibiblio.org/lifepatterns/
http://www.trevorrow.com/lifelab/index.html#features

A useful demonstration of the way complex, often unpredictable
results can "evolve" from (very) simple rules applied over many 
"generations".  Not really a mathematical model of evolution, though.

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Statistics
**********
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Gould, Stephen Jay
"Case One: A Personal Story", in
Full House: the spread of excellence from Plato to Darwin
Three Rivers Press, 1996.

SRLib: HM101 .G67 1996

(an earlier version is
"The Median isn't the Message", in
Bully for Brontosaurus
W.W. Norton & Co., 1991. 

SRLib: QH45.5 .G68 1991)

A practical example of the importance of
a right skew, in the context of Gould's cancer
diagnosis.  There's a happy ending.

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NetLogo Models Library, Northwestern University
Galton Box simulates a binomial distribution (in browser)
(originally an actual box with lead shot,
Natural Inheritance, page 63; 
http://galton.org/, search for "quincunx")
Basis for HW assignment.
http://ccl.northwestern.edu/netlogo/models/GaltonBox

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Genetics (Mendel, DNA)
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Ridley, Matt
Genome: the autobiography of a species in 23 chapters
HarperCollins, 1999.

SRLib: not in the collection, but ordered

Most chapters focus on the effect of a specific gene
(including the official name).  This could be the
basis for group or individual presentations.

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DNA Interactive (Cold Spring Harbor Laboratory)
History, Overview, access to human genome, Applications
http://www.dnai.org/

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National Center for Biotechnology Information (NCBI) Map Viewer
Examine human genome, search for keywords in descriptions of genes 
http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi

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The Biology Project (Univ of Arizona)
Mendel HW multiple-choice problem set, with tutorials
http://www.biology.arizona.edu/mendelian_genetics/mendelian_genetics.html

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Mathematical Association of America (MAA) Digital Library
Biological ESTEEM collection
ABO blood type, calculating allele frequency several ways (Excel)
http://mathdl.maa.org/mathDL/3/?pa=content&sa=viewDocument&nodeId=647

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Queen Victoria homework: tracing hemophilia
adapt from Case Study in Science (Univ Buffalo)
http://ublib.buffalo.edu/libraries/projects/cases/case.html
http://www.sciencecases.org/hemo/hemo.asp

Answer key is password-protected.

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The Tech Museum of Innovation, San Jose CA
One gene for red hair (follow links, too)
http://www.thetech.org/genetics/ask.php?id=44

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Barsh, Gregory S., Howard Hughes Medical Institute, Stanford
What controls variation in human skin color?
Public Library of Science, Biology journal (October 2003)
Barsh GS (2003) What Controls Variation in Human Skin Color? PLoS Biol 1(1): e27
http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0000027
(much murkier than hair color)

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John L. Casti
Paradisms Lost (Chapter 3: It's in the Genes*; 65 pages)
Wm. Morrow & Co., 1989.
*Claim: Human behavior patters are dictated primarily by the genes.

SRLib: Q173 .C35 1989

Milgram shock experiment, the strategy of sociobiology is to explain
all phenotypically altruistic behavior as being genetically selfish acts.
game theory (page 158), coefficient of relatedness,
Wilson's 4-rung ladder, Dawkins: the organism is only DNA's way of making more DNA,
the coevolutionary circuit:
molecular -> cellular -> organismic -> populational(culture) -> molecular,
Boston Group(Lewontin, Gould,...) vs. Wilson

Note also that Casti wrote a follow-up book:
Paradigms Regained
William Morrow/HarperCollins, 2000.

SRLib: Q173 .C353 2000

He reports in particular on recent studies favoring
nature over nurture.

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James D. Watson
The Double Helix
Touchstone/Simon&Schuster, 2001

SRLib: QD345 .W37 1980

See file elsewhere entitled "Double Helix notes".
Watson is exasperating for much of the book, but
redeems himself a bit at the end by doing an about-face
in his description of Rosalind Franklin.

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Basic Chemistry Issues (pH,...)
**********
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The Biology Project (Univ of Arizona)
pH HW multiple choice problem set, with tutorials (need not use all)
http://www.biology.arizona.edu/biochemistry/problem_sets/ph/ph.html

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Evolution
**********
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Gould, Stephen Jay
"Case Two: Life's Little Joke", in
Full House: the spread of excellence from Plato to Darwin
Three Rivers Press, 1996.

SRLib: HM101 .G67 1996

Uses the example of evolution of horses to battle a simplistic
notion of "progress" in evolution.

(an earlier version is
"Life's Little Joke", in
Bully for Brontosaurus
W.W. Norton & Co., 1991. 

SRLib: QH45.5 .G68 1991)
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Barash, David P.
"The Case for Evolution, in Real Life"
Chronicle of Higher Education, 52(31), B10 (April 7, 2006)

A series of ripostes to 10 assertions about evolution.
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Video of the 2005 Holiday Lectures (Howard Hughes Medical Institute)
Sean B. Carroll  and David M. Kingsley  
discuss how Charles Darwin's ideas about evolution ignited a revolution 
in biology that continues to this day. 
http://www.hhmi.org/biointeractive/evolution/lectures.html

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Donald Johanson, Arizona State University
"Origins of Modern Humans:ÊMultiregional or Out of Africa?"
American Institute of Biological Sciences
http://www.actionbioscience.org/evolution/johanson.html
(many links to ways to learn more)

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John L. Casti
Paradisms Lost (Chapter 2: A Warm Little Pond*; 74 pages)
Wm. Morrow & Co., 1989.
*Claim: Life arose out of natural physical processes taking place here on Earth

SRLib: Q173 .C35 1989

Has a bit on DNA/RNA, a bit on Conway's game of Life (page 132), 
Primordial Soup

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Richard Lewontin
The Triple Helix
Harvard Univ Press, 2000.

SRLib: QH506 .L443 2000

129 small pages.  See file elsewhere entitled "Triple Helix notes".

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Andrew H. Knoll
Life on a Young Planet: the first 3 billion years of evolution on Earth
Princeton Univ Press, 2003

Pre-Cambrian

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(for a different perspective)
Dalai Lama
The Universe in a Single Atom
Morgan Road Books, 2005.

SRLib: BQ7935 .B774 U56 2005
 
Use Chapter 1: Reflection (5 pages)
and Chapter 5: Evolution, Karma, and the World of Sentience (19 pages)

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Richard Dawkins
River out of Eden
BasicBooks/HarperCollins, 1995.

SRLib: not in the collection, though we do have Dawkins's
The Selfish Gene, which may overlap.

160 pages, chapter titles are: 
The digital river, All Africa and her progenies,
Do good by stealth, God's utility function, The replication bomb.
Pretty readable, with reasonably frequent quantitative claims 
that are verifiable, in some cases suggesting simulations 
(e.g., for reproductive strategies in chapter 4), and in others
leading to good questions like "What is the average size of a cell?".

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Understanding Evolution
University of California Museum of Paleontology
http://evolution.berkeley.edu/

Overview, lesson plans (K-12 only, often hokey),
"concepts"/theses for 9-12 seem well-stated and useful; see
http://evolution.berkeley.edu/evosite/Lessons/IIConcepts.php
There is a discussion of how to respond to students who believe
that you are trying to get them to forsake their religion, and
a list of potential pitfalls, which I found helpful; see 
http://evolution.berkeley.edu/evosite/Roadblocks/IIStudent.shtml
http://evolution.berkeley.edu/evosite/footshooting/index.shtml

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Light
**********
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Feynman, Richard P., 
QED: the strange theory of light and matter
Princeton University Press, 1985.

SRLib: QC793.5 .P422 F48 1985

Contains rewritten versions of 4 lectures to a general audience.  The
first two of them describe photons.  They're written simply enough to be
accessible, especially if combined with demonstrations and activities
that reinforce the claims made about what will be observed in the
scenarios he describes.  The later two lectures extend the discussion to
electrons and to quarks.  They're handy "enrichment" for the enthusiasts.

Bonus: the "random" behavior of photons feeds into probability and
statistics topics.  This includes the sum (for disjoint events) and
product (for successive events) rules for combining vectors, which mimic
probability axioms.

Video of the original lectures 
(streaming, RealOnePlayer; the UK site sometimes takes a while to load,
but the streamcast once started was pretty smooth)
http://www.vega.org.uk/video/subseries/8

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van Heel, A.C.S. and Velzel, C.H.F,
What is Light?
World University Library, McGraw-Hill, 1968.

SRLib: QC355 .H53

Eight chapters, on Propagation, Reflection and Refraction,
Interference, Diffraction, Polarisation, Production and Detection,
Electromagnetic Field, and Oscillators and Photons.
Some history, lots of diagrams and photographs. The last chapter has a
short and simple explanation of why the photoelectric effect is
incompatible with the wave theory of light.
 
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Teachspin demonstration apparatus (and procedure) Buffalo, NY
http://www.teachspin.com/instruments/two_slit/experiments.shtml