This course has additional materials on a "CourseInfo" site: http://courseinfo.amherst.edu/courses/BIOL-28-00S/
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| January 24 | Introduction: variability in the life sciences | Chapter 1 |
| 26 | Combinations and probabilities | Handouts |
| 28 | Conditional probabilities; Bayesian methods | Chapter 14 |
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| 31 | Binomial distribution and confidence intervals | Chapters 2, 3 |
| February 2 | Using Excel (Webster 102) | |
| 3 | Problem set 1 due | |
| 4 | Quiz 1 | |
| 7 | Normal distribution, confidence interval of the mean, t | Chapters 4, 5 |
| 9 | Presentations | |
| 11 | Survival curves; introduction to paired comparisons | Chapters 6, 7 |
| 14, 16 | The Poisson distribution | Chapter 28, handouts |
| 17 | Problem set 2 due | |
| 18 | Quiz 2 | |
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| 21 | Hypothesis testing | Chapters 10, 11 |
| 23 | Presentations | |
| 25 | Interpretation of p-values; multiple comparisons | Chapters 12, 13 |
| 28, March 1 | Comparisons of central tendency: parametric & non-parametric | Chapters 23, 24, 25 |
| 2 | Problem set 3 due | |
| 3 | Quiz 3 | |
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| 6 | Clinical trials; odds ratio; case control studies | Chapters 8, 9 |
| 8 | Presentations | |
| 10 | More Bayesian methods: linkage, genetics | Chapters 15, 16 |
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| 20, 22 | Correlation | Chapter 17 |
| 23 | Problem set 4 due | |
| 24 | Quiz 4 | |
| 27 | Regression | Chapters 18, 19 |
| 29 | Presentations | |
| 31 | Determining sample size; statistical power | Chapters 20, 21, 22 |
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| April 3, 5 | Chi-square; contingency tables | Chapters 26, 27 |
| 6 | Problem set 5 due | |
| 7 | Quiz 5 | |
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| 10 | ANOVA I | Chapter 30 |
| 12 | Presentations | |
| 14 | ANOVA II | Handouts |
| 17, 19 | Data transformations | Handouts |
| 20 | Problem set 6 due | |
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| 21 | Modeling I: Signals and noise | Handouts |
| 24 | Modeling II: Neuroscience | |
| 26 | Presentations | |
| 28 | Quiz 6 | |
| May 1 | Presentations | |
| 3 | Presentations | |
| 5 | Problem solving/ review for final exam | |
A. Text (available at the Jeffery Amherst College Store):
Intuitive Biostatistics, by Harvey Motulsky (New York, Oxford
University Press, 1995). We will read all but chapters 29, 32,
33, and 34 as part of the course. Chapters 35, 36, 37, and 38
are not mentioned in the course outline, because they cover general
subjects such as common statistical errors; we'll refer to those
chapters from time to time during the course.
B. Handouts: Many scientific papers and excerpts, to be
distributed in class.
C. Reserve Readings:
Heath, D. An Introduction to Experimental Design and Statistics
for Biology, London, UCL Press, 1995. This book contains excellent
conceptual explanations of the thinking behind many statistical
tests and procedures. Some passages will be provided as class
handouts.
Campbell, S. K. Flaws and Fallacies in Statistical Thinking,
Prentice-Hall, 1974.
Fisher, R. A. The Design of Experiments. Hafner, 1971.
Gonick, L. and Smith, W. The Cartoon Guide to Statistics. Harper
Perennial, 1993
Moses, L. E. Think and Explain with Statistics. Addison
Wesley, 1986.
Salsburg, D. S. Understanding Randomness. Lecture Notes
in Statistics, Vol. 6 Marcel Dekker, 1983.
Sokal, R. R. and F. J. Rohlf. Introduction to Biostatistics, 2nd
3ed. Freeman, 1987.
Zar, J. Biostatistical Analysis. Prentice Hall, 1984.
Grading
My goal is to include evaluations based on situations similar
to "real life" use of statistics, i.e. as much emphasis
on problem sets and presentations as on exams. Here is the required
work of the course:
(1) PROBLEM SETS (6% each, total 36% of the grade): 6 problem
sets, involving data presentation, statistical analysis, and experimental
design; you will be asked to explain your approach in addition
to doing the calculations. Problem sets will be due in class on
6 Thursdays during the semester (Feb. 3 and 17; March 2 and 23;
April 6 and 20. For problem sets that you hand in on time (but
not those handed in late), you may submit corrections within within
2 weeks for partial credit.
(2) QUIZZES (7% each, total 28% of the grade): There will
be 6 in-class quizzes on Fridays (Feb. 4 and 18; March 3 and 24;
April 7 and 28). Three of the quizzes will be closed book and
three open book. Quizzes will include both conceptual questions
and calculations. The best 4 scores will be counted towards your
grade, and the lowest two scores will be dropped. Under these
circumstances, there will be no makeups for quizzes missed without
a letter from the Dean of Students verifying personal illness
or family emergency.
(3) PRESENTATION (8% of the grade): Each member of the
class either individually or with a partnerwill make a 20 minute
presentation to the class, with a few minutes for questions afterwards,
on a topic related to scientific method, or cases of interesting
use or misuse of statistics. You will provide a 1 - 2 page abstract,
and a list of references, for each presentation. Sample topics
are listed on an attached pages, but I will be happy to consult
with you if you have a suggestion for a different topic.
(4) PAPER (8% of the grade): A 4 - 6 page paper based on
your presentation; will be done jointly with your partner if your
presentation was a joint presentation.
(5) FINAL EXAM (20% of the grade): A comprehensive, closed
book, scheduled final exam
(6) ATTENDANCE AT PRESENTATIONS: attendance is required
at the presentation sessions.
Prerequisites:
There are no college-level prerequisites for this course. Obviously
we will constantly use numbers (i.e. calculations) and symbols
(i.e. algebra), but the only formal math requirement is at the
level of "pre-calculus" courses.
Applying Bio. 28 to your major:
This is a non-laboratory Biology course that counts as a "List
A" elective for the Neuroscience major. For Biology majors,
Bio. 28 may be used as one of the 5 courses beyond Bio. 18-19
for the major, but it does not fulfill either a lab or an "area"
How dumb can you get!
An article in the December 1999 Journal of Personality and Social
Psychology says that dumber people rate themselves as above average,
while smarter people say the opposite. Maybe we should look at
exactly how the study was done?
The year 2000 census (or should it be a sample?)
The U.S. Constitution says the government has to count the entire
population every ten years, and this is one of those years. However,
those who know statistics say the count would be more accurate
using sampling rather than trying to count everyone - and the
errors from trying to count everyone are by no means random.
The Gulf War syndrome
Many veterans of the Gulf War report debilitating illnesses that
are unlike any described in medical textbooks. Can statistical
methods be used to test what is going on here?
Should women have regular routine mammography screenings
for breast cancer?
A recent high-level panel was asked to answer this question, but
they couldn't reach a unanimous recommendation. How could something
like this not be a good thing?
DNA fingerprinting
How good should a "match" be between DNA at a crime
scene and DNA belonging to an accused person in order to convict?
Refs.: Risch and Devlin, Science 255: 717-720 (1992); Science
256: 593 (1992); Science 254:1745-1750 (1991)
Smoking and cancer
Is it correlation or causation--or is that even the right question?
Evidence of inheritance of acquired characteristics?
A famous early 20th century case of apparent fraud, complete with
sex--in frogs--and the tragic suicide of the scientist involved.
Ref: The Case of the Midwife Toad, by Arthur Koestler.
The homeopathic medicine controversy
Played out in the pages of the distinguished journal Nature, a
French group (Benveniste et al.) claimed that water has a "memory"
of being exposed to certain chemicals that persists even when
the chemical had been successively diluted so many times that
there should be less than one molecule remaining. This was said
to be how some homeopathic remedies work.
The placebo effect
It's one reason why controls are needed in clinical trials. Exactly
what is it, and does it have a physiological explanation? Should
subjects receive placebos to provide a control in clinical trials
when an alternative treatment is available? Science 267: 25-6
(2 Jan. 1995)
Does "oral toleration" using myelin antibodies
cure multiple sclerosis?
A recent clinical trial says yes, critics say no.
Facilitated communication in autism
An autistic person who can't speak a word points to letters on
a keyboard that spell out meaningful sentences--but only when
a "facilitator" gently holds the autistic person's hand.
Real communication by the autistic person, or a "clever Hans"
effect?
Ape language
Do Sarah the Chimp and Koko the gorilla really use sign language,
or are they just going through the motions to get a banana?
Case histories of recent research fraud
Fortunately for students in Bio. 28, but sadly for the integrity
of science, there is ample material here for several juicy presentations
and reports, from an Office of Research Integrity newsletter from
NIH, and from a book by Broad and Wade, Betrayers of the Truth.
Also Science 245: 120-122 (1989).
Do chemists die young, statistically?
An article in Am. J. Industrial Med. 23: 615 (May 1993) analyzes
the data. Perfect for someone seeking revenge for Chem. 12.
Is schizophrenia a genetic disorder?
Four announcements of finding "linkage" have been made--complete
with major press conferences and network TV coverage--in recent
years. All four were later retracted, based on new evidence. What's
going on? Ref: Alper & Natowicz, Trends in Neurosci. 16 387-9,
1993.
Strategic bombing in World War II
During the London blitz, bombs fell in clusters, sometimes near
major military or industrial sites. Statistical analysis was used
to analyze whether the Germans actually had the ability to pick
out particular targets, or whether the bombing was actually random.
Racism by "statistics"
From cranial capacity to intelligence tests, "science"
has sometimes serve to promote belief in racial differences; The
Mismeasure of Man, by Steven Jay Gould; The Bell Curve.
The life of "Student"
W. S. Gosset worked for the Guiness brewery. His employers made
him publish his pathbreaking statistical work under the pseudonym
"Student" because they didn't want the competition to
know they were using heavy brainpower to market their product.
The dance of the bees
Does the bees' dance communicate direction and distance to food
source, as everyone thought--and introductory Biology and Psychology
texts asserted--based on von Frisch's classic experiments? If
the answer were "yes", we wouldn't be asking!
Does prayer work?
A recent study apparently shows that coronary care patients for
whom someone prayed did better than control patients--and the
doctors and nurses taking care of the patients reportedly didn't
know who were the "experimentals" receiving prayer and
who were the controls, so it was a true "double blind"
test.
The frauds of Sir Cyril Burt
Statistical thinking exposed Burt's fake data supposedly showing
a high genetic component of IQ differences in "separated
identical twins." Ref: Letter in Science 204 242-3.
Genes and IQ
Burt's fraud aside, how good are the concepts and data linking
genes and intelligence differences? The Science and Politics of
IQ, by Leon Kamin.
ESP
Some demonstrations of alleged psychokinesis, telepathy, and clairvoyance
have reported astronomical odds against the outcomes happening
by chance. Should we believe?
Animal "super-senses"
Perhaps more plausible than ESP are reports of animals' ability
to detect things humans can't, e.g. that an earthquake is about
to happen, or that their epileptic owner is about to have a seizure.
Still, there is no explanation of how this could be possible.
(Springfield Union News, 17 Aug. 1995).
Psychology of probability
People tend to make systematically skewed judgements of probability;
there is a whole subfield of Psychology to investigate this bias.
Judgment Under Uncertainty, by Kahneman, Slovic, and Tversky.
Feminist science
There are many potential topics here, some more relevant to Bio.
28 than others. The misuse of statistics to justify sexism, and
the claim that women scientists approach science differently,
would be good subjects for this course.
A statistical theory of some kinds of cancer
A "two-hit" model fits very well the data on incidence
of retinoblastoma in one eye vs. both eyes. Ref: Cevence and White,
Sci. Am. March 1995, p. 73.
Attacks on misuse (and perhaps use) of statistics
.. and not because they're boring, either! Refs: Tainted Truth,
reviewed in NYTimes 31 July 1994; a Sci. Am article on "The
Anti-Scientific Attitude".
Can there be a statistical measure of the value of a human
life?
A smoke detector reduces the probablity of dying in a fire by
1 chance in 10,000. People who will buy one for $20 but not for
$50 seem to be placing a value on their own life of between $200,000
($20 x 10,000) and $500,000. Government regulations prohibiting
using asbestos in auto parts cost consumers extra money and save
only a tiny number of lives; the extra cost per life saved is
$1.2 billion. Is the regulation against asbestos justified? Is
this kind of calculation rational in the first place? Refs: NYTimes
29 Jan. 1995; Science 248: 559-564, 1990.
Why are spouses good organ donors?
Kidney transplants between spouses (who of course are genetically
unrelated) are almost as successful as transplants between identical
twins (NEJournal of Medicine, 8 August 1995). Why so?
Optimistic biases about personal risks
When randomly chosen people are polled, on the average they rate
their own risks of various hazards (flu, cancer, poisoning, etc.)
as below average. (Perhaps it's the opposite of the "Lake
Wobegone Effect", where according to Garrison Keillor all
the children of the town are above average.) Can anything be said
in favor of this optimistic bias? Ref: N. Weinstein, Science 246:
1232-3, 1989.
Human behavior and relative risk
People who fear airplane flight regularly put their life in jeopardy
driving, which statistically is much more dangerous than flying.
Others who protest nuclear power plants put themselves at much
higher risk of death from heart disease by eating fatty foods
and not exercising. Are people just irrational, or what?
(NY Times, 6/15/97)
Vaccination risks
When do the risks of vaccination exceed the risks from the disease
that is prevented by vaccination? Should an individual give the
same answer to this question as a public health official would?
(Nature 318: 323-9, 1985; Lancet 335: 641-5, 1990).
Are some infinite, non-repeating decimal numbers more random
than others?
By one newly developed test for randomness, pi was more
random than e, which in turn was more random than the square
root of 2. (Science 276:532, 4/25/97)
The draft lottery wasn't random
As Amherst Prof. Norton Starr has written, the 1970 draft lottery,
on the basis of which many young American men went to war in Vietnam
and some died, was supposed to choose draftees at random based
on birthdates. However, it didn't turn out that way. (http://www2.ncsu.edu/ncsu/pams/info/jse/v5n2)
Benefits of sex
"Study of men finds regular sex may reduce risk of death
by half." Whether this excuse is needed or not, is it true?
(Springfield Union News, 12/23/97.)
Violence and the weather
"Study proves it: Heat makes people violent." Can
it be so? Springfield Union-News, 11/27/97)
Magnetic fields and cancer
For several decades, there have been reports that people exposed
to low-frequency electromagnetic fields have increased risk of
some kinds of cancer. What's the evidence? (Science 277:
29-30, 1997)
Non-random "randomized" trials
Evaluation of new drugs and therapies in medicine depends on randomized
clinical trials. Recently it has come to light that some supposedly
randomized controlled trials weren't random at all. ( JAMA 274:
1456-1458, 1995.)
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