Genomics, Computing,
Economics
10 AM Tue 6-Feb 2007
Barker Center, Room 316 12 Quincy St.
Harvard Biophysics 101
(MIT-OCW Health Sciences & Technology 508)
http://openwetware.org/wiki/Harvard:Biophysics_101/2007
Class outline
(1) Topic priorities for homework since last class
(2) Quantitative exercise
(3) Discuss communication/presentation tools
(4) Topic priorities, homework for next class
(5) Project tools discussion
Shawn & Morten
(1) Topic priorities for homework since last class
(a) Your notes Resmi Charalel, Katie Fifer, Hetmann Hsieh,
Shawn Liu, Christopher Nabel, Zachary Sun, Michael Wang,
Xiaodi Wu
(b) Followup on the "experiment" from Tue:
Tversky & Kahneman (1974) Judgement under Uncertainty:
Heuristics and Biases. Science 185:1124).
(c) Exponential growth Spreadsheet example
Human subject experimentation
(not a test) 7 questions. 5 seconds each
1. Write your name, email, school & year.
2. Estimate 8 x 7 x 6 x 5 x 4 x 3 x 2 x 1
3. From a group "of 70 engineers and 30 lawyers: Dick is a 30 year old man.
He is married with no children. A man of high motivation, he promises to be
quite successful in his field. He is well liked by his colleagues." What is the
probability that Dick is an engineer?
4. Write down a string of 10 random H & T characters.
5. From 10 people, how many different committees of 2 members? 8 members?
6. One person draws 4 red balls & 1 white. Another 12 red & 8 white. What
odds should each individual give that the source is 2/3 red (rather than 2/3
white)?
7. Estimate 1 x 2 x 3 x 4 x 5 x 6 x 7 x 8
Human
experiment
results
3: 70 engineers and 30 lawyers; probability that Dick is an engineer
2 (& 7): 8 x 7 x 6 x 5 x 4 x 3 x 2 x 1 (& rev) Actual: 40320
1974 median: 2250 descending; 512 ascending
2007 median: 3500, 4000, mean 66668, 67646
1974: mostly 0.5, whether 70:30 or 30:70.
2007: 0.3 0.5, 0.7(15), 0.8
4: 1974: more than two in row are rarely chosen. Expect: 2
2007: 6, 4,3,3,2,2,1(4), 0(9) Median: 1, Mean 1.3
5: 10 people, # committees of 2 or 8 members? Actual: C(10,2)=C(10,8)=45
1974 median for 2 was 70; for 8 was 20.
2007 median for 2 was 20; for 8 was 21. Mean: 73, 48. (two said 45)
C(n,i)= n!/[i!(n-i)!]
Human experiment results
6: 4/5 vs 12/20 -- which better supports 2/3 red rather than 2/3 white?
1974: Most people felt 4/5 (80%) is better evidence than 12/20 (60%)
Actual: [C(5,4)(2/3)^4 (1/3) / C(5,1)(2/3)(1/3)^4]= 8 odds ratio
[C(20,12)(2/3)^12 (1/3)^8 / C(20,8)(2/3)^8(1/3)^12]= 16
Monty Hall Experiment
Class discussion:
1car, 2 goats
Tversky & Kahneman (1974)
Judgement under Uncertainty 1974
Science 185:1124
>60% of
15, 45
= 10, 28
p = .151, .068
= 55, 25 days
Hence, programming in statistics &
economics
Mechanical-Analog: slide rule (1620)
Mechanical-Digital: Babbage (1837) DigiComp (1963)
Electronic-Analog: ~1940s
Electronic Digital -- Procedural, imperative languages:
Basic(’63), Lisp(’58), Algol, Cobol(’59), Fortran(’54), C(‘72),
IBM360-Assembly(’64), FORMAC, APL, PL/I
Dynamic languages: Perl(‘87), Python(‘91).
Spreadsheets: double-entry bookkeeping (12th Century)
Electronic Mattessich (’61). PC:Bricklin’s Visicalc (’79),
Excel(’85), public spreadsheets (’70) Wikicalc etc.
http://www.meccano.us/analytical_engine/P1010006.MOV
Exponent.xls
0.035
0.03
A3 =k*A2
0.025
0.02
0.015
A3 =k*A2*(1-A2)
0.01
0.005
0
A3 =MAX(k*A2*(1-A2),0)
try k=
0.9,
1.01, 1.1,
1 5 9 13 17 21 25 29 33 37 41 45 49 53 57 61 65
1.5, 3, 3.67859, 4, 4.03
Class outline
(1) Topic priorities for homework since last class
(2) Quantitative exercise
(3) Discuss communication/presentation tools
(4) Topic priorities, homework for next class
(5) Project tools discussion
Shawn & Morten
Quantitative definition of life
(& utility of such)
"papers incubating where we do
calculate the statistical complexity
of various real-world processes"
http://cscs.umich.edu/~crshalizi/notebooks/complexity-measures.html
James P. Crutchfield and Karl Young,
"Inferring Statistical Complexity," Physical
Review Letters 63 (1989) 105--109
Class outline
(1) Topic priorities for homework since last class
(2) Quantitative exercise
(3) Project level presentation & discussion
(4) Sub-project reports & discussion
(5) Discuss communication/presentation tools
(6) Topic priorities for homework for next class
The Visual Display of Quantitative
Information 1983,2001 Tufte (& Minard 1861)
Other examples
Ben Fry's Genomic Cartography work
http://acg.media.mit.edu/people/fry/
Image and Meaning Initiative
http://web.mit.edu/i-m/intro.htm
The Gettysburg Powerpoint Presentation11/19/1863
http://www.norvig.com/Gettysburg/
Class outline
(1) Topic priorities for homework since last class
(2) Quantitative exercise
(3) Discuss communication/presentation tools
(4) Topic priorities, homework for next class
(5) Project tools discussion
Shawn & Morten