1. Harvard Biophysics 101 (MIT-OCW Health Sciences & Technology 508)MIT-OCW Health Sciences & Technology 508 http://openwetware.org/wiki/Harvard:Biophysics_101/2007 10 AM Tue 6-Feb 2007 Barker CenterBarker Center, Room 316 12 Quincy St.Room 316 Genomics, Computing, Economics

2. 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

3. (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 WuResmi CharalelKatie FiferHetmann Hsieh Shawn LiuChristopher NabelZachary SunMichael Wang Xiaodi Wu (b) Followup on the "experiment" from Tue: Tversky & Kahneman (1974) Judgement under Uncertainty: Heuristics and Biases. Science 185:1124).Science 185:1124 (c) Exponential growth Spreadsheet example

4. 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

5. 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 3: 70 engineers and 30 lawyers; probability that Dick is an engineer 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) Human experiment results C(n,i)= n!/[i!(n-i)!]

6. 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 Human experiment results Monty Hall Experiment Class discussion: 1car, 2 goats

7. Tversky & Kahneman (1974) Judgement under Uncertainty 1974 Science 185:11241974 Science 185:1124 >60% of 15, 45 = 10, 28 p =.151,.068 = 55, 25 days

8. 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.Wikicalc etc. http://www.meccano.us/analytical_engine/P1010006.MOV

9. Exponent.xls try k= 0.9, 1.01, 1.1, 1.5, 3, 3.67859, 4, 4.03 A3 =k*A2 A3 =MAX(k*A2*(1-A2),0) A3 =k*A2*(1-A2)

10. 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

11. 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

12. 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

13. The Visual Display of Quantitative Information 1983,2001 Tufte (& Minard 1861)

14. 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/

15. 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