1. David Evans http://www.cs.virginia.edu/~evans
Class 37:
Secret of Life
CS200: Computer Science
University of Virginia
Computer Science
David Evans

2. Liberal Arts Trivium Quadrivium
From Lecture 15:
Liberal Arts
Grammar: study of meaning in written expression
Rhetoric: comprehension of verbal and written discourse
Logic: argumentative discourse for discovering truth
Arithmetic: understanding numbers
Geometry: quantification of space
Music: number in time
Astronomy
BNF replacement rules for describing languages,
rules of evaluation for meaning
Your PS8 web sites are a discourse
between user and server.
Not yet… Interfaces between
components, program and user
Trivium
Rules of evaluation, if,
recursive definitions
Learned to count in
Lambda Calculus
Not much yet…
wait until April
Curves as procedures,
fractals
Quadrivium
Yes, even if we can’t figure out how to play
“Hey Jude!”
Yes: Neil deGrasse Tyson says so
25 April 2003
CS 200 Spring 2003

3. Today is the 50th anniversary of announcement of the most important scientific discovery of the 20th century!
25 April 2003
CS 200 Spring 2003

4. Eagle Pub, Cambridge UK
“Watson, we have discovered the meaning of life!”
Francis Crick, 28 February 1953
“Watson, come here, I want to see you.”
Alexander Graham Bell, 10 March 1876
25 April 2003
CS 200 Spring 2003

5. Molecular Structure of Nucleic Acids, “A Structure for Deoxyribose Nucleic Acid”, Nature 25 April 1953
It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.
25 April 2003

6. Brief History of Biology
1850
1950
2000
Life is
about
magic.
(“vitalism”)
Life is
about
chemistry.
Life is
about
information.
Life is
about
computation.
Schrödinger (1944)
life is information
crack the information code
Most biologists work on Classification
Aristotle (~300BC) - genera and species
Descartes (1641)
explain life mechanically
Watson and Crick (1953)
DNA stores the information
25 April 2003
CS 200 Spring 2003

7. DNA
Sequence of nucleotides: adenine (A), guanine (G), cytosine (C), and thymine (T)
Two strands, A must attach to T and G must attach to C G C A T
25 April 2003
CS 200 Spring 2003

8. Central Dogma of Biology
Transcription
Translation
DNA
RNA
Protein
Image from
RNA makes copies of DNA segments
RNA describes sequences of amino acids
Chains of amino acids make proteins
25 April 2003
CS 200 Spring 2003

9. Encoding Proteins
There are 4 nucleotides: adenine (A), guanine (G), cytosine (C), and thymine (T) (replaced with uracil (U) in RNA)
There are 20 different amino acids, and a stop marker (to separate proteins)
How many nucleotides are needed to encode one amino acid?
with 2, could encode 16 things: 4 * 4
with 3, could encode 64 things: 4 * 4 * 4
25 April 2003
CS 200 Spring 2003

10. Codons Three nucleotides encode an amino acid
But, there are only 20 amino acids, so there may be several different ways to encode the same one
From
25 April 2003
CS 200 Spring 2003

11. How Big is the Make-a-Human Program?
3 Billion Base Pairs
Each nucleotide is 2 bits (4 possibilities)
3 B pairs * 1 byte/4 pairs = 750 MB
Every sequence of 3 base pairs one of 20 amino acids (or stop codon)
21 possible codons, but 43 = 64 possible
So, really only 750MB * (21/64) ~ 250 MB
25 April 2003
CS 200 Spring 2003

12. 1 CD ~ 650 MB
25 April 2003
CS 200 Spring 2003

13. People are almost all the Same
Genetic code for 2 humans differs in only 2.1 million bases
4 million bits = 0.5 MB
How big is 0.5MB?
1/3 of a floppy disk
~22 times the size of the PS6 adventure game code
25 April 2003
CS 200 Spring 2003

14. Is DNA Really a Programming Language?
25 April 2003
CS 200 Spring 2003

15. Stuff Programming Languages are Made Of
Primitives
Means of Combination
Means of Abstraction
codons (sequence of 3 nucleotides that encodes a protein)
?? Morphogenesis? Not well understood (by anyone).
This is where most of the expressiveness comes from!
DNA itself – separate proteins from their encoding
Genes – group DNA by function (sort of)
Chromosomes – package Genes together
Organisms – packages for reproducing Genes
25 April 2003
CS 200 Spring 2003

16. My Research Group
Build robust, survivable systems from unreliable components
Learn from biological systems that do this
Cell-Based Programming Model
Genes turn on and off  state changes
Emit different chemicals depending on state, sense chemicals in surroundings
Cells can divide asymmetrically
Lots of simplifications: not simulating reality
25 April 2003
CS 200 Spring 2003

17. Example A B state A emits (alive, 1) diffuses (radius, 10) transitions
(alive < 1) from any direction
-> (A, B) in same direction;
-> (A);
state B
emits (alive, 1)
(alive < 1) from any direction & (radius > 1)
-> (B, B) in same direction;
(alive > 0) from any direction -> (B);
-> (radius); A
alive < 1 B
alive > 0
alive < 1
& radius > 1
25 April 2003
CS 200 Spring 2003

18. Simulating Program A B Simulation by Selvin George alive < 1
& radius > 1
Simulation by Selvin George
25 April 2003
CS 200 Spring 2003

19. Simulation by Selvin George
25 April 2003
CS 200 Spring 2003

20. Complexity Molecular map of colon cancer cell
from
25 April 2003
CS 200 Spring 2003

21. Computing with DNA
Leonard Adleman (Mathematical Consultant for Sneakers), 1995
25 April 2003
CS 200 Spring 2003

22. Hamiltonian Path Problem
Input: a graph, start vertex and end vertex
Output: either a path from start to end that touches each vertex in the graph exactly once, or false indicating no such path exists
RIC
start: CHO
end: BWI
BWI
CHO
How hard is the
Hamiltonian path
problem?
IAD
25 April 2003
CS 200 Spring 2003

23. Encoding The Graph
Make up a two random 4-nucleotide sequences for each city:
CHO: CHO1 = ACTT CHO2 = gcag RIC: RIC1 = TCGG RIC2 = actg
IAD: IAD1 = GGCT IAD2 = atgt
BWI: BWI1 = GATC BWI2 = tcca
If there is a link between two cities (AB), create a nucleotide sequence: A2B1
CHORIC gcagTCGG
RICCHO actgACTT
Based on Fred Hapgood’s notes on Adelman’s talk
25 April 2003
CS 200 Spring 2003

24. Encoding The Problem
Each city nucleotide sequence binds with its complement (A  T, G  C) :
CHO: CHO1 = ACTT CHO2 = gcag
CHO’: TGAA cgtc RIC: TCGGactg
RIC’: AGCCtgac
IAD: GGCTatgt IAD’ = CCGAtaca
BWI: GATCtcca BWI’ = CTAGaggt
Mix up all the link and complement DNA strands – they will bind to show a path!
25 April 2003
CS 200 Spring 2003

25. Path Binding CHO’ TGAAcgtc IAD’ CCGAtaca RIC’ AGCCtgac BWI’ CTAGaggt
gcagGGCT
CHOIAD
atgtTCGG
IADRIC
actgGATC
RICBWI
TCGGactg
RIC
BWI
CHO
GATCtcca
ACTTgcag
IAD
GGCTatgt
25 April 2003
CS 200 Spring 2003

26. Getting the Solution
Extract DNA strands starting with CHO and ending with BWI
Easy way is to remove all strands that do not start with CHO, and then remove all strands that do not end with BWI
Measure remaining strands to find ones with the right weight (7 * 8 nucleotides)
Read the sequence from one of these strands
25 April 2003
CS 200 Spring 2003

27. Why don’t we use DNA computers?
Speed: shaking up the DNA strands does 1014 operations per second ($400M supercomputer does 1010)
Memory: we can store information in DNA at 1 bit per cubic nanometer
How much DNA would you need?
Volume of DNA needed grows exponentially with input size
To solve ~45 vertices, you need ~20M gallons
25 April 2003
CS 200 Spring 2003

28. DNA-Enhanced PC
25 April 2003
CS 200 Spring 2003

29. Biology is (becoming) a subfield of Computer Science
Biological mechanisms are mostly understood (proteomics still has a way to go)
What is not understood is how those are combined to create meaning
25 April 2003
CS 200 Spring 2003

30. PS8
Before 10:55am Monday:
Submit a zip file of all your code using a form linked from the CS200 web site
If you want to use a few PowerPoint slides in your presentation, you may submit those also
You only have 3 or 5 minutes: use them wisely
Figure out beforehand what you will do
Recommend: one team member drive web browser, one (or two) talk
Talk about what users should know about your website, not about how you built it (unless there is something especially interesting)
25 April 2003
CS 200 Spring 2003

31. McIntire Symposium Talk: Daniel Kahneman (Psychologist, Nobel Prize in Economics)
When you are 99% sure, how often are you actually right?
85-90% of the time
Some of you will get a sticker on your Exam 2 that will make you 99.5% sure of the lowest grade you could receive in CS200 (the 0.5% is since you still need to do PS8 well)
Humans are overly optimistic and excessively risk averse
No risk in taking the final: it cannot lower your grade
You should be optimistic that it can help your grade
25 April 2003
CS 200 Spring 2003

32. Final Out Monday, due Monday, May 5 (4:55pm)
You have 8 days, but should not spend more than 4 hours on the exam
Will include:
A small programming problem (like a PS)
Some questions about computability and complexity
25 April 2003
CS 200 Spring 2003

33. Graduation Photo
25 April 2003
CS 200 Spring 2003