lecturer: shuki bruck information and logic 331 moore ...paradise.caltech.edu/ist4/lectures/lect...
TRANSCRIPT
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Tuesday Thursday 2:30-4:00
Annenberg 105
Lecturer: Shuki Bruck 331 Moore Office hours: Tuesday, Thursday; 4-5pm
IST 4 Information and Logic
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Office hours at SFL study room, 2nd floor: - Monday (or Friday): 4-5pm; 9-10:30pm - Wednesday: 4-5pm; 9-10:30pm For questions: [email protected] web site: paradise.caltech.edu/ist4/
Secretary: Michelle Chen; 304 Moore
Sidd Grace Chris Jason Lidan
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A request
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What is the most important goal
of your studies
at Caltech?
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Learn to ask questions
The most important goal of your studies at Caltech?
Discover your passion and your gifts!
Do not worry about forgetting the answers
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Escher 1898-1972
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Escher 1898-1972
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Escher 1898-1972
De-familiarize
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“If we start to examine the general laws of perception, we see that as perception becomes habitual, it becomes automatic”
1925
Defamiliarize
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“The purpose of art is to impart the sensation of things as they are perceived and not as they are known”
1925
The purpose of IST4 is to impart the sensation of ideas as they are conceived and not as they are known
Defamiliarize
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How? Teach about the historical innovation process
and the related inventors
Make the subject of Information and Logic
unfamiliar...
The purpose of IST4 is to impart the sensation of ideas as they are conceived and not as they are known
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Teaching Information and Logic
Where should we start?
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Life on earth ~3.7 Billion ya
Earth ~4.5 Billion ya
The Universe ~14 Billion years ago (ya)
Source: Wikipedia
Information
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What is life?
Information
It is a natural
information system
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Source: Wikipedia
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Source: Wikipedia
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Rewriting?
Questions about Life:
Origins?
Memory?
?? DNA
Selection? Mutation? New species?
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Life is a natural
information system
What is an Information System?
memory + intention
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Life is a natural
information system
Replication Development Behavior memory (DNA) + intention = action
present time
future time??
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Life is a natural
information system
memory + intention
future time??
DNA survival
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Production of new information systems via evolution
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Information production
Memory DNA
Selection Mutations New species
Life - Information system
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mutations
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TCATGCA
Mutations - Simple
TCATGCA
TCATGCA
point mutation
TGATGCA
TGCA
deletion
TCATGCA
insertion
TCAAGTTGCA
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Mutations -Duplications
TCATGCA
Duplication (tandem)
TCATCATGCA
TCATGCA
Duplication (interspersed)
TCATGCCATGA
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Duplications are Common
45%
3%3%
49%
Transposons-driven Tandem Other repeats Unique
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
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A Repeat Region from Human Chromosome 1
GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
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GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
A Repeat Region from Human Chromosome 1
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GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
Point Mutations and Duplications
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GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGAGGCT GCTCCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGGGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTCCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG GCTGCGTTACAGGTGGGCGGGGGAGGCG !
Mutations – Questions???
point mutations vs duplications? bug or feature?
recovering the history of mutations?
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Percentage of Genes Shared With Human
ACGT
The Tech Museum of Innovation
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Evolution
ACGT
“The seed of life”
ACGT
ACGTACTTGCGTACTTGCGTACTT
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The History of Mutations
ACGTACTTGCGTACTTGCGTACTT
ACGT
ACGT ACTT GCGT ACTT GCGT ACTT
ACGT ACTT GCGT ACTT
ACGT ACTT GCGT ACTT
ACGT ACTT
ACGT ACTT
ACGT “The seed of life”
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A ‘Binary String’ View of Evolution
ACGT
“The seed of life”
01
0100110101100111Q: Generate any binary string from 01 with tandem duplications?
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A ‘Binary String’ View of Evolution
ACGT
01
0100110101100111
???
010011010110011101 01 0101 01
Q: Generate any binary string from 01 only with tandem duplications? Yes
idea
The target string has to start with 0 and end with 1
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Evolution with Tandem Duplication - Binary 010011010110011101
0101010101010101010101010010101010100110101010100110101101010011010110010100110101100110100110101100111
Proof: We have an algorithm! Generate the 01 blocks and then extend the 0s and 1s
Also: It is true if the duplication length is either 1 or 2.
Seed Thm: Any binary string can be generated from one of the 6 seeds {0,1,01,10,010,101} with tandem duplications
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ACGT
0100110101101
Thm: Any binary string can be generated from one of the 6 seeds {0,1,01,10,010,101} with tandem duplications
What is the seed?
0000000000000
1111111111111
11001101011000100110101100
1100110101101
10
0110
010
101
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ACGT
0100110101101
Thm: Any binary string can be generated from one of the 6 seeds {0,1,01,10,010,101} with tandem duplications
What is the seed?
0000000000000
1111111111111
11001101011000100110101100
1100110101101
10
0110
010
101
Seeds are unique!
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Evolution with Tandem Duplication - Ternary
ACGT
Q: Can we generate with tandem duplications any ternary string from a finite set of seeds?
A: Yes
0121012Can you generate from 012
012101212Can you generate from 012
01210121201212012012101212
A: No
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In Ternary (and higher alphabets) Seeds Are Not Unique
ACGT
012101212Find the seed
012101212
0121012
012101212
01212
01212
012
Irreducible
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Generation of Sequences via Duplications and Point Mutations
ACGT
01210120
012101210121
010101
01210120
0101
01
01010101
2 duplications 2 mutations
2 duplications 3 mutations
0121012001
An active research area
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Metamorphosis
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Megamorphosis
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The appearance of life is the first Information Megamorphosis
What is the second Information Megamorphosis?
The appearance of the human brain is the second Information Megamorphosis
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What is special about the human brain?
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Three Dog 3
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Three Dog 3
??? Languages
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Source: Wikipedia 2Mya
1.2Mya
Verbal languages ~75Kya
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Information system
memory intention
DNA survival Life
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Information system
memory intention
DNA survival Life
Brain human
memory survival
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We are “memory machines” However, our memory sense is
limited... We are doing well because we found a way to augment our memory?
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How do we augment our memory?
collective memory languages stories
teaching external memory
managing our external memory
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How do we augment our memory?
collective memory languages stories
teaching external memory
managing our external memory
IST 4: Explore the evolution of the expansion of our brain
external information and external logic
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IST 4: Explore the evolution of ideas in information and logic
1 Million years
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your first assignment...
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Everyone has a gift!
"I have no special talents I am only passionately curious" Albert Einstein
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• You are invited to write short essay on the topic of the Magenta Question. Extra Credit of 3 points
Everyone has a gift! MQ Due Thursday 4/7/2016 at 10pm
someone you know
you
anyone...
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• You are invited to write short essay on the topic of the Magenta Question. • Recommended length is 3 pages (not more) • Submit the essay in PDF format to [email protected] file name lastname-firstname.pdf • No collaboration. No extensions
Everyone has a gift! MQ Due Thursday 4/7/2016 at 10pm
Grading of MQ: 3 points (out of 105) 50% for content quality, 50% for writing quality Some students will be given an opportunity to give a short presentation for up to 3 additional points
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1. Diana Ardelean - The Gift of Becoming a GO Player
2. Shalini Majumdar - The Gift of Companionship
3. Alex Geffner-Mihlsten - The Gift of Names and Lives
4. Sumana Mahata - The Gift of Laughter
5. Parth Shah - My Mother has the Greatest of all Gifts!
6. Tim Menninger – Colors
7. Nasser Al Rayes - Boo (The Gift of Being Tall)
8. Sophia Yuenchih Chen - The Gift of Uniqueness
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1. Christopher Haack: The gift of resilience
2. Joon Lee: Settling is not an option
3. Spencer Strumwasser: The gift of dyslexia
4. Richard Zhu: The gift of memory
5. Ashwin Hari: The gift of musical composition
6. Jessica Nassimi: Evolution—a gift in disguise
7. Serena Delgadillo: The gift of self-expression
8. Megan Keehan: Gift of motherliness
9. Zane Murphy: Grandmother and the piano
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Organization and Policy
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Class Policy
Homework sets: There are 5 homework sets; all weighted equally. The total weight of the 5 homework set is 94 points
There is no midterm and no final
Essays: There are two essays, 3 points each A selected set of students are given the opportunity to present their essay in class (3 points)
However, to be eligible to receive credit for quizzes/ essays / presentations/ extra credit, a student has to fully attend at least 16 lectures (out of 20), must attend the last two lectures (at least 14+2)
Quizzes: There are 5 in-class pop quizzes, for a total credit of 2 points
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Class Policy Attendance When you attend a class, you should write your initial next to your name on the attendance list provided by the TAs Final Grade The final grade is calculated based on the grades of the homeworks and the quizzes / essays / presentations (if the student is eligible) and will be converted to a letter grade:
94+2+3+3+3
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Class Policy
Collaboration and Open-Book policy Collaboration, in the sense of discussing how to solve the homework problems, is allowed on some, but not all, homework problems. Every homework problem includes a specific statement whether collaboration is allowed or not For all homeworks: • Write the final solutions of the homeworks alone and understand them fully • Books, papers, notes can be consulted, but not copied from • The use of solutions from previous years is not allowed
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Class Policy - Homeworks • Homeworks are to be submitted in class They are due at the start of class on the due date
• A late homework submission should include only solutions to problems that were not attempted in the previous (on-time) submission • We are human... and occasionally make mistakes in grading; corrections of grades should be requested within a week from the time the graded homeworks were returned
• Late homeworks lose 20% of their value immediately and lose 100% of their value a week after the due date except in institute-established cases of illness or emergency
• Homeworks are returned in class. Keep your graded sets until you get the final grade. That’s your record
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There is no Text Reference Books
• The reference books are recommended as sources for extending your knowledge beyond what is covered in class • They are not a required reading
• The list is posted on the class web site • The books are reserved at the Caltech library (SFL)
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mon tue wed thr fri 28 M1 1 4 M1
11 1 2 M2
18 2
25 M2 2 3 9 3 4 16 4 5 23
30 5
x= hw#x out
x= hw#x due
Mx= MQx out
Mx= MQx due
midterms
oh oh
oh oh
oh oh
oh
oh
oh oh
oh
oh
oh
oh
oh
oh
oh
oh = office hours oh
T = today T oh
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Take-homes from today: Information Megamorphosis: Life and the human brain DNA is the language of life... Language is the DNA of ideas...