Lecturer: Shuki Bruck Information and Logic 331 Moore ...paradise.caltech.edu/ist4/lectures/lect...

Tuesday Thursday 2:30-4:00

Annenberg 105

Lecturer: Shuki Bruck 331 Moore Office hours: Tuesday, Thursday; 4-5pm

IST 4 Information and Logic

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

A request

What is the most important goal

of your studies

at Caltech?

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

Escher 1898-1972

Escher 1898-1972

De-familiarize

“If we start to examine the general laws of perception, we see that as perception becomes habitual, it becomes automatic”

1925

Defamiliarize

“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

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

Teaching Information and Logic

Where should we start?

Life on earth ~3.7 Billion ya

Earth ~4.5 Billion ya

The Universe ~14 Billion years ago (ya)

Source: Wikipedia

Information

What is life?

Information

It is a natural

information system

I

I I

I

I I I I

I

I I

I

I

I I

I

I I

I

I

I

I

I

I

I I

I I

I I

I

I

I

I I

I

Source: Wikipedia

I

I

Source: Wikipedia

I

Rewriting?

Questions about Life:

Origins?

Memory?

?? DNA

Selection? Mutation? New species?

Life is a natural

information system

What is an Information System?

memory + intention

Life is a natural

information system

Replication Development Behavior memory (DNA) + intention = action

present time

future time??

Life is a natural

information system

memory + intention

future time??

DNA survival

Production of new information systems via evolution

Information production

Memory DNA

Selection Mutations New species

Life - Information system

mutations

TCATGCA

Mutations - Simple

TCATGCA

TCATGCA

point mutation

TGATGCA

TGCA

deletion

TCATGCA

insertion

TCAAGTTGCA

Mutations -Duplications

TCATGCA

Duplication (tandem)

TCATCATGCA

TCATGCA

Duplication (interspersed)

TCATGCCATGA

Duplications are Common

45%

3%3%

49%

Transposons-driven Tandem Other repeats Unique

A Repeat Region from Human Chromosome 1

GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !


GCTCCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTGCGTTACAGGTGGGCAGGGGAGGCG GCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTCCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGAGGCTGCTCCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGGGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCAGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTCCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCGGCTGCGTTACAGGTGGGCGGGGGAGGCG !


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


Mutations – Questions???

point mutations vs duplications? bug or feature?

recovering the history of mutations?

Percentage of Genes Shared With Human

ACGT

The Tech Museum of Innovation

Evolution

ACGT

“The seed of life”

ACGT

ACGTACTTGCGTACTTGCGTACTT

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”

A ‘Binary String’ View of Evolution

ACGT

“The seed of life”

01

0100110101100111Q: Generate any binary string from 01 with tandem duplications?

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

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

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

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!

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

In Ternary (and higher alphabets) Seeds Are Not Unique

ACGT

012101212Find the seed

012101212

0121012

012101212

01212

01212

012

Irreducible

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

Metamorphosis

Megamorphosis

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

What is special about the human brain?

Three Dog 3

Three Dog 3

??? Languages

Source: Wikipedia 2Mya

1.2Mya

Verbal languages ~75Kya

Information system

memory intention

DNA survival Life

Information system

memory intention

DNA survival Life

Brain human

memory survival

We are “memory machines” However, our memory sense is

limited... We are doing well because we found a way to augment our memory?

How do we augment our memory?

collective memory languages stories

teaching external memory

managing our external memory

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

IST 4: Explore the evolution of ideas in information and logic

1 Million years

your first assignment...

Everyone has a gift!

"I have no special talents I am only passionately curious" Albert Einstein

•  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...

•  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

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

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

Organization and Policy

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

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

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

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

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)

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

Take-homes from today: Information Megamorphosis: Life and the human brain DNA is the language of life... Language is the DNA of ideas...

Lecturer: Shuki Bruck Information and Logic 331 Moore ...paradise.caltech.edu/ist4/lectures/lect...

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