Info atics biologically-inspired computing luisrocha2015 lecture 14 · 2015. 12. 14. · [email protected] biologically Inspired computing INDIANA UNIVERSITY Informatics luisrocha2015

[email protected]://informatics.indiana.edu/rocha/i-bic

biologicallyInspired

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Informatics luis rocha 2015

biologically-inspired computinglecture 14


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course outlook

Assignments: 35% Students will complete 4/5 assignments based on

algorithms presented in class Lab meets in I1 (West) 109 on Lab Wednesdays

Lab 0 : January 14th (completed) Introduction to Python (No Assignment)

Lab 1 : January 28th

Measuring Information (Assignment 1) Graded

Lab 2 : February 11th

L-Systems (Assignment 2) Graded

Lab 3: March 25th

Cellular Automata & Boolean Networks (Assignment 3) Due: April 1st

Lab 4: April 8th

Genetic Algorithms (Assignment 4) Due: April 22nd

Sections I485/H400


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Readings until now

Class Book Nunes de Castro, Leandro [2006]. Fundamentals of Natural

Computing: Basic Concepts, Algorithms, and Applications. Chapman & Hall. Chapters 1, 2, 3.1-3.4, 7.1-7.5, 8.1-8.2, 8.3.10

Lecture notes Chapter 1: “What is Life?” Chapter 2: “The Logical Mechanisms of Life” Chapter 3: “Formalizing and Modeling the World” Chapter 4: “Self-Organization and Emergent

Complex Behavior” posted online @ http://informatics.indiana.edu/rocha/i-

bic Other materials

Flake’s [1998], The Computational Beauty of Nature. MIT Press Chapters 10,11, 14


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final project schedule

Projects Due by May 4th in Oncourse

ALIFE 15 (14) Actual conference due date: 2016 http://blogs.cornell.edu/alife14nyc/

8 pages (LNCS proceedings format) http://www.springer.com/computer/lncs?SGWI

D=0-164-6-793341-0 Preliminary ideas due by April 1st!

Individual or group With very definite tasks assigned per

member of group

ALIFE 15


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Turing’s tape

“On computable numbers with an application to the Entscheidungsproblem” Turing, A. M. Proc. Lond. Math. Soc. s2–42, 230–265 (1936–37).

Turing machine, universal computation, decision problem Machine’s state is controlled by a program, while data

for program is on limitless external tape every machine can be described as a number that can be

stored on the tape for another machine Including a Universal machine

distinction between numbers that mean things (data) and numbers that do things (program)

A fundamental principle of computation

“The fundamental, indivisible unit of information is the bit. The fundamental, indivisible unit of digital computation is the transformation of a bit between its two possible forms of existence: as [memory] or as [code]. George Dyson, 2012.


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computation

Process of rewriting strings in a formal system according to a program of rules Operations and states are syntactic Symbols follow syntactical rules Rate of computation is irrelevant

Program determines result, not speed of machine Physical implementation is irrelevant for result

Computer Physical device that can reliably

execute/approximate a formal computation Errors always exist Design aims to make rate and dynamics irrelevant

some facts

“[…] essential elements in the machine are of a binary […] nature. Those whose state is determined by their history and are time-stable are memory elements. Elements of which the state is determined essentially by the existing amplitude of a voltage or signal are called ‘gates’”. Bigelow et al, 1947


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brief history computing devices

Abacus A counting aid, may have been invented in

Babylonia in the fourth century B.C. Not automatic: memory aid for intermediate

calculations Very used in China and Japan

Each bead on the upper deck has a value of 5, Each bead on the lower deck has value of 1

Beads are considered counted, when moved towards the beam that separates the two decks.

Reconstruction of a Roman abacus in the Cabinet des Médailles, Bibliothèque nationale, Paris.


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Forefathers of the modern computer Wilhelm Schickard (1592- 1635)

In 1623 built the first mechanical calculator can work with six digits, and carries digits

across columns. It works, but never makes it beyond the prototype stage.

Blaise Pascal (1623-1662) built a mechanical calculator in 1642

It has the capacity for eight digits, but has trouble carrying and its gears tend to jam.

10-teeth gears Gottfried von Leibniz (1614-1716)

built a mechanical calculator in 1670 capable of multiplication and division (shift) registers for binary arithmetic Credited Chinese for Binary arithmetic

Closer to abacus Passive register (memory) of states

“The human race will have a new kind of instrument which will increase the power of the mind much more than optical lenses strengthen the eyes… One could carry out the description of a machine, no matter how complicated, in characters which would be merely the letters of the alphabet, and so provide the mind with a method of knowing the machine and all its parts.” Leibniz, 1679.


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The Antikythera Mechanism 2,000-year-old astronomical calculator

bronze mechanical analog computer discovered more than 100 years ago in a Roman shipwreck, was used by

ancient Greeks to display astronomical cycles. built around the end of the second century BC to calculate

astronomical positions With imaging and high-resolution X-ray tomography to study how it

worked. complicated arrangement of at least 30 precision, hand-cut bronze gears

housed inside a wooden case covered in inscriptions. technically more complex than any known device for at least a millennium

afterwards.

Not a universal Turing machine, but an analog computer


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Charles Babbage (1791 – 1871)

Difference Engine Special-purpose digital computing machine

for the automatic production of mathematical tables. logarithm tables, tide tables, and

astronomical tables Steam-driven, consisted entirely of

mechanical components - brass gear wheels, rods, ratchets, pinions, etc.

Numbers were represented in the decimal system by the positions of 10-toothed metal wheels mounted in columns.

Never completed the full-scale machine Completed several fragments. The largest is

on display in the London Science Museum. In 1990, it was built (London Science Museum)

The Swedes Georg and Edvard Scheutz(father and son) constructed a modified version of Babbage's Difference Engine.

For an interesting “what-if” scenario read “The Difference Engine” by Bruce Sterling and William Gibson

Not a universal Turing machine, but an analog computer


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Informatics luis rocha 2015 The analytical engine had an “external tape”

Charles Babbage (1791 – 1871) and Ada Lovelace (1815-1852)

general-purpose mechanical digital computer. Separated memory store from a

central processing unit (or ‘mill’) able to select from among

alternative actions consequent upon the outcome of its previous actions Conditional branching: Choice, information

Mechanical cogs not just numbers Variables (states/configurations)

Programmable Data and instructions on distinct

punched cards

Turing on programs (numbers as instructions) : “[Babbage] had all the essential ideas [and] planned such a machine, called the Analytical Engine. […]

"It is only a question of cards and time, […] and there is no reason why (twenty thousand) cards should not be used if necessary, in an Analytical Engine for the purposes of the mathematician”. Henry Babbage (1888)


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Informatics luis rocha 2015 The external tape as a general principle (system) of universal computing

Charles Babbage (1791 – 1871) and Ada Lovelace (1815-1852)

Analytical engine Separated memory store from a

central processing unit (or ‘mill’) Cogs not just numbers

variables Programmable

instructions on punched cards Inspired by the Jacquard Loom

Ada Lovelace: the science of operations Set of (recursive) rules for producing

Bernoulli numbers (a program) Separation of variable and operational

(data) cards would punch out cards for later use

“the Engine eating its own tail.” (Babbage)

distinction between numbers that mean thingsand numbers that do things.


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John Von Neumann (1903-1957)

realizing the power of Turing’s tape physical (electronic) computers emphasized the importance of the stored-

program concept (the external tape) EDVAC

allows machine to modify its own program von Neumann architecture: The functional

separation of storage from the processing unit. programs can exist as data (two roles)

Converts tape to fixed-address memory (random-access memory)

Turing machines beyond the decision problem

“Let the whole outside world consist of a long paper tape”. —John von Neumann, 1948

“ ‘Words’ coding the orders are handled in the memory just like numbers” --- distinction between numbers that mean things and numbers that do things.

“Since Babbage’s machine was not electrical, and since all digital computers are in a sense equivalent, we see that this use of electricity cannot be of theoretical importance.… The feature of using electricity is thus seen to be only a very superficial similarity.” (Alan Turing)


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Semi-conductor Transistors

Invented by John Bardeen, Walter Houser Brattain, and William Bradford Shockley at Bell Laboratories in December 1947 awarded the Nobel Prize in physics in 1956.

Function as switches A device for making or breaking an electric circuit

Also for amplification in analog devices For choosing between several states

Between “on” and “off”, “1” or “0” Allows the construction of logic gates

Semiconductor device principally silicon, germanium and gallium arsenide.

Better than vacuum tubes Smaller size, Highly automated manufacture, Lower cost,

Lower operating voltage, Absence of a heater Lower power dissipation etc.


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Integrated Circuits

First conceived Geoffrey W.A. Dummer Royal Radar Establishment of the British Ministry of

Defense in 1952. First manufactured independently by two

scientists Jack Kilby of Texas Instruments (Germanium) on

February 6, 1958 Robert Noyce of Fairchild Semiconductor (Silicon)

on April 25, 1961. Thin chip consisting of at least two interconnected

semiconductor transistors, as well as passive components like resistors. Modern-day chips are of size 1 cm2 or smaller, and

contain millions of interconnected devices. Allowed the placement of many transistors in a

small area Typical use as microprocessors

Central Processing Unit (CPU) part of a computer that interprets and carries out the

instructions contained in the software.



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design principles of computationBabbage/Lovelace, Turing’s tape, and roles of information

distinction between numbers that mean things and numbers that do things.


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the eukaryotic cellStructure and organelles

Life is made up of structural and functional units called cells (19th

Century)



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the eukaryotic cellStructure and organelles

Life is made up of structural and functional units called cells (19th

Century)


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more about cells Cell theory

Term coined by Robert Hooke (17th

century) Matthias Schleiden and Theodor

Schwann (19th century) All organisms are composed of

one or more cells. All cells come from preexisting

cells. All vital functions of an organism

occur within cells. Cells contain life’s hereditary

information

phytoplankton


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Term coined by Robert Hooke (17th century) Matthias Schleiden and Theodor Schwann (19th century)

All organisms are composed of one or more cells. All cells come from preexisting cells. All vital functions of an organism occur within cells. Cells contain life’s hereditary information

Types of Cells Prokaryotic (3.5 billion years ago)

in single-celled and colonial organisms Bacteria and Archaea, asexual reproduction,

Eukaryotic cells (aprox. 1.6 - 2.1 billion years ago) Contain organelles with their own membranes

Single (amoeba) and multicelular, slime mold, colonial (sponge) Organisms

Unicellular, colonial, and multicellular Chromosome structure

Haploid: One copy of each chromosome Fungi, male bees, wasps and ants

Diploid: Two copies (homologs) of each chromosome One homolg from each parent


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Unicellular, colonial, and multicellular Chromosome structure

Haploid: One copy of each chromosome Fungi, male bees, wasps and ants

Diploid: Two copies (homologs) of each chromosome One homolg from each parent


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Unicellular, colonial, and multicellular


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Next lectures

Class Book Nunes de Castro, Leandro [2006]. Fundamentals of Natural

Computing: Basic Concepts, Algorithms, and Applications. Chapman & Hall. Chapter 2, 7, 8 Appendix B.3.2-3 - Turing Machines, Computational complexity Chapter 3, sections 3.1 to 3.5

Lecture notes Chapter 1: “What is Life?” Chapter 2: “The logical Mechanisms of Life” Chapter 3: Formalizing and Modeling the World Chapter 4: “Self-Organization and Emergent Complex

Behavior” Chapter 5: “Reality is Stranger than Fiction”

posted online @ http://informatics.indiana.edu/rocha/i-bic Optional materials

Flake’s [1998], The Computational Beauty of Life. MIT Press Chapter 20

Scientific American: Special Issue on the evolution of Evolution, January 2009.

readings

Documents

Info atics biologically-inspired computing luisrocha2015 lecture 14 · 2015. 12. 14. · [email protected] biologically Inspired computing INDIANA UNIVERSITY Informatics luisrocha2015