biologically-inspired computing lecture 14 Informatics luis rocha 2015 biologically Inspired computing INDIANA UNIVERSITY

Size: px

Start display at page:

Download "biologically-inspired computing lecture 14 Informatics luis rocha 2015 biologically Inspired computing INDIANA UNIVERSITY"

Delilah Collins
5 years ago
Views:

1 lecture 14 -inspired

Sections I485/H400 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 14 th

2 Sections I485/H400 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 14 th (completed) Introduction to Python (No Assignment) Lab 1 : January 28 th Measuring Information (Assignment 1) Graded Lab 2 : February 11 th L-Systems (Assignment 2) Graded Lab 3: March 25 th Cellular Automata & Boolean Networks (Assignment 3) Due: April 1 st Lab 4: April 8 th Genetic Algorithms (Assignment 4) Due: April 22 nd

2, 8.3.10 Lecture notes Chapter 1: What is Life?

3 Readings until now Class Book Nunes de Castro, Leandro [2006]. Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications. Chapman & Hall. Chapters 1, 2, , , , 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 Other materials Flake s [1998], The Computational Beauty of Nature. MIT Press Chapters 10,11, 14

final project schedule ALIFE 15 Projects Due

edu/alife14nyc/ 8 pages (LNCS proceedings

4 final project schedule ALIFE 15 Projects Due by May 4 th in Oncourse ALIFE 15 (14) Actual conference due date: pages (LNCS proceedings format) D= Preliminary ideas due by April 1 st! Individual or group With very definite tasks assigned per member of group

A fundamental principle of computation Turing s tape On computable numbers with an application to the Entscheidungsproblem Turing,

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

Universal machine distinction between numbers that mean things (data) and numbers that do things (program) The fundamental,

6 A fundamental principle of computation Turing s tape On computable numbers with an application to the Entscheidungsproblem Turing, A. M. Proc. Lond. Math. Soc. s2 42, ( ). 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) 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.

some facts 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

7 some facts 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 [ ] essential elements in the machine are of a binary [ ] nature. Those whose state is determined by their history and are timestable 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

has a value of 5, Each bead on the lower deck has value of 1 Beads are considered counted, when moved towards the

8 Abacus brief history devices 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.

Wilhelm Schickard (1592-1635) In 1623 built the first mechanical calculator can work with six digits, and carries digits across

Blaise Pascal (1623-1662) built a mechanical calculator in 1642 It has the capacity for eight digits, but has trouble carrying

10-teeth gears Gottfried von Leibniz (1614-1716) built a mechanical calculator in 1670 capable of multiplication and division

states Forefathers of the modern computer The human race will have a new kind of instrument which will increase the power of

9 Wilhelm Schickard ( ) 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 ( ) 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 ( ) 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 Forefathers of the modern computer 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.

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

10 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

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.

11 Difference Engine Special-purpose digital 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 Charles Babbage ( )

Charles Babbage (1791 1871) and Ada Lovelace (1815-1852) The analytical engine had an external tape

machine, called the Analytical Engine. [ ] general-purpose mechanical digital computer.

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

distinct punched cards "It is only a question of cards and time, [ ] and there is no reason why (twenty

12 Charles Babbage ( ) and Ada Lovelace ( ) The analytical engine had an external tape Turing on programs (numbers as instructions) : [Babbage] had all the essential ideas [and] planned such a machine, called the Analytical Engine. [ ] 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 "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)

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

Analytical engine Separated memory store from a central

Programmable instructions on punched cards by the Jacquard

(recursive) rules for producing Bernoulli numbers (a

would punch out cards for later use the Engine eating its

13 Charles Babbage ( ) and Ada Lovelace ( ) The external tape as a general principle (system) of universal Analytical engine Separated memory store from a central processing unit (or mill ) Cogs not just numbers variables Programmable instructions on punched cards 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 things and numbers that do things.

Informatics John Von Neumann (1903-1957) Turing machines beyond the decision

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

the importance of the storedprogram concept (the external tape) EDVAC allows

separation of storage from the processing unit.

(random-access memory) Let the whole outside world consist of a long John von

computers are in a sense equivalent, we see that this use of electricity cannot

14 Informatics John Von Neumann ( ) Turing machines beyond the decision problem Words coding the orders are handled in the memory just like numbers --- distinction between numbers that mean things and numbers that do things. realizing the power of Turing s tape physical (electronic) computers emphasized the importance of the storedprogram 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) Let the whole outside world consist of a long John von Neumann, 1948 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) paper tape.

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.

15 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 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.

First conceived Geoffrey W.A. Dummer Royal Radar Establishment of the British Ministry of Defense in 1952.

Thin chip consisting of at least two interconnected semiconductor transistors, as well as passive components like resistors.

16 First conceived Geoffrey W.A. Dummer Royal Radar Establishment of the British Ministry of Defense in 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, 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. Integrated Circuits

17 design principles of computation Babbage/Lovelace, Turing s tape, and roles of information distinction between numbers that mean things and numbers that do things.

19 Structure and organelles Life is made up of structural and functional units called cells (19 th Century) the eukaryotic cell

20 Structure and organelles Life is made up of structural and functional units called cells (19 th Century) the eukaryotic cell

Cell theory Term coined by Robert Hooke (17 th

century) All organisms are composed of one or more

All vital functions of an organism occur within cells.

21 Cell theory Term coined by Robert Hooke (17 th century) Matthias Schleiden and Theodor Schwann (19 th 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 more about cells phytoplankton

more about cells Cell theory Term coined by Robert Hooke (17 th century) Matthias Schleiden and Theodor Schwann (19 th century) All organisms are composed of one or more cells.

5 billion years ago) in single-celled and colonial organisms Bacteria and Archaea, asexual reproduction, Eukaryotic cells (aprox. 1.6-2.

22 more about cells Cell theory Term coined by Robert Hooke (17 th century) Matthias Schleiden and Theodor Schwann (19 th 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 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

23 more about cells Cell theory Term coined by Robert Hooke (17 th century) Matthias Schleiden and Theodor Schwann (19 th 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 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

24 more about cells Cell theory Term coined by Robert Hooke (17 th century) Matthias Schleiden and Theodor Schwann (19 th 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 billion years ago) Contain organelles with their own membranes Single (amoeba) and multicelular, slime mold, colonial (sponge) Organisms Unicellular, colonial, and multicellular

readings Next lectures Class Book Nunes de Castro, Leandro [2006]. Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications. Chapman & Hall.

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

25 readings 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 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 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.

complex networks and systems i609: advanced PhD seminar I Informatics luis rocha 2019 INDIANA UNIVERSITY

complex networks and systems Informatics luis rocha 2019 i609: advanced PhD seminar I luis m. rocha school of informatics, computing, & engineering indiana university, bloomington, usa and instituto gulbenkian