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Info rm atics biologically-inspired computing luis rocha 2015 lecture 2 biologically Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics course outlook luis rocha 2015 Sections I485/H400  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) biologically Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics readings luis rocha 2015 Until now  Class Book  Nunes de Castro, Leandro [2006]. Fundamentals of Natural Computing: Basic Concepts, Algorithms, and Applications . Chapman & Hall. Chapter 1, pp. 1-23.  Lecture notes  Chapter 1: “What is Life?”  posted online @ http://informatics.indiana.edu/rocha/i-bic  Papers and other materials  Life and Information  Dennet, D.C. [2005]. "Show me the Science". New York Times , August 28, 2005 biologically  Polt, R. [2012]. "Anything but Human". New York Inspired Times , August 5, 2012 computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics 3 types of definitions luis rocha 2015  Organization distinct from inorganic matter  with an associated list of properties  matter controlled by genomic information  Animated behavior  Vitalism  life as a special, incommensurable, quality  Not a viable scientific explanation, because for science nothing is in principle incommensurable.  Pertains to metaphysics.  If the agent of design of the special quality cannot be observed with physical means, then it is by definition beyond the scope of science as it cannot be tested.  See Dennett’s and Polt’s pieces biologically Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics the living organization? luis rocha 2015 how to identify it?  List of properties viruses, candle  Growth flames, the Is life  Metabolism Earth, certain Fuzzy?  Reproduction robots?  Adaptability  Self-maintenance (autonomy)  Self-repair  Reaction  Evolution  Choice  Threshold of complexity  Closure (metabolic, functional) Is there a synthetic criteria? How  Categorization and Control general can it be?  Function (self-reference) biologically  Open-ended evolution Inspired  (genomic) Information computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics how much of life is organization? luis rocha 2015 how much is specific bio-chemistry and history?  Can there be several implementations of life?  To study life do we need to find and synthesize the necessary threshold of complexity?  Hard Artificial Life  Or is it enough to simulate the behavior of life?  Soft Artificial Life  What about implementing “new” life in known biochemistry  Wet Artificial Life or Synthetic Biology  Important to study the living organization  What can be abstracted and implemented in a different medium?  Understanding organization and design principles  Scientific advancement of the essential principles of life  Systems and Computational Biology , Artificial Life  Solving engineering and design problems biologically  Bio-inspired computing Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics life as organization luis rocha 2015 complexity threshold  Science often sees life as the complicated physics of a collection of moving bodies  Reductionist search for answers in the nitty- gritty of biochemistry  When do we reach a threshold of complexity after which matter is said to be living?  Life as (emergent) organization  Systems Thought  Ludwig von Bertallanfy (1980)  What is important are not the actual physical components but the relations amongst them  But what about evolution and history?  Conflict between (general) organization and specific components with their history  What organization explains evolution? “Seeking a connecting link, they had condescended to the preposterous assumption of structureless living matter, unorganized organisms, which darted together of themselves in the albumen solution, like crystals in their biologically mother-liquor; yet organic differentiation still remained at once condition and Inspired expression of all life. One could point to no form of life that did not owe its existence to procreation by parents ”. Thomas Mann [1924]. computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics the roles of information luis rocha 2015 in the living organization organisms act according to information they perceive in an  environment organisms reproduce and develop from genetic information   genetic information is transmitted “vertically” (inherited) in phylogeny and cell reproduction, and expressed “horizontally” within a cell in ontogeny and plain functioning Self-reference   Information relevant to organism/environment: function  Only in reference to an organism/environment does a piece of DNA function as a gene  Biology is contextual and historical, physics is universal  How is purpose/function generated from processes without purpose? “Biology and physics have “Life is a dynamic nothing to do with each state of matter other because biological organized by evolution is essentially biologically information ”. historical, and physical Inspired Manfred Eigen laws must be independent computing of history”. Ernst Mayer [1992] rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics information processes in biology luis rocha 2015 how to best understand life?  Genetic System  Construction (expression, development, maintenance, and response) of cells ontogenetically: horizontal transmission  Heredity (reproduction) of cells and phenotypes: vertical transmission  Immune System “Life is a complex  Internal response based on system for accumulated experience (information) information storage  Nervous and Neurological system and processing”.  Response to external cues based on Minoru Kanehisa memory [2000]  Language, Social, Ecological, Eco-social, etc. biologically Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics information basics luis rocha 2015 observer and choice  Information is defined as “a measure of the freedom from choice with which a message is selected from the set of all possible messages”  Bit (short for binary digit ) is the most elementary choice one can make  Between two items: “0’ and “1”, “heads” or “tails”, “true” or “false”, etc.  Bit is equivalent to the choice between two equally likely alternatives  Example, if we know that a coin is to be tossed, but are unable to see it as it falls, a message telling whether the coin came up heads or tails gives us one bit of information 1 Bit of uncertainty H,T? 1 Bit of information biologically Inspired uncertainty removed , choice between 2 symbols computing information gained recognized by an observer rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Info rm atics Fathers of uncertainty-based information luis rocha 2015  Information is transmitted through noisy communication channels  Ralph Hartley and Claude Shannon (at Bell Labs), the fathers of Information Theory, worked on the problem of efficiently transmitting information; i. e. decreasing the uncertainty in the transmission of information. Hartley, R.V.L., "Transmission of Information", Bell System Technical Journal , July 1928, p.535. C. E. Shannon, “A mathematical theory of communication”. Bell System Technical Journal , 27 :379-423 and 623-656 C. E. Shannon, “A Symbolic analysis of relay and switching circuits” . MS Thesis , biologically (unpublished) MIT, 1937. Inspired computing C. E. Shannon, “An algebra for theoretical genetics.” Phd Dissertation , MIT, 1940. rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY

Let’s talk about choices Info rm atics luis rocha 2015  Multiplication Principle  “If some choice can be made in M different ways, and some subsequent choice can be made in N different ways, then there are M x N different ways these choices can be made in succession” [Paulos]  3 shirts and 4 pants = 3 x 4 = 12 outfit choices biologically Inspired computing rocha@indiana.edu INDIANA http://informatics.indiana.edu/rocha/i-bic UNIVERSITY