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Synthetic biology in a computer science view

  1. Synthetic Biology in a Computer Science view - is it (really) true that “everything is software”? by jones albuquerque iGEM-LIKA-CESAR DEINFO-UFRPE ISI-TICs EPITRACK
  2. in an approach like a story... 1. human, codes, languages and machines 2. genetic engineering like computer science 3. (new?) machines by biology synthetic 4. iGEM-LIKA-CESAR
  3. once was a time… we! 2010, SCIAM, Endangered Species: Humans Might Have Faced Extinction 1 Million Years Ago
  4. codes and languages THE SYMBOLS…
  5. THE ISHAGO BONE, 38.000 BC (???) Origins of Mathematics in the Bunyoro-kitara and Kalahari regions of sub Saharan Africa nearly 40,000 years ago the need to record, compute... using codes !
  6. writing codes... The Blackwell Encyclopedia of Writing Systems DOI 10.1111/b.9780631214816.1999.x 4000 BC origin of LANGUAGES
  7. yet another codes... Ancient Chemical Symbols. Psychoanalytic Review, 14:200-206, 1927 Chineses: pictograms, ideograms, iconically… 1436 BC… 1800 – 1050 BC to 1955…
  8. ALPHABET - codes portuguese Greek arabic
  9. universal codes
  10. lexicon, syntactic, semantic
  11. when a code is wrong? depends of rules… grammatical rules Gramática Da Língua Portuguesa (sebo Amigo) R$ 10,00
  12. Nature 426, 435-439(27 November 2003) doi:10.1038/nature02029 our codes and their rules…
  13. ancient X modern codes… Vale do Catimbau – Buíque - PE are there rules?
  14. interpretation of rules (our codes, rules, and languages…)
  15. new ones? or ancient codes in new rules? X 1453 BC X 2014 AC
  16. a lot of codes… and languages…
  17. our need to count MATHEMATICS…
  18. the need to compute... mathematical codes... the NUMBERS a fact: ISHANGO bone the numerical SENSE the representation of complex  complex codes!
  19. The numerical SENSE How many people in the figures?
  20. and now… how many people? Is it difficult? we must to count, compute… the case of Dantzig´s crow and the case of joa´s chicken 
  21. a summary of the “mathematical language”… o lot of code, rules, … do we understand?
  22. and more complex ones?  dense codes!... é a jacobiana, derivada do gradiente… aplicaçoes???
  23. the need to compute THE MACHINES…
  24. codes + numbers... A LOT OF codes languages and machines... 1912 - 1954 / 1928, Professor in Department of Linguistics & Philosophy at MIT
  25. languages and their grammars…
  26. some grammars are special ones…
  27. simple, but… with some special grammars we can transform languages into machines that recognize them and vice-versa!
  28. BUT we need to understand a code to understand another one…
  29. the need for automatic computation... 1936, the UNIVERSAL AUTOMATA MACHINE by Allan Turing
  30. and we have Computer Science and systems and SOFTWARE
  31. the ASCII (American Standard Code for Information Interchange)
  32. Here’s some machine code from a MIPS processor: 00000000101000010000000000011000 00000000100011100001100000100001 10001100011000100000000000000000 10001100111100100000000000000100 10101100111100100000000000000000 10101100011000100000000000000100 00000011111000000000000000001000 Okay... did that make sense? Probably not. • source: Comp 4 Computer Programming Slide 34
  33. Lets look at it in MIPS assembly language: swap: muli $2, $5,4 add $2, $4,$2 lw $15, 0($2) lw $16, 4($2) sw $16, 0($2) sw $15, 4($2) jr $31 Now does that make sense? Better, but still cryptic. • source: Comp 4 Computer Programming Slide 35
  34. What about a high level language, like C  swap(int v[], int k) { int temp; temp = v[k]; v[k] = v[k+1]; v[k+1] = temp; } This probably still doesn’t make sense to most of you. That’s okay. However, part of us (computer scientists) talk this language. • source: Comp 4 Computer Programming Slide 36
  35. now, we have computer languages a lot of them… and…
  36. several systems (we, now, live “into” software)…
  37. and “into” codes, languages and machines… machines that recognize languages! new machines (2014) DRONESTRAGAM JIBO here, Recife-PE, in we have HEALTHDRONES by EPITRACK/ISI-TICs/CESAR what about the future? “a revolução pode ser antecipada?” by Silvio Meira (in Portuguese) /
  38. NOW, the machines are TALKING with us and among them in a NETWORK: Internet Of Things!
  39. We also have machines that generates their own rules (grammars)… this CODE by a Cellular Automata: Moving Things Around
  40. a cellular automata grammar? Rule 30 - 1000 iterações
  41. Flows in Rule 110!!
  42. is MUSIC a language recognized by machines? take a look at –
  43. basics of our currently digital world: Leibniz 0-1 notation
  44. molecular biology as software… SYNTHETIC BIOLOGY
  45. A Hegelian View of Software Engineering Evolution by Barry Boehm (2005) Autonomy; Bio- Computing 1950's 1960's 1970's 1980's 1990's 2000's 2010's © USC-CSE 47 Engineer Software like Hardware Risk-Based Agile/Plan -Driven Hybrids; Model-Driven Development Value-Based Methods; Collaboration; Global Development; Enterprise Architectures Software Differences, Engineer Shortages Scalability, Risk Mgmt. Many defects Compliance Time to Market, Rapid Change Software Value-Add COTS Process Overhead Scalability Soft SysE Software as Craft Formality, Waterfall Productivity; Reuse; Objects; Peopleware Agile Methods Plan- Driven Software Maturity Models Integrated Sw-Systems Engineering Global Systems of Systems Theses Syntheses Antitheses Prototyping Risk Mgmt. Domain Engr.
  46. do we have the codes!? a 4-ary base…
  47. so, do we have a grammar? Some rules, ok! but… what about a grammar?
  48. Do we have a grammar? a special one? …for example, with no ambiguity… ? In a CNF (Chomsky Normal Form)? Is it possible to write one? • “Diz-se que o código genético é degenerado ou redundante por existirem vários codões que codificam o mesmo aminoácido.”
  49. and… what about the machines? from Synthetic Biology = Molecular Engineering + Computer Science
  50. so… • Genetic engineering • Genetic engineering 2.0 = synthetic biology • Synthetic biology = molecular biology like computer science – Programming DNA like software! – Binary code versus dna code – We have 2 worlds today: a real one and a virtual one by software… – Synthetic biology will generate a NEW world!
  51. Synthetic biology will generate a NEW world! An Open-Source Future for Synthetic Biology Synthetic Animals one.0039054 Preparing the world for synthetic biology for-synthetic-biology/
  52. like in computer science, a philosophical question: IS THERE AN UNIVERSAL GENETIC MACHINE?
  53. “everything is software”by Silvio Meira 
  54. Some real SW initiatives!! ;-) • INCT – INES ( Synthetic Biology as a strategic area • ISI – SENAI Synthetic Biology as a strategic area • LIKA-CESAR (
  55. What is iGEM-LIKA-CESAR? we are trying to build some genetic codes… and some grammars and, who knows, machines… with genetic engineering, robotics, some computer science theory and Innovation, a lot of it!
  56. tks! jones.albuquerque