synthetic biology in a computer science view
DESCRIPTION
is synthetic biology a computer science area and vice-versa?TRANSCRIPT
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Synthetic Biology in a Computer Science view - is it (really) true that “everything is software”?
byjones albuquerque
iGEM-LIKA-CESARDEINFO-UFRPE
ISI-TICsEPITRACK
http://2014.igem.org/ http://2014.igem.org/Team:LIKA-CESAR-Brasil
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in an approach like a story...
1. human, codes, languages and machines2. genetic engineering like computer science3. (new?) machines by biology synthetic4. iGEM-LIKA-CESAR
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2010, SCIAM, Endangered Species: Humans Might Have Faced Extinction 1 Million Years Agohttp://www.scientificamerican.com/article.cfm?id=early-human-population-size-genetic-diversity
once was a time…
we!
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THE SYMBOLS…codes and languages
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the need to record, compute... using codes !
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
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writing
codes...
The Blackwell Encyclopedia of Writing SystemsDOI 10.1111/b.9780631214816.1999.x
origin of LANGUAGEShttp://pandora.cii.wwu.edu/vajda/ling201/test1materials/origin_of_language.htm
4000 BC www.phoenician.org
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yet another codes...
Ancient Chemical Symbols. Psychoanalytic Review, 14:200-206, 1927
Chineses: pictograms, ideograms, iconically…
1436 BC…
1800 – 1050 BC to 1955…
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ALPHABET - codesportuguese
Greek
arabic
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universal codes
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lexicon, syntactic, semantic
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when a code is wrong?depends of rules… grammatical rules
Gramática Da Língua Portuguesa (sebo Amigo)http://produto.mercadolivre.com.br
R$ 10,00
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www.nature.com/
Nature 426, 435-439(27 November 2003)doi:10.1038/nature02029
our codes and their rules…
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ancient X modern codes…
Vale do Catimbau – Buíque - PE
are there rules?
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http://www.historum.com/ancient-history/1001-most-influential-ancient-civilizations-9.html
interpretation of rules (our codes, rules, and languages…)
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X
1453 BC 2014 ACX
new ones? or ancient codes in new rules?
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a lot of codes…and languages…
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MATHEMATICS…our need to count
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the need to compute... mathematical codes...
the NUMBERShttp://pessoal.sercomtel.com.br/matematica/fundam/numeros/numeros.htm
a fact: ISHANGO bonehttp://www.math.buffalo.edu/mad/Ancient-Africa/ishango.html
the numerical SENSEhttp://educar.sc.usp.br/matematica/let2.htm#let2a1
the representation of complex complex codes!http://pt.wikipedia.org/wiki/Hessiano
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The numerical SENSEhttp://educar.sc.usp.br/matematica/let2.htm#let2a1
How many people in the figures?
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the case of Dantzig´s crow
and the case of joa´s chicken
and now… how many people? Is it difficult?
we must to count, compute…
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a summary of the “mathematical language”… o lot of code, rules, … do we understand?http://library.thinkquest.org/22584/emh1000.htm
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and more complex ones? dense codes!...http://pt.wikipedia.org/wiki/Hessiano
é a jacobiana, derivada do gradiente…
aplicaçoes???
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THE MACHINES…the need to compute
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codes + numbers... A LOT OF codes
languages and machines...
/http://www.chomsky.info/1928, Professor in Department of Linguistics & Philosophy at MIT
http://en.wikipedia.org/wiki/Alan_Turing
1912 - 1954
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languages and their grammars…
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some grammars are special ones…
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simple,but…
with some special grammars we can transform languages into machines that recognize them and vice-versa!
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BUT we need to understand a code to understand another one…
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the need for automatic computation...
1936, the UNIVERSAL AUTOMATA MACHINE by Allan Turing
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and we have
Computer Science and systems and
SOFTWARE
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the ASCII (American Standard Code for Information Interchange)
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Comp 4 Computer Programming Slide 34
Here’s some machine code from a MIPS processor:
00000000101000010000000000011000
00000000100011100001100000100001
10001100011000100000000000000000
10001100111100100000000000000100
10101100111100100000000000000000
10101100011000100000000000000100
00000011111000000000000000001000
Okay... did that make sense? Probably not.
• source: http://www.eas.asu.edu/~gupta/intro.html
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Comp 4 Computer Programming Slide 35
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: http://www.eas.asu.edu/~gupta/intro.html
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Comp 4 Computer Programming Slide 36
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: http://www.eas.asu.edu/~gupta/intro.html
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now, we have computer
languages
http://www.levenez.com/lang/
a lot of them… and…
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several systems (we, now, live “into” software)…
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and “into” codes, languages and machines… machines that recognize languages!
new machines (2014)https://www.youtube.com/watch?v=6feEE716UEk
DRONESTRAGAMhttp://www.dronestagr.am/contest/rewards/
JIBOhttp://www.fastcompany.com/3033167/most-creative-people/how-star-wars-influenced-jibo-the-first-robot-for-families
here, Recife-PE, in www.epischisto.org we have HEALTHDRONES by EPITRACK/ISI-TICs/CESAR
what about the future? “a revolução pode ser antecipada?”by Silvio Meira (in Portuguese)http://terramagazine.terra.com.br/silviomeira/blog/2013/10/04/a-revoluo-pode-ser-antecipada/
/
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NOW, the machines are TALKING with us and among them in a NETWORK: Internet Of Things!
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We also have machines that generates their own rules (grammars)… this CODE by a Cellular Automata: Moving Things Around
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Rule 30 - 1000 iterações
a cellular automata grammar?
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Flows in Rule 110!!
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is MUSIC a language recognized by machines?
take a look at– http://tones.wolfram.com/
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Leibniz 0-1 notation
basics of our currently digital world:
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SYNTHETIC BIOLOGYmolecular biology as software…
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© USC-CSE 47
A Hegelian View of Software Engineering Evolution by Barry Boehm (2005)
Autonomy; Bio-Computing
1990's 2010's2000's1970's 1980's1960's1950's
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
SoftSysE
Software as Craft
Formality, Waterfall
Productivity; Reuse;
Objects;Peopleware
Agile Methods
Plan-Driven
Software Maturity Models
Integrated Sw-Systems Engineering
GlobalSystems
ofSystems
Theses
Syntheses
Antitheses
Prototyping
Risk Mgmt.Domain Engr.
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do we have the codes!? a 4-ary base…
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so, do we have a grammar? http://www.sbolstandard.org/ Some rules, ok! but… what about a grammar?
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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.”
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and… what about the machines?
from Synthetic Biology = Molecular Engineering + Computer Science
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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!
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Synthetic biology will generate a NEW world!
An Open-Source Future for Synthetic Biology
http://ieet.org/index.php/IEET/more/bentham20140909
Synthetic Animals
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0039054
Preparing the world for synthetic biology http://www.technologyreview.com/article/403544/preparing-the-world-for-synthetic-biology/
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IS THERE AN UNIVERSAL GENETIC MACHINE?
like in computer science, a philosophical question:
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“everything is software”by Silvio Meira
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Some real SW initiatives!! ;-)
• INCT – INES (http://www.ines.org.br/)Synthetic Biology as a strategic area
• ISI – SENAISynthetic Biology as a strategic area
• LIKA-CESAR (iGEM.org)http://2014.igem.org/Team:LIKA-CESAR-Brasil
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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!
http://2014.igem.org/Team:LIKA-CESAR-Brasil
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tks!
jones.albuquerque