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

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

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!

THE SYMBOLS…codes and languages

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

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

yet another codes...

Ancient Chemical Symbols. Psychoanalytic Review, 14:200-206, 1927

Chineses: pictograms, ideograms, iconically…

1436 BC…

1800 – 1050 BC to 1955…

ALPHABET - codesportuguese

Greek

arabic

universal codes

lexicon, syntactic, semantic

when a code is wrong?depends of rules… grammatical rules

Gramática Da Língua Portuguesa (sebo Amigo)http://produto.mercadolivre.com.br

R$ 10,00

www.nature.com/

Nature 426, 435-439(27 November 2003)doi:10.1038/nature02029

our codes and their rules…

ancient X modern codes…

Vale do Catimbau – Buíque - PE

are there rules?

http://www.historum.com/ancient-history/1001-most-influential-ancient-civilizations-9.html

interpretation of rules (our codes, rules, and languages…)

X

1453 BC 2014 ACX

new ones? or ancient codes in new rules?

a lot of codes…and languages…

MATHEMATICS…our need to count

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

The numerical SENSEhttp://educar.sc.usp.br/matematica/let2.htm#let2a1

How many people in the figures?

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…

a summary of the “mathematical language”… o lot of code, rules, … do we understand?http://library.thinkquest.org/22584/emh1000.htm

and more complex ones? dense codes!...http://pt.wikipedia.org/wiki/Hessiano

é a jacobiana, derivada do gradiente…

aplicaçoes???

THE MACHINES…the need to compute

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

languages and their grammars…

some grammars are special ones…

simple,but…

with some special grammars we can transform languages into machines that recognize them and vice-versa!

BUT we need to understand a code to understand another one…

the need for automatic computation...

1936, the UNIVERSAL AUTOMATA MACHINE by Allan Turing

and we have

Computer Science and systems and

SOFTWARE

the ASCII (American Standard Code for Information Interchange)

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

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

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

now, we have computer

languages

http://www.levenez.com/lang/

a lot of them… and…

several systems (we, now, live “into” software)…

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/

/

NOW, the machines are TALKING with us and among them in a NETWORK: Internet Of Things!

We also have machines that generates their own rules (grammars)… this CODE by a Cellular Automata: Moving Things Around

Rule 30 - 1000 iterações

a cellular automata grammar?

Flows in Rule 110!!

is MUSIC a language recognized by machines?

take a look at– http://tones.wolfram.com/

Leibniz 0-1 notation

basics of our currently digital world:

SYNTHETIC BIOLOGYmolecular biology as software…

© 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.

do we have the codes!? a 4-ary base…

so, do we have a grammar? http://www.sbolstandard.org/ Some rules, ok! but… what about a grammar?

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.”

and… what about the machines?

from Synthetic Biology = Molecular Engineering + Computer Science

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!

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/

IS THERE AN UNIVERSAL GENETIC MACHINE?

like in computer science, a philosophical question:

“everything is software”by Silvio Meira

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

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

tks!

jones.albuquerque