Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL

Codes, Languages, Machines and

Synthetic Biology is it (really) true that “everything is software”?

by

jones albuquerque

iGEM-LIKA-CESAR

DEINFO-UFRPE

ISI-TICs

EPITRACK

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. case iGEM-LIKA-CESAR

THE SYMBOLS…

codes and languages

The Social Life of the Information… http://en.wikipedia.org/wiki/The_Social_Life_of_Information

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 Blackwell Encyclopedia of Writing Systems

DOI 10.1111/b.9780631214816.1999.x

origin of LANGUAGES

http://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 - codes

portuguese

Greek

arabic

www.nature.com/

Nature 426, 435-439(27

November 2003)

doi:10.1038/nature02029

Cúmplice

https://osorrisodogato.wordpress.com/tag/braile/

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

languages

and their grammars…

ancient X modern codes…

Vale do Catimbau – Buíque - PE

are there rules?

X

1453 BC 2014 AC X

a lot of codes…

and languages…

and… the

abstraction of the

COMPLEX

MATHEMATICS…

we need to count

The numerical SENSE http://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…

we 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

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 33

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 34

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 35

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

DRONESTRAGAM

http://www.dronestagr.am/contest/rewards/

JIBO

http://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/

/

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?

is MUSIC a language recognized by

machines?

take a look at

– http://tones.wolfram.com/

COMPUTER SCIENCE VIEW

Humanty in an only one slide

Leibniz 0-1 notation

basics of our

currently digital world:

© USC-CSE 44

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

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.

Education

Applications –

Platforms

Software Engineering –

Methods, processes

and theories

Programming-

Big Data Structures and

Algorithms

Science

Technology

Diffusion

http://www.ines.org.br/

SYNTHETIC BIOLOGY

molecular biology as software…

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

Synthetic Biology

based on standard parts https://www.igem.org/Main_Page

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

http://2014.igem.org/Team:LIKA-CESAR-Brasil

Synthetic Biology and Robotics - The Integration that can Save Lives

The LIKA-CESAR BRASIL proposes the development of a biosensor for the

detection of breast cancer with the help of synthetic biology and robotics. The idea

was to build a robotic system linked to genetic engineering capable of processing

and prepare small samples of blood in an automated manner.

For this our team, created the Coli Alert for the BreastBotSensor. This system is

one robot to DNA/RNA extraction coupled by an electrochemical biosensor and

linked to one quality control, the ColiAlert, responsible to confirm the process of

nucleic acid extraction.

The team believes that the best way to solve problems is joining technologies. For

this, we think that synthetic biology should go hand in hand with robotics and

information technology. Then our project was to join the synthetic biology with the

robots, aiming to fight against to the one of biggest health problems: The Breast

Cancer.

http://2014.igem.org/Team:LIKA-CESAR-Brasil

http://www.epitrack.com.br/

https://www.ufpe.br/lika/

http://startupbio.com.br/website/

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!

– 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:

http://www.simulation-argument.com/

http://www.simulation-argument.com/

“everything is software”by Silvio Meira

tks!

jones.albuquerque