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

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

once was a time…
we!
2010, SCIAM, Endangered Species: Humans Might Have Faced Extinction 1 Million Years Ago
http://www.scientificamerican.com/article.cfm?id=early-human-population-size-genetic-diversity

codes and languages
THE SYMBOLS…

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 !

writing
codes...
The Blackwell Encyclopedia of Writing Systems
DOI 10.1111/b.9780631214816.1999.x
4000 BC www.phoenician.org
origin of LANGUAGES
http://pandora.cii.wwu.edu/vajda/ling201/test1materials/origin_of_language.htm

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

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?

interpretation of rules (our codes, rules, and languages…)
http://www.historum.com/ancient-history/1001-most-influential-ancient-civilizations-9.html

new ones?
or ancient codes in new rules?
X
1453 BC X 2014 AC

a lot of codes…
and languages…

our need to count
MATHEMATICS…

the need to compute...
mathematical codes...
the NUMBERS
http://pessoal.sercomtel.com.br/matematica/fundam/numeros/numeros.htm
a fact: ISHANGO bone
http://www.math.buffalo.edu/mad/Ancient-Africa/ishango.html
the numerical SENSE
http://educar.sc.usp.br/matematica/let2.htm#let2a1
the representation of complex  complex codes!
http://pt.wikipedia.org/wiki/Hessiano

The numerical SENSE
http://educar.sc.usp.br/matematica/let2.htm#let2a1
How many people in the figures?

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 

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 need to compute
THE MACHINES…

codes + numbers... A LOT OF codes
languages and machines...
http://en.wikipedia.org/wiki/Alan_Turing
1912 - 1954
/http://www.chomsky.info/
1928, Professor in Department of Linguistics & Philosophy at MIT

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)

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
Comp 4 Computer Programming Slide 36

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/
/

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

a cellular automata
grammar?
Rule 30 - 1000 iterações

Flows in Rule 110!!

is MUSIC a language recognized by
machines?
take a look at
– http://tones.wolfram.com/

basics of our
currently digital world:
Leibniz 0-1 notation

molecular biology as software…
SYNTHETIC BIOLOGY

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.

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.p
one.0039054
Preparing the world for synthetic biology
http://www.technologyreview.com/article/403544/preparing-the-world-
for-synthetic-biology/

like in computer science, a philosophical question:
IS THERE AN UNIVERSAL
GENETIC MACHINE?

“everything is software”by Silvio Meira


Some real SW initiatives!! ;-)
• INCT – INES (http://www.ines.org.br/)
Synthetic Biology as a strategic area
• ISI – SENAI
Synthetic Biology as a strategic area
• LIKA-CESAR (iGEM.org)
http://2014.igem.org/Team:LIKA-CESAR-Brasil

What is iGEM-LIKA-CESAR?
http://2014.igem.org/Team:LIKA-CESAR-Brasil
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!

tks!
jones.albuquerque