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
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