codes languages, machines and synthetic biology and one case lika-cesar-brazil
TRANSCRIPT
![Page 1: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/1.jpg)
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
![Page 2: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/2.jpg)
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
![Page 3: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/3.jpg)
THE SYMBOLS…
codes and languages
![Page 4: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/4.jpg)
The Social Life of the Information… http://en.wikipedia.org/wiki/The_Social_Life_of_Information
![Page 5: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/5.jpg)
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
![Page 6: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/6.jpg)
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
![Page 7: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/7.jpg)
yet another
codes... Ancient Chemical Symbols. Psychoanalytic Review, 14:200-206, 1927
Chineses: pictograms, ideograms, iconically…
1436 BC…
1800 – 1050 BC to 1955…
![Page 8: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/8.jpg)
ALPHABET - codes
portuguese
Greek
arabic
![Page 9: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/9.jpg)
www.nature.com/
Nature 426, 435-439(27
November 2003)
doi:10.1038/nature02029
![Page 10: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/10.jpg)
Cúmplice
https://osorrisodogato.wordpress.com/tag/braile/
![Page 11: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/11.jpg)
universal codes
![Page 12: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/12.jpg)
lexicon,
syntactic,
semantic
![Page 13: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/13.jpg)
when a code is wrong?
depends of rules… grammatical rules
Gramática Da Língua Portuguesa (sebo Amigo)
http://produto.mercadolivre.com.br
R$ 10,00
![Page 14: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/14.jpg)
languages
and their grammars…
![Page 15: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/15.jpg)
ancient X modern codes…
Vale do Catimbau – Buíque - PE
are there rules?
![Page 16: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/16.jpg)
X
1453 BC 2014 AC X
![Page 17: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/17.jpg)
a lot of codes…
and languages…
and… the
abstraction of the
COMPLEX
![Page 18: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/18.jpg)
MATHEMATICS…
we need to count
![Page 19: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/19.jpg)
The numerical SENSE http://educar.sc.usp.br/matematica/let2.htm#let2a1
How many people in the figures?
![Page 20: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/20.jpg)
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…
![Page 21: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/21.jpg)
a summary of the
“mathematical
language”…
o lot of code, rules, …
do we understand? http://library.thinkquest.org/22584/emh1000.htm
![Page 22: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/22.jpg)
and more complex ones?
dense codes!... http://pt.wikipedia.org/wiki/Hessiano
é a jacobiana, derivada do gradiente…
aplicaçoes???
![Page 23: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/23.jpg)
THE MACHINES…
we need to compute
![Page 24: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/24.jpg)
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
![Page 25: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/25.jpg)
![Page 26: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/26.jpg)
some grammars are special ones…
![Page 27: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/27.jpg)
![Page 28: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/28.jpg)
simple, but…
with some special grammars we can transform languages
into machines that recognize them and vice-versa!
![Page 29: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/29.jpg)
BUT we need to understand a code to understand another one…
![Page 30: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/30.jpg)
the need for automatic computation...
1936, the UNIVERSAL AUTOMATA MACHINE by Allan Turing
![Page 31: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/31.jpg)
and we have
Computer Science and
systems and
SOFTWARE
![Page 32: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/32.jpg)
the ASCII (American Standard Code for
Information Interchange)
![Page 33: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/33.jpg)
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
![Page 34: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/34.jpg)
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
![Page 35: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/35.jpg)
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
![Page 36: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/36.jpg)
now, we have computer
languages
http://www.levenez.com/lang/
a lot of them… and…
![Page 37: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/37.jpg)
several systems (we, now, live “into”
software)…
![Page 38: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/38.jpg)
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/
/
![Page 39: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/39.jpg)
We also have machines that generates their own rules
(grammars)…
this CODE by a Cellular Automata: Moving Things Around
![Page 40: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/40.jpg)
Rule 30 - 1000 iterações
a cellular automata
grammar?
![Page 41: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/41.jpg)
is MUSIC a language recognized by
machines?
take a look at
– http://tones.wolfram.com/
![Page 42: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/42.jpg)
COMPUTER SCIENCE VIEW
Humanty in an only one slide
![Page 43: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/43.jpg)
Leibniz 0-1 notation
basics of our
currently digital world:
![Page 44: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/44.jpg)
© 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.
![Page 45: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/45.jpg)
Education
Applications –
Platforms
Software Engineering –
Methods, processes
and theories
Programming-
Big Data Structures and
Algorithms
Science
Technology
Diffusion
http://www.ines.org.br/
![Page 46: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/46.jpg)
SYNTHETIC BIOLOGY
molecular biology as software…
![Page 47: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/47.jpg)
do we have the codes!?
a 4-ary base…
![Page 48: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/48.jpg)
so, do we have a grammar?
http://www.sbolstandard.org/
Some rules, ok! but… what about a grammar?
![Page 49: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/49.jpg)
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.”
![Page 50: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/50.jpg)
and… what about the machines?
from Synthetic Biology = Molecular
Engineering + Computer Science
![Page 51: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/51.jpg)
Synthetic Biology
based on standard parts https://www.igem.org/Main_Page
![Page 52: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/52.jpg)
![Page 53: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/53.jpg)
![Page 54: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/54.jpg)
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
![Page 55: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/55.jpg)
http://2014.igem.org/Team:LIKA-CESAR-Brasil
![Page 56: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/56.jpg)
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
![Page 57: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/57.jpg)
![Page 58: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/58.jpg)
http://www.epitrack.com.br/
https://www.ufpe.br/lika/
http://startupbio.com.br/website/
![Page 59: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/59.jpg)
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/
![Page 60: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/60.jpg)
IS THERE AN UNIVERSAL
GENETIC MACHINE?
like in computer science, a philosophical question:
![Page 61: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/61.jpg)
http://www.simulation-argument.com/
![Page 62: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/62.jpg)
http://www.simulation-argument.com/
![Page 63: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/63.jpg)
“everything is software”by Silvio Meira
![Page 64: Codes languages, machines and synthetic biology and one case LIKA-CESAR-BRAZIL](https://reader033.vdocument.in/reader033/viewer/2022042716/55ad627d1a28ab681b8b45ff/html5/thumbnails/64.jpg)
tks!
jones.albuquerque