Storing Digital Binary Data in Cellular DNA

Storing Digital Binary Data in Cellular DNAThe New ParadigmDr. Rocky Termanini
Copyright
Dedication
About the author
Acknowledgments
Prologue
The big escape to the cloud
Cloud hardware
Why is silicone important?
The silicon addiction
DNA—the holy grail
1 . Discovery of the book of life—DNA
Initial thoughts
DNA—the code of life
DNA, the Columbus discovery
The DNA pioneers
DNA as an organic data castle
Music is also one of the DNA's talents
Appendix
How was DNA first discovered and who discovered it? Read on to find out …
Glossary (courtesy of MERIT CyberSecurity—archive)
Suggested readings
2 . The amazing human DNA system explained
“Magical DNA” found in King Tut study
Fighting chaos
Anatomy of DNA
The central dogma of genetics
The genetic code
Properties of the genetic code
Another blessing of DNA, biological profiling
The holy grail of DNA: gene editing
The yogurt story
How gene editing works
Anatomy of CRISPR
Social and ethical issues in DNA fingerprinting
DNA's other dark side, the hacking nightmare
DNA is a warm place for music
DNA can hack computers
Appendices
Glossary (MERIT CyberSecurity engineering archives)
Get down with the lingo
References
3 . The miraculous anatomy of the digital immunity ecosystem
Introduction
What is the Smart Vaccine?
Smart cities are like the human body
What is a smart city?
CEWPS is the intelligent smart shield of the smart city
The 3D nanoattack scenario
Anatomy of CEWPS and its intelligent components
Anatomical composition of CEWPS (the digital immunity ecosystem)
CEWPS component 1: The Central Coordination Center
CEWPS component 2: The knowledge acquisition component
What is experience?
What is knowledge?
The six stages of a cybercrime episode
Cybercrime raw data distillation process
CEWPS component 3: the reasoning engine
What is causality?
What is prediction?
We can forecast weather; why cannot we predict crime?
Anatomy of the causality reasoning engine
CEWPS component 4: reverse engineering center
CEWPS component 5: smart city critical infrastructure
The critical infrastructures in smart cities
What is criticality?
What is a critical infrastructure?
CEWPS component 6: the Smart Vaccine center
CEWPS component 7: the vaccine knowledge base
CEWPS component 8: the virus knowledge base
CEWPS component 9: CEWPS smart Nanogrid
The smart grid model
Connectivity of critical systems to a city's smart Nanogrid
Anatomy of the autonomic adapter
A smart city is an idealistic hype
Sample system performance screens on the city dashboard
Appendices
Appendix 3.A Glossary (extracted from MERIT cybersecurity library)
References
4 . Hacking DNA genes— the real nightmare
A glimpse of the bright future
Stuxnet is the devil's key to hell
The DNA stuxnet (DNAXNET)
Criminals could alter their DNA to evade justice with new genetic editing tools
DNA digital data hacking
DNA crime
Gene hacking
MyHeritage website leakage
Appendices
Appendix 4.A The complete story of Stuxnet
The stuxnet strategy of attack
Two attack strategies
The crack in the door
Damages
Historical background
Appendix 4.B Glossary (extracted from MERIT CyberSecurity archives)
Suggested readings
5 . The digital universe with DNA—the magic of CRISPR
For your own information
What is our digital universe?
How big is our digital universe?
Why is the digital universe growing so fast?
Data storage capacity is becoming asymptotic
Dubai is the magical smart city with its Achilles' heel
Dubai embracing DNA storage
The hyper data center of the world
Five types of data centers
The top 10 hyperscale data centers
How did DNA digital storage start?
From DNA genetic code to DNA binary code
Total size of the human genes in bytes
Why ASCII was so important to DNA coding—A glimpse of history
The Huffman compression rule
Example: the gopher message
Summary of the data storage in DNA
The CRISPR magic
How to hack DNA
Anatomy of CRISPR—the smart cleaver
Word on word processing
Artificial intelligence–centric text editing
Ethical concerns
CRISPR is the Holy Grail of data deluge
Appendices
Appendix 5.A Glossary of data center terms (MERIT CyberSecurity engineering)
Appendix 5.B Glossary for big data (prepared by MERIT CyberSecurity Engineering)
Appendix 5.C Glossary of CRISPR (MERIT Cybersecurity knowledge base)
Appendix 5.D A list of features standard in current word processing programs
Suggested readings
6 . Getting DNA storage on board: starting with data encoding
Some mathematical ideas that we all need to know
And DNA does that!
Data nomenclature
The random access method
Other existing encoding methods
Bancroft encoding method
The Huffman encoding method
The Goldman encoding method
XOR encoding method
The tunable (balanced) redundancy method
Selecting the best encoding method
DNA storage with random access
The simulation method
Experiment description
Experiment results
File recovery (back to binary) method
What is sequencing depth (number of sequence times)
Reduced sequencing depth
Naive encoding method
Comparison of reliability versus density
Test result 1: percent of file recovery as a function of strand density
Test result 2: density as a function of strand length in bits
Test result 3: desired reliability as a function of time span and number of copies needed to achieve the desired reliability
DNA the Rosetta stone
Silicon is getting scarce
What is silicon?
Artificial gene synthesis
Amazon's flying warehouses
Church's DNA storage
DNA computing—the tables turned
DNA is the new supercomputer
Appendix 6.A Glossary of DNA encoding (from merit CyberSecurity library)
Suggested readings
7 . Synthesizing DNA-encoded data
One trillionth of a gram!
The DNA writer
DNA Fountain software strategy
Fountain software architecture
A reliable and efficient DNA storage architecture
DNA computing is around the corner
The adleman discovery
Dr. Jian-Jun Shu discovery
The BLAST algorithm software
BLAST software architecture
One word on FASTA software system
The story of binary code
Nondeterministic universal turing machine
Video and audio media features
Digital video
Binary to DNA code, revisited
Anatomy of text and binary
Quantum computing
The QC entanglement process
The D-wave systems
Quantum computer versus DNA computer
Coding malware into a strand of DNA
Mechanics of the buffer overflow
Method 1: spilled data
Method 2: launch pad
Sherlock software
The creative mind of the hacker
The next generation of DNA hacking
CRISPR, the gene editor
Who is the DNA cyber hacker?
Type 1: artificial intelligence–powered malware
DeepLocker—The smart software
Type 2: nanopowered malware
DNA malware-as-a-service
DNA hacking with nanorobots
How could DNA attack a computer?
Appendices
Appendix 7.A Bioinformatics
Goals of bioinformatics
Appendix 7.B IBM's DeepLocker—the AI-powered malware
Appendix 7.C FASTQ software
Appendix 7.D The Bachand DNA story
Marlene and George Bachand pioneers of DNA-encrypted data (Fig. 7.15)
Appendix 7.E Deep neural network
Appendix 7.F Sherlock detective software
Appendix 7.G Glossary (deep neural networks)
Appendix 7.H Glossary (DNA terms)
Suggested readings
8 . Sequencing DNA-encoded data
The grandiose design of our digital universe in the 21st century
Smart City ontology
The bright sun of DNA is coming up
How to retrieve your Illumina Solexa sequencing data
Mac OS X
Linux
What is the Illumina method of DNA sequencing?
Illumina DNA sequencing operations?
The disruptive industry of digital DNA sequencing
From cell atlas project to DNA storage libraries
Blockchained cannabis DNA
The hidden second code in our DNA
Get on the A-train for blockchain
The sunrise
Unseen sinkholes
Blockchain's competitionethereum
Disadvantages of blockchain
Malware is hovering over DNA code
Case 1: blockchained malware inside DNA
Case 2: biohacking—malware hidden in DNA
Case 3: DNA malware trafficking
DNA satellite hacking
DNA drone hacking
Appendices
Appendix 8.A The cannabis dilemma
Appendix 8.B Dr. Church's Regenesis book
Appendix 8.C The miracle of making protein
Appendix 8.D Unit conversion table
How to convert text to binary code using JavaScript software?
How can we encode the digital data into DNA?
Appendix 8.E Glossary for blockchain (From MERIT CyberSecurity knowledge base)
Suggested readings
9 . Decoding back to binary
Introduction
Dynamic equilibrium
Structure DNA
The central dogma of genetics
Key players in DNA synthesis/sequencing and storage
Academic research
University of Washington
Harvard University
Columbia University
University of Illinois, Urbana–Champaign
Swiss Federal Institute of Technology (ETH), Zurich
Research consortium
Industry
Microsoft Research
Micron Technology
More Research
Start-ups
Catalog
Iridia
Helixworks
US Government
Defense Advanced Research Projects Agency
Intelligence Advanced Research Projects Activity
National Institutes of Health
National Science Foundation
Foreign research
European Bioinformatics Institute
Decoding DNA sequence back into binary
Copying DNA sequences with polymerase chain reaction
Molecular information storage (MIST) story
Just so you know, your DNA can be a wallet for bitcoin data
BioEdit software, sequence editing
The next-generation sequencing technology
Malware Technology
DNA malware
The Two-way malware of binary data and DNA
Method 1: binary malware, inject into DNA
Method 2: infected DNA, converted to binary
Blockchain malware
A rainstorm of grasshoppers; now we have a rainstorm of blockchain
Appendices
Appendix 9.A
Appendix 9.B Glossary for DNA sequencing (from MERIT Cyber Library)
Suggested readings
10 . Fusing DNA with digital immunity ecosystem
How did human immunity come about?
Plague at the Siege of Caffa, 1346
The plague of Athens, 430 BC
DNA digital storage meets the Digital Immunity Ecosystem
Anatomy of Digital Immunity Ecosystem and its intelligent components
Anatomical composition of Digital Immunity Ecosystem
Component 1: the central coordination center
Component 2: the knowledge acquisition component
Component 3: reverse engineering center
Component 4: the causality reasoning and predictor
Machine learning component
Component 5: smart city critical infrastructures
Component 6: the smart vaccine center
Component 7: the vaccine knowledge base
Component 8: the virus knowledge base
Component 9: CEWPS smart nanogrid
The smart grid model
The DNA component
How did encryption get into DNA?
Cryptology evolution of time
The miracle of cryptology in DNA
DNA cryptology
The encryption algorithm
Malware going after DNA storage
DNA computing
DNA computing applications
DNA computer
Case study: demographic and data storage growth of Dubai
Dubai digital data forecast
Appendices
Appendix 10.A Cryptography: one-time pad
Appendix 10.B DNA cryptography with data encryption standards
Appendix 10.C DNA cryptography with advanced encryption standard
Appendix 10.D Advanced encryption standard algorithm
Appendix 10.E DNA encoding
Appendix 10.F Cryptology glossary (From MERIT CyberSecurity library)
Suggested readings
11 . DNA storage heading for smart city
Introduction
Why do we need molecular information storage?
Smart city needs smart data
The smart city will switch from hardware to bioware
DNA potentialities
Concluding revelation
Appendices
Appendix 11.A Glossary Smart Cities (MERIT Knowledge Library)
Suggested readings
12 . DNA Data and Social Crime
Sources of social crime
Poverty as a pervasive social crime
Key information stored in DNA data storage
DNA can interpret the behavior of a mass killer
Can we reverse engineer DNA and predict a crime?
Smart cities and eradication of cybercrime
Final thought
Some interesting numbers about DNA data storage
Some interesting numbers about datacenter power consumption
Justification for using DNA storage
Appendices
Appendix 12.A Poverty State of the Health
Appendix 12.B Glossary for Social/Hate Crime
Appendix 12.C Glossary (Courtesy MERIT CyberSecurity Library)
Suggested readings
13 . DNA data and cybercrime and cyberterrorism
Opening thoughts
DNA is our binary Holy Grail of data storage
Behavior of the cybercriminal
Adding insult to injury
Anatomy of cyberterrorism
Cybercrime runs on steroids; antivirus technology runs on diesel
Where did the word cyber come from?
Cybercrime data repositories
The storage supply is killing the storage demand
DNA is the holy grail of digital storage
Back to smart city
What is cyberterrorism?
DNA is the holy grail of smart city
Appendices
Appendix 13.A The human cell atlas
Appendix 13.B DNA computing explained
The experiment
Biochemistry-based information technology
Real case of chemical DNA computer
Appendix 13.C Glossary for smart city (MERIT cybersecurity engineering)
Suggested readings
14 . DNA is a time storage machine for 10,000 years
A special genre of time machine
DNA time clock can predict when we will die
The link between biological clock and mortality
The telomere story
Time travel is within reach
The amazing storage phenomenon
Storage evolution over time
DNA storage random access retrieval
Appendices
Appendix 14.A Svalbard Global Data Vault
Appendix 14.B Glossary (Courtesy http://www.genesinlife.org/glossary)
Suggested readings
15 . DNA and religion
DNA and religion galaxies are intersecting
We all ride our personal boat
The blessing of bacteria
Peace between science and religion—injecting “scriptural” DNA into the body
The magic of CRISPR
DNA and bacteria are allies
The magic of CRISPR, the futuristic phenomenon
Stepping into God's domain
What is more important—DNA or religion?
Some atheistic arrogance
The Collins defense
Dr. Crick and Churchill arguments
Religious communities are not happy
Personal and medical data used as DNA fingerprint
DNA is human future diary, cannot be fooled
Finally, CODIS was born
Now religion speaks about DNA
The story of evolution
Concluding thoughts
The last words of Einstein
Appendices
Appendix 15.A The God Gene… how faith is hardwired into our genes (extracted from wikipedia)
Appendix 15.B Some laws and principles in evolutionary biology (from library of MERIT CyberSecurity)
Appendix 15.C Holy Quran refers to DNA
The programming in genes
Holy Quran reference to DNA
Appendix 15.D The information capacity of DNA
Advantages of knowing DNA
Appendix 15.E Glossary for research ethics (from library of MERIT CyberSecurity)
Suggested readings
Index
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