Biomedical Defense Principles to Counter DNA Deep Hacking

By Rocky Termanini

Biomedical Defense Principles to Counter DNA Deep Hacking presents readers with a comprehensive look at the emerging threat of DNA hacking. Dr. Rocky Termanini goes in-depth to uncover the erupting technology being developed by a new generation of savvy bio-hackers who have skills and expertise in biomedical engineering and bioinformatics. The book covers the use of tools such as CRISPR for malicious purposes, which has led agencies such as the U.S. Office of the Director of National Intelligence to add gene editing to its annual list of threats posed by "weapons of mass destruction and proliferation."

Readers will learn about the methods and possible effects of bio-hacking attacks, and, in turn the best methods of autonomic and cognitive defense strategies to detect, capture, analyze, and neutralize DNA bio-hacking attacks, including the versatile DNA symmetrical AI Cognitive Defense System (ACDS). DNA bio-hackers plan to destroy, distort and contaminate confidential, healthy DNA records and potentially create corrupted genes for erroneous diagnosis of illnesses, disease genesis and even wrong DNA fingerprinting for criminal forensics investigations.

• Presents a comprehensive reference for the fascinating emerging technology of DNA storage, the first book to present this level of detail and scope of coverage of this groundbreaking field
• Helps readers understand key concepts of how DNA works as an information storage system and how it can be applied as a new technology for data storage
• Provides readers with key technical understanding of technologies used to work with DNA data encoding, such as CRISPR, as well as emerging areas of application and ethical concern, such as smart cities, cybercrime, and cyber warfare
• Includes coverage of synthesizing DNA-encoded data, sequencing DNA-encoded data, and fusing DNA with Digital Immunity Ecosystem (DIE)

• Language: English
• Publisher: Academic Press
• Release date: Dec 2, 2022
• ISBN: 9780323985406

Rocky Termanini

Dr. Rocky Termanini, CEO of MERIT CyberSecurity Group, is a subject matter expert in IT security and brings 46 years of cross-industry experience at national and international levels. He received his Ph.D. in Computer Science, Artificial Intelligence, from Yale University. He is the designer of the "Cognitive Early-Warning Predictive System" and "The Smart Vaccine™" which replicates the human immune system to protect the critical infrastructures against future cyber wars. Dr. Termanini spent five years in the Middle East working as a security consultant in Saudi Arabia, Bahrain, and the UAE. Professor Termanini’s teaching experience spans over 30 years. He taught Information Systems courses at Connecticut State University, Quinnipiac University, University of Bahrain, University College of Bahrain, Abu Dhabi University, and lectured at Zayed University in Dubai. Dr. Rocky Termanini is a senior advisor to the Department of Homeland Security and other Federal Law Enforcement agencies, as well as an advisor to the FBI on Cyber-terrorism and global malware. Dr. Termanini was the security manager of the Saudi e-Government project for the Saudi Ministry of Interior. Presently, Dr. Termanini helps companies set up cyber-security plans to protect their information assets and to monitor employee loyalty. He is a visiting professor to several universities in the Persian Gulf region, giving short courses in Digital Forensics and ethical hacking. Dr. Termanini has experience in preparing DARPA solicitations for cyber security grants and is the author of two books on Cybersecurity from CRC Press. He is the author of Storing Digital Binary Data into Cellular DNA: The New Paradigm from Elsevier Academic Press.

Book preview

Chapter 1: The miraculous architecture of the gene pyramid

Abstract

It is said that life would be easier if we had the source code. Well, Crick, and Watson discovered the code of life in DNA. Physicist Richard Feynman said at the annual American Physical Society meeting at Caltech on December 29, 1959, that There's Plenty of Room at the Bottom … which also inspired researchers like George Church and Feng Zend to pursue the road leading to DNA genetic engineering. Also, DNA open the door for Doudna and Chatelier to create a mechanism to edit the genes. In this chapter, we introduce the story of genetic revolution and DNA emerged as the most powerful factor that impact out humanity. DNA is the most awesome knowledge mine in our existence. The chapter covers the hierarchical structure of DNA gene, anatomy of chromosomes, Central Dogma mechanism, and the transcription process.

Keywords

Base pairs; Central dogma; CRISPR; Double helix; Genetics; Genome; Nucleic acid; Short tandem repeat (STR)

There is enough storage capacity in the DNA of a single lily seed or a single salamander sperm to store the Encyclopedia Britannica 60 times over. Some species of the unjustly called primitive amoebas have as much information in their DNA as 1000 Encyclopedia Britannica.

Richard Dawkins.

The results suggest a helical structure [of DNA] (which must be very closely packed) containing probably 2, 3, or 4 coaxial nucleic acid chains per helical unit and having the phosphate groups near the outside.

Dr. Rosalind FranklinDouble Helix Discoverer.

DNA is like Midas’s gold, everyone who touches it goes mad.

Dr. Maurice Wilkins.

Blind individuals who have tried these artificial retinas have been amazed that they can see colors and outlines of images. It is only a matter of time before we have artificial retinas that can rival human sight.

Dr. Michio Kaku.

My name is DNA

For life to exist, an information system is needed to produce and regulate life functions. This information system must also be able to accurately copy itself for the next generation. DNA (deoxyribonucleic acid) is the information system for life.

Initial thoughts

Imagine a world where you could go outside and take a leaf from a tree and put it through your personal DNA sequencer and get data like music, videos, or computer programs from it. Well, this is all possible now. It was not done on a large scale because it is quite expensive to create DNA strands, but it is possible.

Here's an interesting anecdote that will catch you eye: A French high schooler has allegedly bioengineered DNA based on verses from the Bible and Quran and injected it into his own leg. Adrien Locatelli, 16, from Grenoble, France, posted a short paper to the Open Science Framework preprint server in which he claimed to produce strands of DNA that corresponded to verses from the Bible and the Quran. According to Locatelli, he then injected the DNA containing the Bible verses into his left thigh, and the DNA with the Quranic verses into his right thigh. I did this experiment only for the symbol of peace between religions and science, Locatelli told me in an email. It's just symbolic. The proteins created by Locatelli are basically just short strands of DNA, which is made of nucleotides that can only be combined in specific ways.

Anatomy of DNA

Deoxy-ribo-nucleic acid is a large molecule in the shape of a double helix. That's a bit like a ladder that's been twisted many times. Many people believe that American biologist James Watson and English physicist Francis Crick discovered DNA in the 1950s. In reality, DNA was first identified in the late 1860s by Swiss chemist Friedrich Miescher. Then, in the decades following Miescher's discovery, other scientists—notably, Phoebus Levene and Erwin Chargaff—conducted a series of research efforts that revealed additional details about the DNA molecule, including its primary chemical components and the ways in which they joined with one another. Without the scientific foundation provided by these pioneers, Watson and Crick may never have reached their groundbreaking conclusion of 1953: that the DNA molecule exists in the form of a three-dimensional double helix.

The fact is 1869 was an important milestone year in genetic research. It was the year in which Friedrich Miescher, the Swiss physiological chemist first, identified what he called nuclein inside the nuclei of human white blood cells. Miescher's discovery of nucleic acids was unique among the discoveries of the four major cellular components (i.e., proteins, lipids, polysaccharides, and nucleic acids) in that it could be dated precisely … [to] one man, one place, one date. DNA is actually a biological USB drive, a carrier of genetic instructions for the development and life of an organism to another organism.

Watson and crick story

It is worth mentioning few words about two formidable minds that leapfrogged the human mind by 1000 years. They revealed DNA's double-helix structure in 1953, Francis Crick and James Watson helped to invent biotechnology, provided the foundation for understanding the diversity of life on Earth. Now that they revealed that DNA is the blueprint of life, Watson and crick have a hair-raising dogma about the Supreme Being and not giving him credit for the creation of the universe. Dr. Crick, 86, said recently in Sydney Morning Herald in March 22, 2003: The God hypothesis is rather discredited. Indeed, he says his distaste for religion was one of his prime motives in the work that led to the sensational 1953 discovery. It puzzles the mind that Watson and Crick deviated from the mainstream theology. In 1961 Crick resigned as a fellow of Churchill College, Cambridge, when it proposed to build a chapel. When Winston Churchill wrote to him, pointing out that none need enter [the chapel] unless they wish, Dr. Crick replied that on those grounds, the college should build a brothel, and enclosed a cheque for 10 guineas. Also, Mr. Watson boldly claimed Only with the discovery of the double helix and the ensuing genetic revolution have we had grounds for thinking that the powers held traditionally to be the exclusive property of the gods might 1day be ours.

DNA double helix

Let's go back and describe the miraculous module. In 1953 James Watson and Francis Crick published their theory that DNA must be shaped like a double helix. A double helix resembles a twisted ladder. Each upright pole of the ladder is formed from a backbone of alternating sugar and phosphate groups. Each DNA base (adenine, cytosine, guanine, thymine) is attached to the backbone and these bases form the rungs. There are 10 rungs for each complete twist in the DNA helix. Fig. 1.1 shows the 3D representation of DNA. The notation 5′- and -3′ is used to show that DNA has a direction where 5′ is the head of the DNA string while 3′ is the tail of the DNA string. (5′ is read as five-prime and 3′ is read as three-prime.). The total length of DNA strands in the human body is equivalent to: 120 billion miles.

Biology has earned a global reputation because of the discovery of DNA structure and composition. The sequencing of the human genome has given a new view to biology as an information science. Two attributes of DNA structure have created an impressive influence on science:

Digital nature: (The order of bases on each strand makes up the digital code that carries the instructions for life), whereby one strand of the helix binds perfectly with its partner. DNA has two types of digital information—the genes that encode proteins, which are the molecular machines of life, and the gene regulatory networks that specify the behavior of the genes.

Base complementarity: (In other words, the nucleotides of the DNA have the property of base pairing), where the letter A (Adenine) forms a hydrogen bond with the letter T (Thymine) and the letter C (Cytosine) forms a hydrogen bond with the letter G (Guanine). Let's use an example of a string of DNA like this: ACGT.

Figure 1.1  Here's some statistics that will not only blurs your vision, but also you mind: The human body consists of some 37.2 trillion cells. The total number of chromosomes that are found in each and every human cell is 46. DNA exists inside the nucleus of each of the body's cells. DNA is arranged as a coil of coils of coils of coils of coils! This allows the three billion base pairs in each cell to fit into a space just 6 microns across. The sequence goes like this: genes in DNA in chromosomes in cells.

What is a gene?

By analogy, a gene is like a word that carries some inheritance knowledge of every living soul. Genes in DNA encode protein molecules, which are the workhorses of the cell, carrying out all the functions necessary for life. Genes are attached to the helix twisted ladder legs strand-1 and strand-2. The two strands (the sides of the ladder) are tightly connected together with steps (bases). Genes make up sentences with a total of 1000–25 million words. These sentences with variable lengths are tightly packed into one of the 46 chromosomes (23 from male parent, 23 from female parent). We can compare the chromosomes to files stored in file cabinet. These chromosomes files are used in crucial forensic crime investigations. The chromosomes files are continually retrieved and copied; and then returned to the file cabinet. Our analysis have shown that defining a gene is problematic because on gene can code for several protein products, some genes code only for RNA, two genes can overlap, and other unpredictable complications. The information in our genes is presently programmable; this is no longer a fear. Research has now demonstrated that our destiny is not predefined: it is set by the choices we make every day.

What is the chromosome?

Simplistically speaking, it is a heavy-duty file cabinet with a lock, to store DNA genes. Chromosomes always remain in the nucleus, but proteins are made at ribosomes. Chromosomes are identical in every cell, which contain a person's genes (DNA data). A chromosome contains hundreds to thousands of genes which are tightly wrapped around inside histones. DNA, of fully extended, its length would be 1.7m long. Unwrapping all the DNAs in all our cells, it would equal to the distance from Earth to moon 6000 times. A normal human cell contains 23×2 pairs of chromosomes, for a total of 46 (male and female) chromosomes. Females have two X chromosomes in their cells, while males have one X and one Y chromosome. We can use this mathematical formula in (Fig. 1.1) to symbolize the number of genes in every cell.

Chromosomes in forensics

Crime doesn't pay is a justice board that DNA created and hanged in every courtroom. A Y-STR is a short tandem repeat (STR) on the Y-chromosome. Y-STRs are powerful toll used in forensics. There are regions on DNA that are made up of multiple copies of short repeating sequences of bases (e.g., TATT) which repeat a variable number of times depending on the individual. These repeat regions are examined when conducting STR analysis. It is extremely rare to find two people having the same number of repeated sequences. Forensic scientists use the polymerase chain reaction (PCR) to make millions of copies of repeated genes in the STR regions. Gel electrophoresis then yields the number of times each repeat unit appears in the fragment.. Forensic crime analysts used this technique to isolate the criminal. Forensic experts around the world recognized the potential of the method for sexing and exclusion and promoted Y-chromosome analysis for sex crimes.

The central dogma

Central Dogma is a very complex and deep term indeed, which was coined by Francis Crick discoverer of the structure of DNA in 1958. Dr. Francis Crick eloquently stated "I called this idea the central dogma, for two reasons, I suspect. I had already used the obvious word hypothesis in the sequence hypothesis, and in addition I wanted to suggest that this new assumption was more central and more powerful. The central dogma concept (pretty much like a production line) explains how the flow of genetic data (bases) from DNA to RNA and to ribosomes which uses amino acid instructions to make customized to protein. The ribosomes serve as factories in the cell where the information is translated" from a code into the functional product.

Let us go a little deeper to understand the mechanics of the central dogma and DNA as shown in (Fig. 1.2). It starts with the protein which is essential nutrient for the human body. Protein is one of the building blocks of body tissue and can also serve as a fuel source. As fuel supplier, proteins provide as much energy density as carbohydrates. So, if a certain part of the body needs muscle build up and it will inform the DNA of the cell about the need for protein. Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together between the carboxyl atom of one amino acid and the amine nitrogen of another. The diagram (Fig. 1.3) gives a visual representation of the whole cycle of this phenomenon central dogma.

Figure 1.2  This is the miraculous product line of making protein. Six phases starting from Crude DNA all the way to a refined protein.

Figure 1.3  The diagram clearly shows the three phases, starting with the initiation phase where RNA gets the message from DNA. In the elongation phase, mRNA is built. In the termination phase where mRNA leaves a healthy DNA on its own.

Proteins

Proteins are the chief actors within the cell, and they carry out the duties specified by the information encoded in genes. The sequence of amino acids in a protein is defined by a gene and encoded in the genetic code. The best-known role of proteins in the cell is as enzymes, which acts as a catalyst for chemical reactions. Conclusively, the number of protein molecules in a cell was calculated to be 42 million.

Amino acid

As Dr. Lawrence C. Brody, Ph.D. eloquently defined amino acid: Amino acids are the small molecules with 20 different flavors that make proteins. These amino acids get linked together like beads on a string to make long chains that we call polypeptides which are the building blocks of proteins. The neat thing about amino acids is that they make the final shape of the protein which in turn dictates what it can do in the cell.

RNA structure

It is called ribonucleic acid (RNA). It is the bridge that carries DNA protein instructions to the ribosome (assembly engine) where protein is manufactured. The order of the DNA bases (ATGC) determines the genetic code, similar to the way the order of letters in the alphabet is used to form words. DNA's words are three letters (or bases) long, and used specifically as code for genes, which in the language of the cell, is the blueprint for proteins to be manufactured.

To read protein blueprints, DNA is unzipped to expose the individual strands and an enzyme translates the instruction into a massage called messenger RNA (mRNA) which carries the instructions for making proteins. The mRNA is then leaving the nucleus and moves to a molecular machine responsible for manufacturing proteins called ribosome. The ribosome translates the mRNA instructions to three-letter words called codons. The three letter codons are loaded into the codon table, and they extract a specific amino acid which is a polypeptide chain that will eventually become a protein.

The ribosome assembles a protein in three phases—The first step called initiation ; a transfer RNA (tRNA) brings the specific amino acid that was selected from the codon table into the ribosome. The second step called elongation ; each amino acid is sequentially connected to a link in a chain called polypeptide. The order each amino acid is crucial to the functionality of the future protein; errors in adding an amino acid can result in disease. The third step called termination , the completed polypeptide chain, is released from the ribosome and is folded into its final protein state. Proteins are required for the structure, function, and regulation of the body's tissues and organs; their functionality is seemingly endless.

Transcription (phase-1 of central dogma)

Merriam-Webster dictionary defines the term transcript as an official copy of a student's educational record. In biochemistry, it is the process to copy genetic sequence information of DNA nucleotides into newly synthesized molecules of RNA, while DNA serves as a template. There are three agents of RNA with distinct functions during DNA transcription:

• mRNA (messenger RNA) which sends a DNA message to the ribosome).

• rRNA (ribosomal RNA) which makes up the ribosome.

• gRNA Gets instructions from DNA and guides Cas9 to the target location.

• tRNA (transfer RNA) which transfers amino acids building supplies of protein to the ribosome.

The transcription process

It takes place in three consecutive steps: initiation, elongation, and termination. The steps are illustrated in (Fig. 1.3).

Initiation (step-1): As DNA is being transcribed by the polymerase, a transcription bubble forms. RNA enzyme at the beginning of transcription binds to the promoter at the beginning of the gene chain. This triggers the beginning of a read message which creates the strand of mRNA.

Elongation (Step-2): It occurs when RNA polymerase starts building mRNA molecule with DNA complementary base pairs reads, where adenine (A) nucleotides become uracil (U) in mRNA.

Termination (Step-3): is the ending of transcription and occurs when RNA polymerase crosses a stop (termination) sequence in the gene. The mRNA strand is complete, and it detaches from DNA.

Translation (phase-2 of central dogma) process

Within all cells, the translation central unit is called the ribosome which contains two subunits that contain proteins and the two specialized RNA molecules: ribosomal RNA (rRNA) and transfer RNA (tRNA). Within the ribosome, the mRNA and tRNA complexes are held jointly to facilitate base-pairing. The rRNA catalyzes the attachment of each new amino acid to the growing chain.

Figure 1.4  This is another view of the Central Dogma process. (1) The pre-mRNA is ready to creates the messenger RNA (mRNA) (2) Polymerase builds the mRNA (3) which sends the mRNA to rRNA (ribosomal RNA) which makes up the ribosome. (4) Transfer RNA (tRNA) transfers amino acids building supplies of protein to the ribosome. (5) Amino acid chain polypeptide is created. (6) The codon table extracts the amino acids codes. (7) The selected protein id created.

Translation is the second part of the Central Dogma miracle which comes after the transcription step is complete. Information from messenger mRNA created during transcription gets decoded and turned into a series of amino acids (through the codon table), and later they produce selected proteins. We use the term expression as the process of disassembling a gene and assembling its corresponding protein. Fig. 1.4 gives a magnified view of the Central Dogma process.

Anatomy of CRISPR machine

Let me explain the meaning of a miracle: The religions interpret a miracle as divine intervention. But this is not what we're interested in. In science, we do not have miracles—the term is drastically abused and twisted. We do have unexpected surprises due to an unearthed, unscheduled event, which will be scientifically explained later. A scientific miracle is a steppingstone for further miracles which will enhance human endeavor for further progress. A scientific miracle is a means and not an end.

Muslim's focus on medicine was fostered by the Qur'an and the hadith, as indicated in the following saying the Prophet Muhammad: Allah has not sent any disease without sending a cure for it. CRISPR and its future generations have been secretly hidden in the Qur'an and will be all discovered to eradicate all the diseases of the Earth.

CRISPR is the mini name of (clustered regularly interspaced short palindromic repeats) which is a crazy—long name that we probably will not need to remember. CAS stands for CRISPR-Associated gene. CRISPR got its name because scientists noticed that it contained lots of small palindromic sequences repeated through the DNA. A palindromic is a word that reads the same forward and backward as taco cat. A palindromic DNA sequence could be AATTAA, miraculously powerful genome editing tool. CRISPR since its creation hat created a new dimension on genetic engineering for editing genomes (see Fig. 1.5 for additional explanation). We all are familiar with word processing. We add, cut, paste, search, delete, and replace words in a text with utmost simplicity. Well, CRISPR is a gene processor, doing exactly what word processors do.

Having said that, we can say that CRIPSR is a scientific miracle with great momentum for helping humanity. Fixing DNA defects and eliminating complex disorders such as autism, Alzheimer's disease, and diabetes is an incredible achievement comparable to the discovery of vaccine. Jerry Lewis will be crying in his grave from joy when he finds out that his muscular dystrophy children will be able to walk in 5years. CRISPR is truly a Holy Grail.

Figure 1.5  (1) A DNA has a corrupt strip of genes and needs to be replace with a healthy one (2) Under the orders of RNA, Cas-9 is built (3) RNA learns the location of the defect (4) and (5) Cas9 cuts the defect strip (6) The repair of the target DNA starts (7) The healthy strip is inserted as a replacement of the mutated one.

CRISPR structure

CRISPR technology is a simple yet powerful tool for editing genomes. It allows researchers to easily alter DNA sequences and modify gene function. CRISPR is like a gun in the hand of the deranged mind. In popular usage, Cas9 CRISPR-associated is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA. In a paper published Nov. 10, 2017, in the journal Nature Communications, Mikihiro Shibata of Kanazawa University and Hiroshi Nishimasu of the University of Tokyo showed in a video what it looks like when a CRISPR is in action for the very first time.

Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune called CRISPR-Cas, which provides sequence-specific adaptive immunity and fundamentally affect our understanding of virus–host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell allowing it to remember, recognize, and clear infections.

CRISPR using enzymes as scissors to slice and splice sections of DNA as they are unwanted segments and patch in substitutes. In theory, it also might make it possible to create designer babies that are smarter or better-looking than other individuals. But some people have questioned whether such tinkering with human cells would be like playing god. Many people also worry that editing is not safe.

Nature Magazine in its November 15, 2016 announced that On 28 October, a team led by oncologist Lu You at Sichuan University in Chengdu delivered the modified cells into a patient with aggressive lung cancer as part of a clinical trial at the West China Hospital, also in Chengdu. The team of researchers removed immune cells from the recipient's blood and then they used CRISPR–Cas9, to cut a DNA-cutting enzyme with a molecular guide called gRNA tells the enzyme precisely where to cut. The procedure was to cut off the gene codes protein PD-1, which stops the cell's immune response and allows cancer function to proliferate. The team allowed grow culture the number healthy DNA molecules and injected them back into the patient, who has large lung cancer. Without PD-1, the edited cells will become part of the native cells and will attack and defeat the cancer.

It has happened. The first children genetically engineered with the powerful DNA-editing tool called CRISPR-Cas9 have been born to a woman in China. Their altered genes will be passed to their children, and their children's children. Join Jennifer Doudna, as we explore the perils and the promise of this powerful technology. It is not the first-time human ingenuity has created something capable of doing us great good and great harm. Are we up to the challenge of guiding how CRISPR will shape the future?

Drawbacks and unethical issues

The phenomenon genome vandalism as specified by Dr. Church, Professor of Genetics at Harvard Medical School, is where DNA is to cut at sites other than the intended target. Even when the system cuts on target, there is a chance of not getting a precise edit. The phenomenon of off-target effects can lead to the introduction of unintended mutations. There's plenty of room to tarnish the success of CRISPR. Making genetic modifications to human embryos and reproductive cells such as sperm and eggs is known as germline editing. Since changes to these cells can be passed on to subsequent generations, using CRISPR technology to make germline edits has raised a number of ethical concerns.

Not since the atomic bomb has a technology so alarmed its inventors that they warned the world about its use. Not, that is, until the spring of 2015, when CRISPR's co-discoverer microbiologist Jennifer Doudna called for a worldwide moratorium on the use of the new gene-editing tool CRISPR—a revolutionary new technology that she helped create—to make heritable changes in human embryos. The cheapest, simplest, most effective way of manipulating DNA ever known, CRISPR may well give us the cure to HIV, genetic diseases, and some cancers, and will help address the world's hunger crisis. Yet even the tiniest changes to DNA could have myriad unforeseeable consequences—to say nothing of the ethical and societal repercussions of intentionally mutating embryos to create better humans.

When Alfred Nobel, the Swedish inventor of dynamite and more powerful explosives, died in 1896, he bequeathed the bulk of his fortune to create five annual prizes honoring ingenuity. The chemistry, medicine, and physics prizes have come to be widely regarded as the most esteemed in their fields. The two others, literature, and peace are more controversial.

Bio-hacking CRISPR, cracking the biological atom

DNA Bio-hacking is a mischievous component of genome vandalism. It is the central focus of the book and will be discussed in greater detail. CRISPR/Cas9 has already been hacked much more than just gene editing. Chris Lowe, Head of Research Operations at Horizon Discovery in Cambridge, Cambridge shire, United Kingdom explained: I see the CRISPR system not so much as an editing tool but more as a targeting system. It allows us to precisely target tools to specific locations in the genome—and this ability is challenging our imagination, allowing the investigation of much more subtle effects on the genome compared to the fairly blunt technique that was brought out a couple of years ago where you just damage the DNA and let it repair.

When Dr. Jonathan S. Weissman, Professor of Cellular Molecular Pharmacology at the University of California, San Francisco (UCSF), in an attempt to demonstrate bio-hacking, got hold of CRISPR/Cas9, the first thing he did was break the scissors. His team modified Cas9 (CRISPR associated protein 9) enzyme scissors by activating/and deactivating gene expression, giving the team a simple system to turn genes on or off. Cyber criminals specializing in molecular pharmacology and bioinformatics developed formidable CRISPR/Cas9 tools to mangle the sequence of DNA genes and created new hacking paradigm that gave these criminals a leading advantage to corrupt biomedicine.

CRISPR could 1day enable scientists to cure myriad genetic diseases, eradicate mosquito-borne illnesses, create pest-resistant plants and resurrect extinct species. But it also raises the specter of customizable designer babies and lasting changes to the human genetic code through so-called germline editing, or edits made to reproductive cells that are transmitted to future generations. This bioethics nightmare scenario was realized last fall when a Chinese researcher declared that he had used CRISPR to edit the genomes of twin girls in order to make them resistant to HIV. Doudna decried the act but allows that her own views on germline editing are still evolving. I've gone from thinking ‘never, ever’ to thinking that there could be circumstances that would warrant that kind of genome editing, she said. But it would have to be under circumstances where there was a clear medical need that was unmet by any other means and the technology would have to be safe.

The true ramifications of gene editing technology (i.e., CRISPR) could be far more serious than the realization of mythical creatures. In 2016, for the first time, the Office of the Director of National Intelligence added gene editing to its annual list of threats posed by weapons of mass destruction and proliferation. An article authored by Amrit P. Acharya and Arabinda Acharya in the June 2017 issue, and under the provocative headline, When ISIS Meets CRISPR—explores the ramifications of gene editing technologies and techniques somehow finding themselves in the wrong hands.

Many cyber terrorists are turning into bio terrorists and could hold an entire city for ransom or DNA genome vandalism. This is an open-ended area that will excite the imagination of biohackers who will be energized to step into this new type of vandalism. What is more frightening is, while federal biodefense strategies have largely focused on anthrax, smallpox, HIV, and Ebola, biotech software and gene editing AI-centric tools will open up a new domain of bioterror with genetically modified viruses.

CRISPR/Cas9 is a fast-evolving gene editing technology that enables geneticists and clinicians to remove, add or change sections of DNA sequences with unprecedented ease and efficiency. Its versatility and wide array of potential uses have caused a lot of excitement in the healthcare and life sciences industry—and also some deep concerns about its misuse.

For all the promise of being able to prevent or cure inheritable diseases such as muscular dystrophy, Huntington's disease or sickle cell anemia, after all, many ethicists have also sounded the alarm about gene editing technology being used for eugenic designer babies—or potentially even a wholesale revision of the natural world as we know it. We can generalize and add the corollary "for any existing and emerging technology, we created two polarized sides, a good side that will benefit humanity, and a wicked side that will eclipse human progress and global prosperity".

CRISPR cyber hacking

Using cyber hacking in bioinformatics is the devil's hatchet in his right arm. Cyber terrorists are learning the potentialityof DNA binary storage to replace silicone technology. They are getting ready to create a cyber pandemic that will vandalize DNA storage libraries, in addition to poisoning confidential hospital genomic repositories and topple the privacy of citizens DNA medical files. CRISPR developers will curse the day they announced this magical scissors to the world.

Appendix

Appendix-A Glossary of DNA

Appendix-B Landmine Nobel Sweet Irony

Appendix-C CRISPER Pioneers

Appendix-A: Glossary of DNA (courtesy MERIT CyberSecurity technical library)

Allele    One of several possible versions of a gene. Each one contains a distinct variation in its DNA sequence. For example, a deleterious allele is a form of a gene that leads to disease.

Amino acid    The chemical building block of proteins. During translation, different amino acids are strung together to form a chain that folds into a protein.

Archaea    Microbes that look similar to bacteria but are actually more closely related to eukaryotes, such as humans. Archaea are single-celled organisms that don't have a nucleus and can only be seen with a microscope. They're found in many different habitats, and many of the first known examples were found in extreme environments.

Bacteria    An abundant type of microbe. These single-celled organisms are invisible to the naked eye, don't have a nucleus, and can have many shapes. They're found in all types of environments, from Arctic soil to inside the human body. Most bacteria are not harmful to human health, but certain pathogenic bacteria can cause illness.

Base    The four letters of the genetic code (A, C, T, and G) are chemical groups called bases or nucleobases. A=adenine, C=cytosine, T=thymine, and G=guanine. Instead of thymine, RNA contains a base called uracil (U).

Base pair    Different chemicals known as bases or nucleobases are found on each strand of DNA. Each base has a chemical attraction for a particular partner base, known as its complement. C matches up with G, while A pairs with T or U. These bonded genetic letters are called base pairs. Two strands of DNA can zip together to form a double-helix shape when complementary bases match up to form base pairs.

Cancer    A type of disease caused by uncontrolled growth of cells. Cancerous cells may form clumps or masses known as tumors, and can spread to other parts of the body through a process known as metastasis.

Cas    Abbreviation of CRISPR-associated, may refer to genes (cas) or proteins (Cas) that protect bacteria and archaea from viral infection.

Cas12    A protein derived from the CRISPR-Cas bacterial immune system that has been co-opted for genome engineering. Uses an RNA molecule as a guide to find a complementary DNA sequence. Once the target DNA is identified, Cas12 cuts both strands. It has been compared to molecular scissors or a genetic scalpel. In CRISPR immunity, cutting viral DNA prevents it from destroying the host cell. In genome engineering, cutting genomic DNA initiates a repair process that ends up making a change or edit to its sequence.

Cas9    A protein derived from the CRISPR-Cas bacterial immune system that has been co-opted for genome engineering. It uses an RNA molecule as a guide to find a complementary DNA sequence. Once the target DNA is identified, Cas9 cuts both strands. It has been compared to molecular scissors or a genetic scalpel. In CRISPR immunity, cutting viral DNA prevents it from destroying the host cell. In genome engineering, cutting genomic DNA initiates a repair process that ends up making a change or edit to its sequence.

Cell    The basic unit of life. The number of cells in a living organism ranges from one (e.g., yeast) to quadrillions (e.g., blue whale). A cell is composed of four key macromolecules that allow it to function (protein, lipids, carbohydrates, and nucleic acids). Among other things, cells can build and break down molecules, move, grow, divide, and die.

Chromosome    The compact structure into which a cell's DNA is organized held together by proteins. The genomes of different organisms are arranged into varying numbers of chromosomes, and human cells have 23 pairs.

Cleave    The scientific term for cut or break apart. Typically refers to splitting apart a long polymeric molecule like DNA, RNA, or protein. For example, a nuclease like Cas9 can be directed to cleave DNA at a specific location.

Complementary    Describes any two DNA or RNA sequences that can form a series of base pairs with each other. Each base forms a bond with a complementary partner. T (DNA) and U (RNA) bond with A, and C complements G. For example, in CRISPR immunity, the spacer sequence in a guide RNA is complementary to a sequence found in a viral genome. When the RNA bases pair with complementary DNA bases from an invading virus, the Cas9 protein will cut the target to stop the viral infection.

CRISPR    Pronounced crisper. An adaptive immune system found in bacteria and archaea, co-opted as a genome engineering tool. Acronym of clustered regularly interspaced short palindromic repeats, which refers to a section of the host genome containing alternating repetitive sequences and unique snippets of foreign DNA. CRISPR-associated surveillance proteins use these unique sequences as molecular mugshots as they seek out and destroy viral DNA to protect the cell. During CRISPR immunity, the host cell generates crRNA molecules, each containing one spacer that is complementary to a portion of a viral genome. crRNAs guide CRISPR immune proteins to find and destroy matching invader sequences.

CRISPR screening    A technique that lets scientists see the effects of turning gene expression up or down with CRISPRa and CRISPRi. Instead of checking one gene at a time, a single CRISPR screen can provide information about thousands of different genes at a time.

CRISPRa and CRISPRi    CRISPRa stands for CRISPR activation and CRISPRi stands for CRISPR interference or inhibition. Both are methods for fine-tuning gene expression. If a gene were a car, CRISPRa is the gas pedal and CRISPRi is the brake. Using CRISPRa to activate a gene increases protein production. Using CRISPRi to turn down a gene reduces the number of protein products made from that gene.

dCas9    Catalytically inactive, or dead, Cas9. This mutated version of the Cas9 protein cannot cut, but still binds tightly to a particular DNA sequence specified by the guide RNA. It can be used to physically block the process of transcription, turning off a specific gene, or to shuttle other proteins to a particular site in the genome.

DNA    Abbreviation of deoxyribonucleic acid, a long molecule that encodes the information needed for a cell to function or a virus to replicate. Forms a double-helix shape that resembles a twisted ladder. Different chemicals called bases, abbreviated as A, C, T, and G, are found on each side of the ladder, or strand. The bases have an attraction for each other, making A stick to T while C sticks to G. These rungs of the ladder are called base pairs. The sequence of these letters is called the genetic code. Double-strand break (DSB) When both strands of DNA are broken, two free ends are created, may be made intentionally by a tool such as Cas9. The cells repair their DNA to prevent cell death, sometimes changing the DNA sequence at the site of the break. Initiating or controlling this process with the intent to alter a DNA sequence is known as genome engineering.

Enzyme    A molecule, typically a protein, that causes or catalyzes a chemical change. Usually an enzyme's name describes a molecule involved in the activity it performs and ends with the suffix -ase. For example, lactase is a well-known enzyme that breaks down lactose, a sugar found in milk. Cas9 is a nuclease, an enzyme that breaks apart the backbone of nucleic acids (RNA or DNA).

Epigenetic    Refers to changes to a cell's gene expression that do not involve altering its DNA code. Instead, the DNA and proteins that hold onto DNA are tagged with removable chemical signals. Epigenetic marks tell other proteins how to read the DNA, which parts to ignore, and which parts to transcribe into RNA. Comparable to sticking a note that says SKIP onto a page of a book—a reader will ignore this page but the book itself has not been changed.

Eukaryote    A domain of organisms whose cells contain a nucleus and other organelles. Eukaryotes are often large and multicellular (e.g., elephants) but can also exist as microscopic, single cells (e.g., yeast). This category of life includes humans compared to prokaryotes (bacteria and archaea).

Expression    A product being made from a gene; can refer to either RNA or protein. When a gene is turned on, cellular machines express this by transcribing the DNA into RNA and/or translating the RNA into a chain of amino acids. For example, a highly expressed gene will have many RNA copies produced, and its protein product is likely to be abundant in the cell. CRISPRi and CRISPRa are methods for turning gene expression down or up, respectively, image of gene expression. Starting with a gray chromosome, DNA nucleosomes are acetylated and chromatin is exposed. The chromatin then exposes a DNA segment that is translated into RNA to then be transcribed into a protein.

Gene    A segment of DNA that encodes the information used to make a protein. Each gene is a set of instructions for making a particular molecular machine that helps a cell, organism, or virus function.

Gene drive    A mechanism for preferential inheritance of a particular DNA sequence. Usually, offspring have a semi-random chance of inheriting a given stretch of DNA from either parent. In a scientist-designed gene drive, a gene is engineered to have a 100% chance of being passed on. Gene drives can force the inheritance of a desirable trait through a population of organisms. For example, this approach could potentially make all mosquitoes incapable of transmitting the malaria parasite.

Gene therapy    Delivering corrective DNA to human cells as a medical treatment. Certain diseases can be treated or even cured by adding a healthy DNA sequence into the genomes of particular cells. Scientists and doctors typically use a harmless virus to shuttle genes into targeted cells or tissues, where the DNA is incorporated somewhere within the cells' existing DNA. CRISPR genome editing is sometimes referred to as a gene therapy technique.

Genetically modified organism (GMO)    A GMO has had its DNA intentionally altered using scientific tools. Any organism can be engineered in this manner, including microbes, plants, and animals.

Genome    The entire DNA sequence of an organism or virus. The genome is essentially a huge set of instructions for making individual parts of a cell and directing how everything should run.

Genome editing    Intentionally altering the genetic code of a living organism. It can be done with ZFNs, TALENs, or CRISPR. These systems are used to create a double-strand break at a specific DNA site. When the cell repairs the break, the sequence is changed. Can be used to remove, change, or add DNA.

Genome surgery    Repairing harmful DNA through a one-time genome editing procedure. Unlike taking a drug that will temporarily reduce long-term symptoms, altering a patient's genetic code with the CRISPR-Cas9 molecular scalpel would permanently and directly reverse the cause of a genetic disease.

Genomics    The study of the genome, all the DNA from a given organism. Involves a genome's DNA sequence, organization and control of genes, molecules that interact with DNA, and how these different components affect the growth and function of cells.

Germ cells    The cells involved in sexual reproduction: eggs, sperm, and precursor cells that develop into eggs or sperm. The DNA in germ cells, including any mutations or intentional genetic edits, may be passed down to the next generation. In contrast, the genetic material in somatic cells (all the cells in the body except for germ cells) cannot be inherited by offspring. Note that genome editing in an early embryo is considered to be germline editing since any DNA changes will likely end up in all cells of the organism that is eventually