“CRISPR making it a defense mechanism” (Lacoma,

“CRISPR refers to a naturally occurring DNA sequence that help and protect organisms by identifying threats and attacking them, making it a defense mechanism” (Lacoma, Tyler). CRISPR is also an acronym for “clustered regularly interspaced short palindromic repeats”. It was first observed in bacteria around 1980s when scientists observed one DNA sequence repeating all the time. The sequences between the repeats were the DNA of viruses that invade the bacteria. When bacterial cells are invaded by a foreign virus, a part of the virus’s DNA is inserted into the CRISPR sequence. The DNA of the virus undergoes transcription (the process of copying DNA into RNA) and this RNA chain is cut into pieces called CRISPR RNA (“CRISPR:A game”). This allows the bacteria to remember the virus for future attacks. In this defense mechanism, there is also a set of enzymes called Cas (CRISPR-associated proteins). According to Carl Zimmer, “together the viral RNA and Cas enzymes drift through the cell and if they they encounter genetic material from a virus that matches the CRISPR RNA, the Cas enzymes cuts the DNA of the virus, disabling the virus”.
CRISPR-Cas9 was adapted from the naturally occurring genome editing system which means that this technology allows scientists to change an organism’s DNA by adding, removing, and/or altering (“What are genome”). One of the only differences is that researchers create a piece of RNA called guide RNA which is designed to find and attach itself to only a specific sequence in the DNA (the target sequence) and not a bacteria. The Cas9 enzyme goes with the guide RNA in the same location which acts as a pair of molecular scissors to cut across both strands of the DNA (“What is CRISPR-Cas9”). The cell recognizes that the DNA is damaged so the researches can use the repair machinery of the cell itself to change the genetic material by replacing with a customized DNA sequence. 
The CRISPR-Cas9 has a lot of potential applications because of its ability to accurately edit the building blocks of life. The medical applications of CRISPR technology is being looked at currently to understand, prevent and treat human diseases such as cystic fibrosis, hemophilia, Huntington’s disease and many more. However ethical problems are brought up when technologies such as CRISPR-Cas9 is used to alter human DNA.       
Cystic Fibrosis
“Cystic fibrosis is an inherited disease characterized by the buildup of thick, sticky mucus that can damage many of the body’s organs” (“Cystic”). It  is caused by changes in the CFTR gene in which to little amount of the CFTR protein reaches the cell surface. This particular gene provides information so that negatively charge particles called chloride ions can be transported in and out of cells. Chloride ions are important because the flow of these ions help control the movement of water in tissues. More movement of the ions means there is more thin and easily moving mucus. Where there are mutations in this gene, “cells that line the passageways of the lungs, pancreas, and other organs produce mucus that is usually thick and sticky” (“Cystic”). This causes damage slowly to the respiratory and digestive system. This condition is inherited in an autosomal recessive pattern which means there is a 50% of you being a carrier but not have the gene if one is born to parents who carry the same autosomal recessive mutation. There is also a 25% of having the disease and 25% chance having normal genes so no trace of disease. 
The F508del mutation is most common and when this happens the CFTR protein does not reach the cell surface in the required quantity. The G551D mutation is when the protein is location on the surface of the cells but doesn’t work. The most recently approved medication is Ivacaftor which works by “keeping the CFTR channels open to enable transportation of chloride ions across the cell membrane in CF patients” (“Kalydeco”). It prevent chloride ions from leaving the cell and keeps the salt levels balance in the body by keeping the chloride gateway open. Most medication before this only concentrated on the symptoms such as mucus-thinning drugs to take out the mucus and antibiotics to treat lung infections.
How CRISPR will help
Therapies for cystic fibrosis can be directed to one of three levels in the cell: DNA, RNA, or protein. DNA is in the nucleus of the cell, contains all the instructions to create the required proteins however, it cannot move out of nucleus. “Therefore, the instructions contained in DNA are transcribed into RNA, which travels out of the nucleus to create the necessary protein” (Shannon, S). Proteins then are the final stage because they help cells stay alive. So, DNA is used to create RNA and that creates protein. This also means if there is a mutation in one’s DNA, there will also be a mutation in the RNA and in the protein.
In cystic fibrosis there can only be a cure if the mutation is treated in the DNA level. Ivacaftor, which help to restore the function of the protein, do not go in depth to the RNA or DNA. This means that medication like Ivacaftor restores the function of the protein, the cell continues to be dysfunctional since the mutation is in the DNA and not only the protein.
A cure and goal of cystic fibrosis therapies is to use CRISPR-Cas9 to replace mutated genes in those with the genetic disease. The CRISPR-Cas9 system can target a specific sequence of DNA and cut it out then replace it with the correct gene sequence. The process is already explained in the first two paragraphs of this essay. This is a better solution because the DNA is targeted instead of only the symptoms or the proteins. This could prevent the mutation to be passed onto future generations also. 
The use of the CRISPR-Cas9 system has already begun for example in a study in 2013 published in Cell by Gerald Schwank and colleagues titled “Functional Repair of CFTR by CRISPR-Cas9 in Intestinal Organoids of Cystic Fibrosis Patients”, used CRISPR to correct the CFTR gene in intestinal cells (Shannon, S). In the study, intestinal organoids were taken from two donor patients who were homozygous for the F508del mutation. What the study tested was if it its possible to replace a mutated CFTR gene with the correct gene sequence which would restore the function of the gene. With use of the CRISPR-Cas9, the study was successful in so the function of the CFTR was restored fully, allowing a proper flow of mucus to cross the intestinal cells.
The success of the study shows the potential use of CRISPR-Cas9 in the future for medical purpose like those living with cystic fibrosis. Although it has a bright future, there are still issues to address before this type of technology is used everywhere. 
Ethical Negative
Researchers led by Junjiu Huang attempted to modify the gene called HBB, which encodes the human ?-globin protein and is responsible for ?-thalassaemia (a dangerous blood clotting disorder), using CRISPR-Cas9. From 86 embryos that were injected, 71 had survived, just 28 of those had removed the defect part of the DNA and just a small fraction had the replaced genetic material, making this experiment very unsuccessful. Huang himself said: “if you want to do it in normal embryos, you need to be close to 100%. That’s why we stopped. We still think it’s too immature.” This experiment proves that it was good healthy embryos weren’t used or else a lot of them would’ve died and a lot wouldn’t be healed. (Woollaston, V)
Huang’s team also found a lot ‘off-target’ mutations which CRISPR-Cas9 caused. This is the main safety problem related to gene editing because these unintended mutations could be harmful. “Off-target mutations could potentially result in the development of cancer and other pathologies” (Gyngell, C). The rates of the off-target mutations were much higher than those in studies with human adult cells or mouse embryos. Huang’s team only tested a part of a DNA sequence where they found the unintended mutations and according to Huang “if we did the whole genome sequence, we would get many more (off-target mutations)”. The reason a larger DNA sequence is a problem is because “large genomes may contain multiple DNA sequences identical or highly homologous to intended target DNA sequence” which means there should be no off-target mutations in small sequences to ensure the organism will be healthy (Rodriguez, E). 
CRISPR-Cas9 promotes the usage of stem cells and scientist and religious groups have debated over if stem cells should be used since 1999 which is one year after the research paper stating that stem cells can be taken from human embryos was published (Phillips, Theresa). In the beginning the research method was to take embryonic stem cells from an aborted embryo. This was done a few days days after conception or between the 5th and 9th week. The research method involves using a blastocyst. which gets from a lab rotary fertilization of an egg. This way the possibility of life can be gone. The main ethical problem was that “a life is a life and that should never be compromised. A fertilized egg should be valued as a human life even if it is in its very first weeks. Destroying human life in the hopes of saving human life is not ethical” (“Stem Cell Research”). So CRISPR-Cas9 could possibly be killing potential babies when trying to save lives.
Ethical Positive 
Huang’s study was not conducted with real healthy embryos that even had the potential to be born. The researchers used triploid embryos (embryos that have an extra set of chromosomes) so these embryos wouldn’t have survived pregnancy. Even by using CRISPR in these embryos, they would’ve still had no chance of survival. The study turned out unsuccessful and there was a lot of off-target mutations however, these did not have a significant harm so technically Huang wasn’t being unethical. 
Huang also has future plans to decrease the number of off-target mutations using adult human cells or animal models first then moving to embryos when the results are better. He is specifically thinking of “tweaking the enzymes to guide them more precisely to the desired spot, introducing the enzymes in a different format that could help to regulate their lifespans and thus allow them to be shut down before mutations accumulate, or varying the concentrations of the introduced enzymes and repair” (Cyranoski, D). This would help save the amount of embryos that would’ve been destroyed and increased the chances of his study to be successful. 
Embryos aren’t free and easy to use because there are regulations that control embryo research in several countries. This protects future people from the safety risks. For example the UK has laws that only allows some forms of genetic research to be conducted, the embryo should destroyed by 14 days after research and not implanted into a woman. This legal requirement will decrease every risk that could potentially harm any future child. (Gyngell, C)
Using CRISPR-Cas9 may be the only way to avoid passing on genetic disorders. Approximately 19% of women produce only one working embryo (“Human Fertilization”). One of those women could be carrier of the gene for cystic fibrosis and their partner is too but they wish to have a child together. They have a 25% of having a child with cystic fibrosis. They would want to  avoid this outcome and have a healthy baby so by using the new technology, they could prevent cystic fibrosis and many other genetic disorders.