Modifying the Genome: What is Genetic Engineering?

What is Genetic Engineering?

The genome is our genetic code and is made of all the DNA that determines how our bodies are put together and maintained (learn more about genomes). The genome is like an instruction manual for an organism, and the DNA is like the script from beginning to end. If you were able to change the DNA script in an organism's genome, then you would be able to alter that organism's characteristics or function.

Genetic engineering or genetic modification "is the process of altering the DNA in an organism's genome. . . Genetic engineering is used by scientists to enhance or modify the characteristics of an individual organism."[1]

Technically speaking, humans have been modifying the genomes of organisms for thousands of years through methods like selective breeding.[2] In selective breeding, if a desirable characteristic appears in a plant or animal, a farmer can try to breed animals or select and plant seeds with the desired trait to try and grow that trait among their herds or crops. If the farmer keeps mating organisms with the desired trait, the number of organisms with the desired trait will grow, eventually creating whole new varieties of crops or herds.[2]

Evolution of corn [4]

Corn as we know it today—with its rows of bright yellow, juicy kernels—is the result of selective breeding. Archaeologists have traced corn's ancestry to teosinte, a tough type of grass that bears little resemblance to corn.[3] When these plants would produce new, desirable characteristics through a mutation (like larger plants or tastier kernels) farmers would choose seeds from the preferred plants to try and produce crops with the same desired traits. This artificial evolution of crops over thousands of years is what eventually lead to a type of corn that is incredibly different from how it used to be.

But when we hear "genetic engineering," or "genetically modified organisms," or "genome editing," we generally don't think of thousands of years of selective breeding. What separates these methods from selective breeding?

The World Health Organization defines a genetically modified organism or GMO as "organisms (i.e. plants, animals or microorganisms) in which the genetic material (DNA) has been altered in a way that does not occur naturally by mating and/or natural recombination."[5]

These genetic engineering methods can involve "changing one base pair [a single "rung" on DNA's ladder-shape], deleting a whole region of DNA, or introducing an additional copy of a gene. It may also mean extracting DNA from another organism's genome and combining it with the DNA of that individual.[1] There are different techniques for genetically modifying organisms. Some are older technologies dating back to the 1970s, and some are new, cutting-edge techniques.[7]

A Few Examples of Genetic Engineering Methods. . .

Agrobacterium
Agrobacterium is a bacteria that infects plants. When it infects a plant, it inserts and integrates some of its own DNA into the DNA of the host plant's cells.[2][7] In the early 1980s, scientists developed Agrobacterium strains without the disease-causing genes that remained able to "infect" the plant and transfer DNA.[2] By replacing the disease-causing DNA with other DNA, scientists could use Agrobacterium to deliver DNA of their choosing into the plant to become part of its own DNA.

Gene editing methods in plants [6]

The "gene gun"
Scientists in 1987 discovered that DNA could be delivered to plant cells by "shooting" seeds or plant tissue with gold or tungsten micro-particles coated in the desired DNA.[2][7] The DNA, after injection, would integrate with the plant's DNA.

These methods of genetic engineering introduce DNA to an organism and allow it to integrate with the organism's DNA. When DNA is added or changed, a new trait may then develop in an organism. Other methods target and edit specific pieces of DNA. These methods are referred to as genome or gene editing, and are defined as "the use of biotechnological techniques to make changes to specific DNA sequences in the genome of a living organism."[8] [Italics added.]

Zinc Finger Nucleases (ZFNs)
ZFNs are a type of genome editing technology referred to as engineered nucleases.[9][10] Engineered nucleases have two parts: a part that targets and binds to a specific part of the DNA, and a nuclease (enzyme) part to "cut" the DNA.[10] The "binding" part of ZFNs are "zinc finger" proteins. ZFNs were effectively developed in 2005 and are a method of targeting and cutting a specific piece of DNA in the genome.[9] The "cutting" part of the ZFN is a FokI enzyme, and the cut occurs when the two FokI come together across the DNA strand.[11]

Image credit: Genome Research Limited [10]

Transcription activator-like effector nucleases (TALENs)
TALENs are also a type of engineered nucleases, effectively developed in 2010.[9] The binding part of TALENs are proteins called "transcription activator-like effectors" that come from bacteria that infect plants.[10] The cutting part of TALENs, like ZFNs, are a FokI nuclease and cut DNA in an identical manner.[11]

Image Credit: Genome Research Limited [10]

TALENs are able to be engineered to bind to the correct part of DNA more easily than ZFNs.[10] However, TALENs still don't always bring about the desired change, and the nucleases can be difficult to make.[10]

Engineered nucleases produce a "double strand" break in the DNA. The cell will repair the DNA strand either by rejoining the broken ends (deleting the DNA section that was cut from the sequence), or by deleting and then inserting a new piece of DNA to fill the gap (adding a DNA section, usually chosen by the scientist, to the sequence).[10][11]

CRISPR-Cas9
"CRISPR" stands for "clustered regularly interspaced short palindromic repeats" and is a type of immune system found in bacteria that protects them against viruses.[12] Cas9 is a protein (Cas9 stands for "CRISPR-associated protein 9) and cuts invasive viral DNA into pieces to protect the cell.[12]

In 2012 it was discovered that this system could be used as a genome editing technology.[12] CRISPR consists of an RNA molecule that is able to seek out DNA with a matching sequence. (RNA is a single-stranded molecule that is almost identical to DNA.)[13] It is able to search through all DNA in the cell and bind to the specific DNA bases that match its own sequence.[11][12] Cas9 is the part of the system that then cuts the DNA targeted by the RNA molecule.[11][12]

This system is "programmable," and scientists discovered that they could program CRISPR-Cas9 to "seek out" and then "cut" specific pieces of DNA that they wanted to target.

CRISPR-Cas9 is regarded as a groundbreaking genome editing technology, because prior methods were considered either too inefficient or too difficult for scientists to frequently use them in their laboratories.[12] CRISPR-Cas9 is currently considered the most inexpensive and efficient method of genome editing today.[11]

Results of Genetic Engineering

There are many crops grown today that have been genetically modified to have certain traits. According to the World Health Organization, the vast majority of genetically modified crops are modified to have one of three traits: "resistance to insect damage; resistance to viral infections; and tolerance towards certain herbicides."[5] Some crops include genetically modified corn, soybeans, cotton, alfalfa, and canola.[14]

There are fewer examples of genetically modified animals that are on the market. For human consumption, a variety of genetically modified salmon was approved for sale in the United States (2015) and in Canada (2016) (but has yet to officially reach the market in the U.S.).[15] As pets, a zebra fish genetically modified to glow in the dark was permitted for sale in the United States in 2003.[16] For laboratory experiments, many genetically modified rats and mice are used within labs around the world.[16]

There are even fewer examples of human genetic engineering that seek to make permanent, inheritable changes to a human genome. The first-ever genome editing experiment to alter a human embryo took place in China in 2015.[17] Most experiments that have used genome editing techniques on human DNA performed the experiments on early embryos, which were later destroyed after the experiment ended.[17] Genome editing on human DNA is tightly regulated around the world, and is even criminalized in some countries. The United Nations has even called for a world-wide moratorium on editing human DNA until ethical and safety issues can be resolved.[18]

Public Attitudes towards GMOs

Genetically modified organisms continue to provoke concerns from people around the world. Some people believe genetically modified crops are not safe for human consumption, or are less healthy than "natural" foods. Some people believe that releasing genetically modified organisms into the environment could harm ecosystems. Some also claim that the potential to genetically modify animals or humans violates nature and could have serious implications for the future of the human race and society as we know it.

On the opposing side, many argue that most applications of genome editing are safe, can benefit humanity and the environment, and can be prudently implemented to have a positive impact on the future. The questions created here are worth exploring, and I hope to touch on some of them in later blog posts!

 Have anything to add? Additional sources, helpful and relevant resources, and professional insights are welcome! Share in the comments below.


SOURCES

[1] yourgenome. (c2017). What is Genetic Engineering? yourgenome. [Online]. [Accessed 15 November 2017]. Available from: https://www.yourgenome.org/facts/what-is-genetic-engineering.

[2] National Research Council (US) Committee on Identifying and Assessing Unintended Effects of Genetically Engineered Foods on Human Health. (2004). Methods and Mechanisms for Genetic Manipulation of Plants, Animals, and Microorganisms. In: Safety of Genetically Engineered Foods: Approaches to Assessing Unintended Health Effects. Washington (DC): National Academies Press (US).  Available from: https://www.ncbi.nlm.nih.gov/books/NBK215771/

[3] Carroll, SB. (2010). Tracking the Ancestry of Corn back 9,000 Years. The New York Times. [Online]. May 24. [Accessed 02 November 2017]. Available from: http://www.nytimes.com/2010/05/25/science/25creature.html.

[4] Photo credit: © Robert S. Peabody Museum of Archaeology, Phillips Academy, Andover, Massachusetts. All Rights Reserved. {Accessed 02 November 2017]. Available from: http://learn.genetics.utah.edu/content/selection/corn/.

[5] World Health Organization. (2014). Frequently Asked Questions on Genetically Modified Foods. [Online]. [Accessed 02 November 2017]. Available from: http://www.who.int/foodsafety/areas_work/food-technology/faq-genetically-modified-food/en/.

[6] Powell, C. (2015). How to Make a GMO. Harvard University: The Graduate School of Arts and Sciences. [Online]. Available from: http://sitn.hms.harvard.edu/flash/2015/how-to-make-a-gmo/.

[7] Nuffield Council on Bioethics. (1999). The Scientific Basis of Genetic Modification. In: Genetically Modified Crops: The Ethical and Social Issues, pp. 22-23. [Online]. [Accessed 02 November 2017]. Available from: http://nuffieldbioethics.org/report/gm-crops-2/chapter-downloads/.

[8] Merriam Webster. [Online]. s.v. Gene Editing. [Accessed 02 November 2017]. Available from: https://www.merriam-webster.com/dictionary/gene%2Bediting.

[9] Nuffield Council on Bioethics. (2016). Genome Editing. In: Genome Editing: An Ethical Review. London: Nuffield Council on Bioethics, p. 8. [Online]. [Accessed 02 November 2017]. Available from: http://nuffieldbioethics.org/wp-content/uploads/Genome-editing-an-ethical-review.pdf.

[10] Nature Video. (2011). Method of the Year 2011: Gene-editing Nucleases. [Online]. [Accessed 02 November 2017]. Available from: https://www.youtube.com/watch?v=zDkUFzZoQAs.

[11] yourgenome. (c2017). What is Genome Editing? yourgenome. [Online]. [Accessed 02 November 2017]. Available from: http://www.yourgenome.org/facts/what-is-genome-editing.

[12] Doudna, J. 2015. How CRISPR Lets Us Edit Our DNA. TEDGlobal, September 2015, London. [Online]. [Accessed 02 November 2017]. Available from: https://www.ted.com/talks/jennifer_doudna_we_can_now_edit_our_dna_but_let_s_do_it_wisely#t-48530.

[13] Nature Education. (c2014). Ribonucleic Acid/RNA. Scitable. [Online]. [Accessed 02 November 2017]. Available from: https://www.nature.com/scitable/definition/ribonucleic-acid-rna-45.

[14] Johnson, D. and O'Connor, S. (2015). These Charts Show Every Genetically Modified Food People Already Eat in the U.S. Time. [Online]. [Accessed 03 November 2017]. Available from: http://time.com/3840073/gmo-food-charts/.

[15] Gallegos, J. (2017). GMO Salmon Caught in U.S. Regulatory Net, but Canadians have Eaten 5 Tons. Washington Post. [Online]. [Accessed 03 November 2017]. Available from: https://www.washingtonpost.com/news/speaking-of-science/wp/2017/08/04/gmo-salmon-caught-in-u-s-regulatory-net-but-canadians-have-eaten-5-tons/?utm_term=.c42f83a8c469.

[16] U.S. Food and Drug Administration. (2015). Consumer Q&A. U.S. Food and Drug Administration. [Online] [Accessed 03 November 2017]. Available from: https://www.fda.gov/AnimalVeterinary/DevelopmentApprovalProcess/GeneticEngineering/GeneticallyEngineeredAnimals/ucm113672.htm.

[17] Spicer, C. (2017). US Lab May Have Edited Human Embryos for First Time. BioNews. [Online]. [Accessed 15 November, 2017]. Available from: http://www.bionews.org.uk/page_866686.asp.

[18] International Bioethics Committee. (2015). Report of the IBC on Updating Its Reflection on the Human Genome and Human Rights. UNESCO. [Online]. [Accessed 15 November, 2017]. Available from: http://unesdoc.unesco.org/images/0023/002332/233258E.pdf .

Interview with a Synthetic Biologist: Michael Flanagan of Genspace

(1)

Michael Flanagan is an electrical engineer, synthetic biologist, and instructor for the Biohacker Boot Camp course offered through Genspace. He is a current member of the lab at Genspace, where he works on his own independent synbio projects. 

After taking the biohacker course with Michael and becoming intrigued by the concept of "biohacking," I asked Michael for an interview to learn more about it.

I wanted to ask you what “biohacking” means to you.

To me personally, “biohacking” is a buzz expression that is sometimes used to generate a hype or excitement. 

In many contexts, hacking implies some level of crudeness and brute force: such as might be associated with the use of an axe.  In contrast, I find that synthetic and molecular biology will often require the level of finesse and skill more closely associated with a scalpel than an axe.

I’d be lying to you if I said that I was a big fan of the term “biohacking,” and the irony is not lost on me that the class I teach technically has the word “biohacking” in it!  I think that from a marketing perspective, there is a certain wisdom in selecting terms that are getting people to look twice, or to think about it, or to get excited about it—I get that. But from a personal perspective, it’s not a term that deeply resonates with what I do .

What is your background and how did you get involved in (as I call it) DIY biology?

I normally call what I do “synbio,” or synthetic biology.

I am a trained electrical engineer. I have a PhD in electrical engineering from Caltech, and also have a master’s degree and a bachelor’s degree in electrical engineering.  I have worked in both large industrial research facilities like NASA’s Jet Propulsion Laboratory and Bell Labs as well as in smaller startups.

But then, after leaving my last startup, Arieso, I realized that if I didn’t make a significant change with my life, and begin to focus on synthetic biology—which I had been admiring from a distance for about a decade—I might never do it!  Never would I find a better time in my life to take the plunge and to retool myself to fully engage in synthetic biology.  I wanted to see first-hand what it was about, where the state of the art was, and what I might be able to contribute to it.

What was the first step you took to get involved in synthetic biology? 

It started with reading popular books, technical papers, and textbooks on molecular biology and biochemistry.  I then started taking classes at Genspace, the community biology laboratory of New York City, including the one that I teach now.  After running out of classes to take at Genspace, I became a member in late 2014 to pursue my investigations and to learn more about synthetic biology in a hands-on fashion.

In a way, these early efforts in synthetic biology reminded me of when I was a young teenager learning to program computers.  I learned early on that there is a unique thrill associated with getting an automaton (such as a digital computer) to do what you wanted it to do, especially after countless – sometimes frustrating! -  hours of effort.  In some sense, I am still programming, but I often only use four letters on my keyboard (ATCG)!  More importantly, I am still trying to get automatons to carry out desired tasks – except they are now carbon-based bacteria, instead of silicon-based computers.

If you are okay with sharing, what kind of projects do you work on in synbio?

I primarily work on biomaterials projects. I am particularly interested in cellulose production and trying to teach bacteria to act like trees by reprogramming their DNA.

Regardless of the end-product, I am intrigued by how you can edit DNA sequences from different organisms to work in concert to accomplish tasks in new ways that have never occurred before in nature.

So you already made clear that you don’t really like the term “biohacking/biohacker”, would you call yourself a DIY biologist?

I’m a synthetic biologist. Although to be honest with you, when I wake up in the morning I still think of myself as an engineer. And what is the difference between a scientist and an engineer? A scientist will look at a phenomenon and say, “Well I wonder how that works. I wonder what the underlying mechanism is and how that fits in with existing models of the way the world works.”  An engineer will look at the same phenomenon and say, “I wonder how I could use that. I wonder if I could predictably and reliably put something together that makes use of that phenomenon.”  Don’t get me wrong: I’m a big fan of understanding underlying mechanisms (I wouldn’t have spent four years in graduate school at Caltech otherwise!)  But I’m a bigger fan of doing something useful.

Working in community labs; do you think that you or others like you have any advantages developing biotech or synbio over scientists working in more traditional settings?

I guess one advantage is that you’re doing it for yourself. You’re working hard each day because you want to be there and you’re trying to set a course and direction yourself. There can be something very empowering, and certainly very personally satisfying, in working for those reasons.  I have found traditional research and development settings to often be more risk-averse.    In this environment, improvements and new efforts are often incremental rather than revolutionary.  But it will take many different types of environments (traditional and non-traditional) for synbio to achieve its full potential.

If we saw more people join community labs, or if we saw more hobbyists in synbio, what does the future look like to you?

I think the future would be very bright! If you have more people knowing about how to work in community labs and taking some part in it, it enables them to be more knowledgeable citizens, especially about topics that will have an increasing impact in their world.  They will be able to look beyond the polarizing hype that cripples so much public discourse today.

From what I read online and from people I talk to in my life, I get this feeling that there’s a lot of dystopian fear around this [synthetic biology]. “What if this person that makes a lab in their basement creates this bacteria that destroys mankind?” What would you say to thoughts and feelings like that?

What I would say is that we need to be vigilant regarding all technological threats.  But this vigilance must be balanced and rational so that we do not delay the considerable benefits that these technologies will allow.   We can best see this with an example: over 200 years ago Benjamin Franklin was literally taking the first steps in a new world of electrical engineering.  In particular, he was conducting experiments with a kite and a key in a lightning storm. You can imagine people coming up to him and saying, “Electricity comes from the heavens: doesn’t that make it divine? Should base mortals really be playing around with electricity? What if someday they put electricity into every home? Electricity could cause countless houses to burn down!  Couldn’t electricity be used to make electronic devices that effectively turn our families, friends and ourselves into zombies because we stare into them all the time?  Couldn’t electricity enable future weapons systems that could destroy all of humanity?”

And then Ben Franklin would have looked at them and said something along the lines of, “I’m a guy with a kite in a rainstorm. The manifestation of your concerns and fears is very far off from where we are technologically right now.  And the ultimate measure of this (or any technology) requires a consideration of the pros as well as the cons.” 

We are still in the early days of synbio, but it is not difficult to see how the ultimate benefits could outweigh the risks.  The primary task of synthetic biologists is to pave a path towards these benefits so that our efforts will be on the right side of history.

 What are some of the biggest goods you think DNA reprogramming could potentially produce?

The potential good staggers the imagination!  In brief: longer and healthier life, (including the eradication of cancer and other genetic diseases), improved biodiversity, novel biomaterials, and reduced pollution.


Very special thanks to Michael Flanagan for taking the time to talk for an interview, and for all the additional work in helping put the transcript together.


(1) Background photo from Scientific Times Journal of Microbiology. Available at: http://scientifictimes.org/journals/Microbiology/index.html.

What is a Genome?

Image from: blogs.nature.com

What is a genome?

"A genome is the complete set of genetic information in an organism."(1)  It is the entirety of our DNA—the molecule that contains our biological code. (2)  In my favorite analogy, the genome is like an instruction manual containing the information for how to put your body together and then maintain it. Every living organism—from single-celled to human—has a genome, but your genome is unique to you. (3)

Image 1: Map of a Cell (2)

Where is my genome?

Copies of your genome exist inside your cells. Most of the genomic information will be inside the nucleus of a cell, clustered into 46 structures called chromosomes. A very small part of the genomic information is in the mitochondria of the cell— structures outside of the nucleus that give energy to the cell and help it to function properly. (4)

Cells with no nucleus, like red blood cells, will not have a copy of the genome inside of them. Cells with only 23 chromosomes, like egg and sperm, will also not have a complete copy of the genome in them. (3)

What is my genome made out of?

Our genome is the complete set of our DNA. (2)  Each chromosome inside of a nucleus is made of a single strand of coiled DNA. (4)  DNA is shaped like a twisted ladder; the "sides" of the ladder are made of sugar and phosphate, and the "rungs" are made of four chemical bases (adenine, guanine, cytosine, and thymine) that form pairs called base pairs. (3)

Image 2: DNA in the Nucleus (5)

There are about 3 billion base pairs in human DNA. (2) Adenine and thymine are always paired together, and cytosine and guanine are always paired together.

Codons are groups of three base pairs that have the instructions to make a specific amino acid—the building blocks of proteins. Genes are groups of codons that provide the instructions to make a protein. (3)

As mentioned in the introduction, the genome is like an instruction manual. Our DNA can be thought of as the string of all letters in the instruction manual from beginning to end, and chromosomes can be thought of as chapters that divide the DNA. (3)

Instead of 26 letters of the alphabet, our imaginary genomic book is written with only 4 letters (A, G, C, and T) that represent DNA's four chemical bases. Codons are like words that are built from three chemical letters, and genes are like sentences built from a stretch of codons that provide the instructions for how to make a protein. (3)

What are proteins? 

"Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body's tissues and organs." (6)

Proteins can function as antibodies (that protect the body from foreign particles), enzymes (that perform different chemical reactions), and messengers (such as hormones, that transmit signals). (6) They can also provide structure for cells, or store and transport atoms and small molecules throughout the body. (6)

Proteins are essential for creating a functional organism, and their production is the central purpose of DNA. (3)

How does my genome make proteins?

Ribosomes are structures in a cell where proteins are made. They are outside of the nucleus and assemble the protein when they receive the instructions for making it. (In Image 1, the ribosomes are the small red dots that surround the nucleus and are scattered throughout the cell.)

DNA—and its genes that provide the instructions for building proteins—cannot leave the nucleus of cells. DNA in the nucleus can be thought of like a reference book that cannot be checked out of a library. (3)  To get information from a reference book out of a library, it needs to be photocopied. Similarly, to get the genetic information to the ribosomes to assemble a protein, the information inside the nucleus needs to be copied. (3)

Image 3: Transcription (Building messenger RNA) (2)

The copying process is called transcription and it uses molecules called RNA. RNA is very similar to DNA, but it is single-stranded, contains a different sugar, and has the chemical uracil (U) instead of thymine (T) as a base. There are different types of RNA. (3)

Transcription begins with RNA polymerase; an enzyme that attaches to the start of the gene and "unzips" the DNA strand. Using the base chemicals of the unzipped DNA strand as a template, free-floating base chemicals that match each base on the DNA strand are brought together to form an RNA strand. (3)(7)

Image 4: Translation (Building the Protein) (8)

This RNA is called "messenger RNA" (mRNA) and carries a copy of the gene that can leave the nucleus. But before mRNA can be "read" in the ribosome, it must keep only the "coding" information that directs production of amino acids (the building blocks of proteins) and remove any "noncoding" information that does not direct production of amino acids. (3)(7)

When mRNA leaves the nucleus, a ribosome binds to it for the step known as translation. Translation is when the mRNA is "read" to assemble the chain of amino acids that will create the protein. Every codon (three bases) on the mRNA strand corresponds to a single amino acid. Another type of RNA, called transfer RNA (tRNA), carries an amino acid to the ribosome by matching its chemical bases to the corresponding chemical bases on the mRNA strand. (3)(7)

As the tRNA brings amino acids to the ribosome, the amino acids bind together to form a chain. Once the last amino acid is added, the chain folds together and makes the final product; a protein. (7)  And from these proteins, we get the building blocks of life that put our bodies together and allow us to function.

(An excellent 3D explanation of transcription, translation, and how a protein is built can be found at https://www.youtube.com/watch?v=gG7uCskUOrA.) (7)


Have anything to add? Additional sources, helpful and relevant resources, and professional insights are welcome! Share in the comments below.


SOURCES

(1) Scitable. (c2014). Genome. Nature [Online]. [Accessed Mar 05, 2017]. Available at: http://www.nature.com/scitable/definition/genome-43.

(2) National Human Genome Research Institute. (2010). The Human Genome Project Completion: Frequently Asked Questions. [Online]. [Accessed Mar 05, 2017]. Available at: https://www.genome.gov/11006943/human-genome-project-completion-frequently-asked-questions/.

(3) Health Education England. (2016). Week 1: The Genome and How We Explore It. Whole Genome Sequencing: Decoding the Language of Life and Health. Sept 19, 2016, FutureLearn Online course.

(4) Wellcome Trust Centre for Mitochondrial Research. (n.d.) What is Mitochondrial DNA? [Online]. [Accessed Mar 05, 2017]. Available at: http://www.newcastle-mitochondria.com/patient-and-public-home-page/what-is-mitochondrial-dna/.

(5) Image from: Murphy, E. (2013). The Hunt for a Diagnosis: The Science Bit. Little Mama Murphy. [Online]. [Accessed Mar 05, 2017]. Available at: http://www.littlemamamurphy.co.uk/2013/04/the-hunt-for-diagnosis-science-bit_10.html.

(6) Genetics Home Reference. (2017). What are Proteins and What Do They Do? U.S. National Library of Medicine. [Online]. [Accessed Mar 05, 2017]. Available at: https://ghr.nlm.nih.gov/primer/howgeneswork/protein.

(7) yourgenome. (2015). From DNA to Protein - 3D. [Online]. [Accessed Mar 05, 2017]. Available at: https://www.youtube.com/watch?v=gG7uCskUOrA.

(8) Image from: Norman, H. (n.d.) What Function do Ribosomes Serve in Polypeptide Synthesis? Quora. [Online]. [Accessed Mar 05, 2017]. Available at: https://www.quora.com/What-function-do-ribosomes-serve-in-polypeptide-synthesis.

Becoming a Biohacker: My Four Days in a Community Lab

I was determined to get "hand's on" with my genome editing bioethics research, so I enrolled in a four-day lab course that was being offered at a community lab in Brooklyn, NY.

What is a "community" lab? A lab that anyone can join to work on their own projects. Much like a gym membership, becoming a member gives you access to the lab, the equipment, and some supplies to get you started. This particular lab is called Genspace, and is “a nonprofit organization dedicated to promoting citizen science and access to biotechnology. . . providing educational outreach, cultural events, and a platform for science innovation at the grassroots level.” (1)

I signed up for the "Biohacker Boot Camp" course, which promised to teach me how to "extract our own DNA, analyze ancestry through bioinformatics, splice genes into bacteria, and learn all the standard techniques such as using pipettors, gel electrophoresis, amplifying DNA with PCR reactions, working with restriction enzymes to build plasmids, and growing and transforming bacteria." (2)

Day 1: Pipettes, isolating DNA, and "polymerase chain reaction"

On the first day, I met my instructor, Dr. Mike Flanagan, and the fellow students I would be working with for the next four days. It was interesting to see that we all came from different backgrounds (even my instructor revealed he had a Ph.D. in electrical engineering!) and some, like me, had no prior experience in a lab. I also learned that some of the current members of Genspace got started with the same class I was taking, and went on to join the lab to pursue projects as biotech entrepreneurs, synthetic biology hobbyists, and artists.

We started with an hour-long introduction to some of the basic concepts in molecular biology, and while the content was robust, the explanations were designed for learners with limited biology knowledge, so I was able to learn quite a bit. The big goal for the class was to test our mitochondrial DNA; a small portion of DNA that we inherit from our mothers. We were also instructed on how to use a pipette (a tool used to transfer tiny and precise amounts of liquid) which we would be using a lot in the next four days. Then, the hands-on work began.

We swabbed the inside of our cheeks with a Q-tip and then inserted it into a small test tube filled with saline. For the next two hours, we were in the lab spinning, pipetting, shaking, and boiling our small sample. Our instructor guided us through each movement, and told us what each step was supposed to accomplish to help us learn more about the structure of cells at the molecular level.

For instance, since most DNA is inside the nucleus of the cell, the cells need to be ruptured to free the DNA. And because rupturing the cell also frees enzymes that will destroy the DNA, these enzymes need to be neutralized by an additive.

By the end of the process, I was staring at a tiny test tube that had my DNA strands floating freely inside. The more I looked, the more I felt an odd feeling creep over me— I was holding my DNA, my genetic code, isolated from my cells, in a test tube. . . It can only be described as the strangest feeling of vulnerability I've ever experienced.

The final step we covered was "polymerase chain reaction" (PCR) where a chosen segment of DNA is replicated exponentially. By replicating the specific segment of DNA we want tested (in our case, a small portion of the mitochondrial DNA), we get a rich sample to send off for testing.

PCR requires adding “primers” to the sample; short DNA molecules that will guide an enzyme that copies DNA to exactly the right spot in the 3 billion letters that make up the human genome. If DNA can be thought of like a book, the primers are the bookmarks that show the pages in the book where a photocopy is supposed to begin and end. The PCR starts after putting the sample in a thermocycler (a machine that raises and lowers the temperature over and over) and turning it on to the correct setting. The temperature changes create a reaction where the DNA strands separate into two halves, and build new halves onto all the old halves.

Day 2: Gel electrophroesis

On day two, we were introduced to “gel electrophroesis”: using a slab of thick gel submerged in a salt solution connected to an electrical power supply to check the quality of our DNA sample.

We learned the recipe for making and molding the gel, and made one of our own together in the lab. We also learned which additives we needed to pipette into our sample to prepare it for the gel, and where to put our DNA sample in the gel once it was set. 

The glowing clusters of each of our DNA, 

suspended in gel.

Once the gel was set, positioned in its salt bath, and the DNA had been added, we were ready to safely apply an electric current to the gel using electrodes at both ends of the gel connected to the power supply. Because DNA is negatively charged, it migrates towards the positive electrode, with short strands moving faster, and long strands moving slower as they tangle in the molecular obstacle course that is part of the structure of the gel.

After letting the gel sit for awhile in the magnetic field, we turned off the electricity, removed the gel, and put it under UV light, where the DNA and its additives started to glow inside the gel.

Under the UV light, we were able to see the concentration of different sizes of DNA from our sample, which allowed us to assess its quality. The heavily concentrated clusters of DNA glowed brightest, and the less concentrated clusters glowed dimmest. And depending on how far the clusters had advanced through the gel, we were able to determine the length of the DNA within that cluster. According to our instructor, all of our samples appeared to be good.

Day 3: Plasmids, restriction enzymes, and transforming bacteria

On day three, we learned about plasmids and restriction enzymes in preparation for an experiment with bacteria. This was a completely new topic for me, so it was a lot to learn, but I was able to grasp the basics: plasmids are circular forms of DNA, and restriction enzymes are proteins inside cells that evolved in bacteria to search and destroy any DNA that doesn’t belong. Because restriction enzymes “search and destroy” DNA in a very targeted way, they can be used like molecular scissors to cut and paste DNA to literally ‘build’ a plasmid.

This introduction prepared us for our experiment: modifying E. coli plasmids to produce E. coli colonies that were bright red. We learned about the structure of the particular plasmid we were targeting and how introducing the restriction enzymes would change the plasmid. We returned to the lab and were guided through introducing the restriction enzymes, plasmids, and bacteria together in the right order before putting it all on a petri dish and placing it in our incubator to grow overnight. 

The positive control is the only petri dish 

glowing bright red under UV light, but a 

closer look shows that my team’s dish has 

a few colonies going strong!

By the end of this experiment, I had officially genetically modified my first organism!

Day 4: Bioinformatics and analyzing ancestry

On our final day together, our first activity was to examine the petri dishes we had left in the incubator. The results? Bright red colonies of E.coli bacteria that glowed under a UV light! The experiment was a success.

Our next activity was to sit together to review the results of having our mitochondrial DNA sequenced. Before viewing our results, we learned a bit about bioinformatics—the task of taking the DNA sample and sequencing it into a string of letters that can be analyzed. 

At last, it was time to view our results, and I was first to be put on the spot. Our instructor pulled up a Word document containing a string of 329 letters. A portion of my mitochondrial DNA sequence was displayed on the projector.

If I thought holding my DNA in a test tube was a surreal experience, seeing a piece of my mitochondrial DNA that connected me to my maternal ancestors was equally so. What did each letter on that Word document determine about my body? How did this string of letters connect me to my mother, grandmother, great-grandmother, and beyond?

The thought about my great-grandmother made me remember a story that was told at the family dinner table only a few weeks before: how as a young, unmarried woman in the 1920s, my great-grandmother made the unthinkable journey of traveling from Minnesota to New York City alone by car. And here I was, sitting in a lab in Brooklyn after my own first-ever solo road trip to New York City. Musing on our shared experience while staring at our shared DNA created a sense of oneness and connection to my maternal heritage that I had never felt before.

Next, we looked at my maternal "haplogroup.” A haplogroup is an ancestral group based on a common line of lineage. Our maternal haplogroup is our ancestry line traced through the mitochondrial DNA we inherit from our mothers.

Each student had their turn to look at their maternal haplogroup, and together we researched the geographic areas in the world that are associated with our particular maternal haplogroup to get a picture of where in the world our maternal ancestors may have come from. And while we were all from different haplogroups, I learned that human mitochondrial DNA is incredibly similar; in the approximately 200 base pairs of mitochondrial DNA that we looked at, between the eight of us there were only about 6 total differences.

A DIY thermocycler

To finish, we learned that some of the lab equipment we used, such as a thermocycler and a centrifuge (used for spinning test tubes really fast) can actually be made by hand for a DIY lab. We looked at a few examples of DIY lab equipment, and while they still required some complex assembly, anyone with the motivation to learn how to assemble this equipment could possibly create a decent makeshift lab on a limited budget.

2 months later. . .

This four-day class gave me an incredible introduction to molecular biology and working in a lab. I picked up new skills like pipetting, using various pieces of lab equipment, and how to be safe, organized, and sterile while working with different lab materials. The lab has become a less-intimidating place for me as a non-scientist, and I feel ready to try any other lab-based experiences when given an opportunity in the future.

I also felt like this class helped me commit more biological concepts to memory than any textbook I had ever studied. My instructor gets part of the credit for being a great presenter, but a lot of the educational magic was being able to “see” firsthand how each concept tied into our experiments as we were performing them. (Its hard to forget what a restrictive enzyme is after it featured in two lab projects you performed yourself!)

And finally, I felt inspired to become a “citizen scientist.” I don’t know if I will be building a DIY lab in a basement or joining a community lab just yet, but I do have a new desire to continue experiencing and learning science first-hand.

And as for bioethics, through this experience I've become very intrigued by the idea of "citizen scientists" or amateur biologists working on independent biology projects. Where will DIY biology take the future of biotechnology? How will it impact society? Is a humble entrepreneur capable of creating the next great invention to cure the ills of humanity, or unknowingly unleashing devastation on the human race? I’m interested in hearing more from the biohackers and citizen-scientists themselves to hear their thoughts.

Special thanks to Dr. Ellen Jorgensen of Genspace for editing help!

SOURCES

(1) Genspace. (n.d.). About. Available at: http://genspace.org/page/About

(2) Genspace. (n.d.) Biohacker Boot Camp. Available at: http://genspace.org/event/20150706/1800/Biohacker%20Boot%20Camp.

Upcoming: Biohacking in Brooklyn

Photo credit: Brooklyn Bridge At Night by Paslier Morgan

The CRISPR Drawer has taken a long break (first for the December holidays, then for time to complete a separate writing project), but now, the blog is back and ready to delve into "biohacking" in the upcoming weeks.

What is "biohacking"?

According to Wikipedia, biohacking is: "Do-it-yourself biology, a social movement in which individuals and organizations pursue biology and life science with tools equivalent to those of professional labs."

First, I'll describe my experience in a Brooklyn "community lab"—a lab that anyone can join to work on their own, independent biology projects—and what it was like to learn how to isolate my own DNA and genetically modify my first organism.

Next, I'll interview some "biohackers" to ask questions such as:

-What is biohacking, really?

-What kinds of projects are biohackers working on?
-How could biohacking impact the field of biology?

-How could biohacking impact society?
-What ethical issues do you think matter most?

The writing as already begun, so stay tuned for upcoming posts about biohacking in Brooklyn!

What is Bioethics?

Image Source: Center for Bioethics and Human Dignity

The CRISPR Drawer is a bioethics blog. But what is bioethics? 

First and foremost, bioethics is a subfield of ethics, which is a branch of philosophy concerned with determining what kinds of human conduct are right/wrong, moral/immoral, permissible/impermissible, or justified/unjustified. Its concerned with what humans "should" or "should not" do.

Stick "bio" to the front of "ethics," and you have "bioethics." "Bio" comes from the Greek bíos meaning "life," and can pertain to living organisms (like in biology), or to the course of human life (like in biography). (1)

If bioethics somewhat-literally translates to "the ethics of life," wouldn't that just be. . . ethics? Not quite, because bioethics, as an academic discipline, has a more particular meaning.

Defining bioethics and its issues
Philosophy writer Lewis Vaughn, in the textbook Bioethics: Principles, Issues, and Cases, defines bioethics as: "Applied ethics focused on health care, medical science, and medical technology." (2)

The Center for Bioethics and Human Dignity defines bioethics as "a branch of ethical inquiry that examines the nature of medical, scientific, and technological discoveries and their subsequent responsible use, with particular emphasis upon their moral implications for individuals and our common human humanity" [sic] (3).

Monash University's bioethics program describes bioethics as ethics that focuses on "the growth of scientific knowledge and technical ability in medicine, genetics and the biological sciences" as well as "the healthcare field." (4)

Based on the above, bioethics can be understood as a discipline concerned with ethical questions in medicine, biological research, genetics, biotechnology, and healthcare.

Ethical issues in medicine and healthcare can include questions about who can make medical decisions on behalf of patients, questions about the limits of patient autonomy, or questions about the scope of a doctor's oath to "do no harm." Beyond the clinic or hospital, there are also bigger societal questions about healthcare and medicine, such as questions about what kinds of medical procedures people should have a right to access or questions about how healthcare should be paid for.

Ethical issues in biological research or biotechnology can include the use of genome editing and cloning in organisms, experimenting with human embryos or stem cells, or designing clinical trials for new medicines. These concerns often focus on the bigger impact to humanity, and how such research or technological developments will benefit or harm society.

While attempting to define bioethics, its important to note that its not easy to conclusively draw defining lines between what "is" or "isn't" bioethics. Bioethics can concern itself with issues that don't fit neatly into the above categories, such as animal rights. (5)  There are also issues not generally considered to be covered by bioethics, such as climate change, that some argue should be included. (6)  Bioethics is an umbrella category that can cover or partially-cover many different topics, and the boundaries of bioethics can be always be expanded into new territory.

(For more examples of issues of interest in bioethics, the list of issues in the Bioethics article on Wikipedia and the blog archive at Bioethics.net can be helpful starting points!)

So now that bioethics has been somewhat defined, how do bioethicists ultimately decide what is right or wrong? A lot can go into ethical analysis, but here I will focus on two parts: moral theory, and research.

Moral theory
A moral theory, simply defined, tries to define or outline right or wrong action by providing a kind of moral criteria.

Utilitarianism focuses on the consequences of actions, and says that right or wrong action depends on whether the consequences maximize overall well-being in the world. (7)

Principlism focuses on four principles—autonomy, beneficence, non-maleficence, and justice—and argues that right action is guided by adherence to these principles. (8)

Deontological theories focus on moral duties or moral norms, and argues that right action is determined by acting in accordance with these duties or norms. (9)

There are other many other moral theories in addition to those mentioned above, and there can also be multiple versions of a single moral theory.

Research in bioethics
Ethical analysis relies strongly on philosophical inquiry and theory, but examining the ethics of an issue wouldn't be complete without additional background research.

If the ethical concern is a technology, understanding how it works, how it would be used, and how safe or effective it is matters a great deal when we question whether its use should or shouldn't be permitted.

If the ethical concern is a hospital policy towards patients, understanding the needs of the patient, the doctor, the healthcare provider, and the hospital could help determine whether the policy is fair.

If the ethical concern is a proposed bill regulating some aspect of medicine or healthcare, knowing the legal context, the detail and scope of the bill, and the potential consequences of its implementation could offer insight when asking whether the bill should or shouldn't be endorsed.

The additional background and contextual questions surrounding ethical issues can sometimes only be answered by science, law, history, medicine, or social science, which can make bioethics somewhat interdisciplinary in practice.

What is bioethics?

• Bioethics is concerned with answering ethical questions in biological research, medicine, biotechnology, and healthcare.

• Bioethics can be defined by its tradition, but can always expand into new areas.

• Bioethics often uses moral theories to analyze the ethics of a given issue.

• Bioethics may incorporate research from many different fields in order to formulate a fully thought-out ethical analysis.

This concludes my brief introduction to bioethics, but since this is a bioethics blog, there will certainly be more to come!

Have anything to add? Additional sources, helpful and relevant resources, and professional insights are welcome! Share in the comments below.


SOURCES

(1) Dictionary.com. [Online]. (n.d.). Bio-. [Accessed Jan 03, 2017]. Available at: http://www.dictionary.com/browse/bio-.

(2) Vaughn, L. (2013). Bioethics: Principles, Issues, and Cases. Second Edition. Oxford: Oxford University Press. 

(3) Center for Bioethics and Human Dignity. (n.d.). FAQs. [Online]. [Accessed Jan 03, 2017]. Available at: https://cbhd.org/about-cbhd/faqs.

(4) Monash University. (2016). Bioethics. [Online]. [Accessed Jan 03, 2017]. Available at: https://www.monash.edu.au/pubs/handbooks/aos/bioethics/ug-arts-bioethics.html.

(5) Blumenthal-Barby, J. S. (2014). Philosopher Calls for End to Animal Experimentation (And More): Is There a "Reasonable" Conception of Animal Rights? Bioethics.net Blog. [Online]. [Accessed Jan 03, 2017]. Available at: http://www.bioethics.net/2014/05/philosopher-calls-for-end-to-animal-experimentation-and-more-is-there-a-reasonable-conception-of-animal-rights/.

(6) Macpherson, C. C. (2013). Climate Change is a Bioethics Problem. Bioethics. [Online]. 27(6), pp. 305-308. [Accessed Dec 30, 2016]. Available at: http://onlinelibrary.wiley.com/doi/10.1111/bioe.12029/full.

(7) Savulescu, J. and Birks, D. (2012). Bioethics: Utilitarianism. eLS. John Wiley & Sons, Ltd: Chichester, pp. 1-7. [p. 1]

(8) Beauchamp, T. L. (2010). The Four Principles Approach to Health Care Ethics. In: Beauchamp, T. L. ed. Standing on Principles: Collected Essays. Oxford: Oxford University Press, pp. 35-49.

(9) Alexander, L. and Moore, M. (2016). Deontological Ethics. In: Zalta, E. N. ed. The Stanford Encyclopedia of Philosophy. 2016 Winter Edition.  [Online]. [Accessed Jan 03, 2017]. Available at: https://plato.stanford.edu/entries/ethics-deontological/#DeoThe.

Name change!

I first conceived of this blog when I discovered that you could buy simple CRISPR kits online.

My first thought: I could buy CRISPR online and do genome editing experiments from my kitchen??

My second thought: How fun would it be to write about this, as a bioethicist?

My third thought: I'm making a blog, and I'm calling it, "The CRISPR Kitchen."

I absolutely loved the name I came up with. It had alliteration, it was short and catchy, and the word "kitchen" elicited mental images of DIY home experiments to cook up something new and interesting. But then I discovered that there is another website called "CRISPR Kitchen". . .

After about two weeks of struggling with what to do about the name conflict, it became obvious that a name change was necessary, and that this moment in time (just starting out) was the best time to do it.

And so I present to you my blog in its new form: "The CRISPR Drawer."

As disappointed as I am in the loss of the name I loved so much, the new name is starting to grow on me. Its still linked to my much-loved kitchen metaphor of DIY experimentation and research, and its literal in that I hope to have a CRISPR experiment in my actual refrigerator in the near future.

I'm also hoping that the name change will fit better with the direction I hope to take my writing; I still plan on experimenting, but I also hope to write about other topics beyond CRISPR that are connected to genome editing.