Imitation to Creation: The Revolutionizing Effects of Synthetic Biology Fading a Once Fine Line
Walking down the streets of our homes, we always look at nature in awe, saying things such as, “Oh I wish I could fly like a bird!” Or, it would be so cool to be able to camouflage like a chameleon. Seems impossible for us to have applications such as these taking place in human bodies, but a long time ago airplanes were non-existent, and we learned to make them by looking at nature!
It’s quite amazing to see how by using our understanding of biology, we are now at a point where we are able to create it. This almost sounds like a scene from a sci-fi movie, where we don’t fully understand the entirety of biology and have moved on to making our own takes on biology!
Synthetic biology, however, is not just about science, it includes ethics as well as philosophy.
In all of our time on Earth humans have only discovered a fifth of all species on the planet. Once we discover a species we immediately dive into finding all there is to know about it. We discover how and what it eats, how it reproduces, and give it characteristics such as a name to be able to identify it. So, why not reverse this process? Spend time making your own organism and knowing exactly how it works, and in the end give it a name! Welcome to the beautiful world of synthetic biology.
Synthetic Biology: The Rundown
It is clear that nature is the best engineer out there. Producing organisms that have reproductive abilities, not to mention adaptation and survival instincts. Using the evolution of nature over centuries, we have now classified the same way in which we do this through synthetic means as SynBio. There are several definitions of SynBio floating around; to summarize them all, Synbio is the creation of creatures that do not exist in our environments or the technological enhancement of organisms.
To understand SynBio is is crucial to look at 3 key parts.
- DNA Sequencing
- Protein Design
- Genome Design
DNA Sequencing
DNA essentially is what has allowed us to quantify life. Standing for deoxyribonucleic acid it is a molecule shaped like a double helix and houses the instructions living organisms need to live. DNA resides with proteins in the nucleus of cells and makes up the 23 pairs of chromosomes we have in each cell. The helix of DNA is made up of paired chemical letters known as bases.
These 4 letters are G, C, A, T and are the basis of life! A = Adenine, G = Guanine, C = Cytosine, T = Thymine. What is key here, is that going back to our first point DNA is made up of a double helix shape due to the chemical letters bonding to each other. You see, the parts that make up DNA bind together when they are the opposite, so A’s bind to the T’s, and the G’s bind to the C’S. So, if the sequence of these 4 letters in a strand are the opposite they will essentially stick together. If we take a look at this sequence: AATTTGGCCAATCCCGG, and another one: TTAAACCGGTTAGGGCC, putting them vertically you will see that since the opposite letters are in the same sequence it would be two long strands that intertwine to form the double helix shape.
DNA makes up our genes and our genes make up our genome. Essentially our genome is the accumulation of all of our genes and tells our cells how to act and what to do, similar to how codes in tell a computer program what to do.
Now, once we have learned what DNA is and looks like, we can learn how to read and sequence it. Although all DNA is made up of these 4 chemical letters, the sequence in which they occur in each organism is completely different. This is what causes the person beside you to have darker or lighter eyes. This is because your DNA may come in the sequence: AATTTCGGGAATTCCCGG, but the other person’s DNA sequence may look like this: AAATTCCGGAATCCCGG. This is exactly what DNA sequencing is; learning the sequence in which these 4 letters appear in your DNA because it is what makes you, you! Even with just 4 letters, there are millions of ways in which they can form!
Finding the sequence may appear difficult, as it was a decade ago, but it is now far more efficient. Because our genome is made up of four chemical letters that are coupled in millions, it is both vast and little. The A’s, T’s, C’s, and G’s are just 8–10 atoms wide and packed together like a tiny ball of yarn at the molecular level. So, the amount of information we need to take out is extremely large, but the space is itty bitty. You can have a sequence that is 1 million base pairs long, but the technology we have currently does not support that, so we break it down into smaller more feasible pieces to work with. Now, if we break DNA, how do we put it back together? Well, the process is definitely one to gaze upon and will explain it all:
- DNA samples, most often blood or saliva, are collected and placed in a sequencing device.
2. The DNA is subsequently broken down into smaller fragments of roughly 600 base pairs in length by high-frequency soundwaves.
3. The smaller DNA samples are then mixed with plasmid DNA, which is a circle-shaped molecule that can function on its own. It has few genes and is useful for cloning.
4. The samples are then placed in a spot plate with bacteria so that it may generate several copies of the DNA, making detection of the sample simpler. Once the DNA has been duplicated, it is removed from the bacteria and ready for sequencing.
5. Following that, various items are added to sequence the base, beginning with loose individual bases, terminator bases that have been labelled with fluorescent tags, polymerase enzyme, and DNA primer.
6. The DNA is heated to 96 degrees, causing the helix to break into two lengthy strands. The temperature is then reduced to 50 degrees, causing the DNA primer to attach to the plasmid DNA in the long strand on top, as opposing bases will bind.
7. After that, the temperature is raised by 10 degrees, allowing the polymerase enzyme to attach to the primed DNA. The enzyme will next begin to add the free bases to the DNA. It will only cease adding when a terminator base is added since it has been chemically and physically engineered with fluorescent tags to do so. The length is determined when the terminator base was added, which then causes the enzyme to fall off.
9. Then the temperature is put up to 96 degrees again, and the new strand of DNA falls away from the original strand. Now, to read. Since our DNA strands had the terminator bases added at different times, they are different lengths, some are long and some are short. So, using a process called electrophoresis the strands are “read” from shortest to longest. A capillary tube is put over each spot and gives the samples in it an electric charge.
10. The tubes have a gel in them, that allows the small strands to move through faster and longer ones slower. Remember that A binds with T and C binds with G, and so once the strands reach the end, there is a laser that makes the terminator base light up, and from here each of the 4 letters have a special colour given to them. The camera will capture and record this, and then seeing how opposites bind you can put together the original DNA sequence.
In comparison to what DNA sequencing was like before this process, has been improved greatly. It may seem that this process is slow, as it recognizes each terminator base’s letter one by one. With the research advancing It is astonishing how we are able to break up our DNA in such a manner and put it back together in this way to learn how complex life really is at the start the beginning when our DNA was forming in the specific sequences. Who knows we might be able to sequence the entire genome without having to go one by one in the future.
Protein Design
Proteins are undoubtedly one of the most important aspects of cells. They are responsible for the structure and produce energy so that cells can carry out their intended functions.
It is due to this that proteins have so much unlocked potential, and designing proteins to carry out tasks is already underway! More on this later though! First, let’s learn what proteins actually are.
Think of proteins as a string of beads. Let’s try to think of what is specific about a string of beads. Well, it is made of round balls, and it can be folded, curved and shaped in many different ways with our hands.
This is how we can think of proteins, you know in the appropriate situations! Proteins are made up of amino acids, these amino acids are the beads! The string is a peptide bond that keeps these round spheres of amino acids together.
The peptide bond is formed due to a chemical reaction in our body, when we consume proteins these proteins are broken down into individual amino acids.
Proteins are constant working molecules that are the blocks of our cells. However, these proteins are not just in our bodies always hanging out and working every second, we actually need to have them in our body first. This is where the 3 specific types of proteins come in. The first non-essential meaning our body produces these proteins on its own. Essential meaning our body cannot produce these on its own and we must get these from food, and finally conditionally essential, where healthy bodies can but in starvation or errors in metabolism systems they cannot.
What is key about proteins is that the string of beads form a protein shape when they come together in a cluster, so imagine your strings are in a basket, and you bunch them up in your hand as you pick them up. When we pick up a cluster of beaded strings a few times we can see how each time, the order in which they overlap will not be the same. Proteins are so complex for this reason, the amino acid strings fold and overlap, in millions of formations throughout our body, and this all depends on the order of the amino acids joining together. Although they fold randomly, if they were to fold incorrectly this can cause huge complications.
The way in which we have moved so far, where we are working to follow the way in which amino acids appear in proteins, and the way in which they fold, is our evolution in this field, as proteins within our bodies have evolved in relation to changes in DNA — proteins work to serve you, so this is just the beginning!
DNA Synthesis — Designing Genomes
Did you ever think it was possible to create an organism the way you want? Creating artificial life is not as fun and easy as it seems, but it has some amazing benefits, so how do we actually create life?
So, if you are learning about SynBio for the first time you might think that this talk is new, but the first artificial cell was actually created in 2010, and it took more than a decade! All life needs to start at the origin: DNA, so to create this cell the DNA was sequenced, so they knew what it was made of, but that’s not all they needed.
You see, cells have a membrane that protects them from the outside world, this cell membrane decided what comes in and what goes out. Although, we can create living organisms the cell membrane is too complex and so can’t be made in a lab. So, when we claim we created an organism, we mean we obtained its genome and then hollowed out the DNA of a normal cell and inserted the genome. The cell membrane then identifies this as regular DNA and operates normally!
Making a genome where we can control exactly how it behaves, is how this is dropping jaws, synthetic biology goes beyond this though. With synthetic biology we can program organisms to be able to adapt based on different environments, embed survival instincts, all of the characteristics that make life unique, this is a game changer don't you agree?
Applications
Synthetic biology ever since being initiated by Dr. Craig Venter, and Dr. Hamilton Smith, has pumped out dozens of applications in the process.
Over the years SynBio has stirred up a lot of talk in ethics, saying that scientists who are trying to make a life are way in over their heads. Making an organism or tweaking an organism for the greater good is an amazing thing, we should be gearing our attention towards. Once we treat the application and potential of SynBio as a tool, we can sidetrack the negatives, and move forward together to solve some of the world’s biggest problems.
My explanation of these give them no justice, but here we go. First off my favourite. How we are using SynBio to design proteins to be effective killers of viruses and diseases. Programming and designing proteins to kill diseases come with many factors though. Take cancer, for example, chemotherapy is effective at killing cancerous cells, however, this process does not only target the cancerous cells and ends up killing healthy cells in the process. With more research in this field, we can potentially program proteins to only come after diseased cells. This is called smart therapeutics and is not just for cancer, but if we can potentially program a small batch of proteins to engage when they detect these unhealthy cells, we could protect the health of our immune system much longer.
Another application is arsenic water. In poverty-stricken areas water can be contaminated easily due to inefficient infrastructure. However, before we discovered we can make organisms that can help to detect the arsenic levels, these tests were extremely difficult and expensive to do. Synthetic biology has allowed us to make inexpensive and dependable tests. How did this happen? Well, we took the bacterium E. Coli and changed only two genes! The first gene detects the arsenic and needs to detect it in order to release the genes that will boot it out. The second gene then allows bacteria in the cell to consume lactose sugar, thus making lactic acid. Now the modified cells of E.Coli will carry this out as the lactose consumption is put under the control of the arsenic detecting gene. So, only once it detects the lactose can be digested or else, the cell would be producing lactic acid unnecessarily.
The Future
The great philosopher Aristotle stated, “Technology imitates nature.” Of course, Aristotle was way ahead of his time and makes an excellent point. We have to ask would we even have the efficient technology we have today without looking for inspiration from nature. One of the most efficient trains in the world that you can find in Japan, were not invented because someone had an idea that with a more narrow tip, it can push through the air better, but looking at the kingfisher’s beak.
The most amazing part though, we have gone past imitation, and have now arrived at the point of creation. Revolutionizing definitions we keep in our books, the once fine line of technology and nature is merging into synthetic biology where we get the best of both worlds. Technology is now becoming more “biological” than ever, and if we continue to look at the negatives we’ll miss our opportunities to create a better world.
Every great invention has started at a very low point. Looking at the applications of SynBio so far has provided a new perspective on technology and life for me.
I began thinking about the applications of the many other diseases out there. Starting with ischemic heart disease, when the arteries become clogged with fats and cholesterol due to an imbalanced diet is the leading cause of mortality worldwide. There are a lot of solutions out there from medicines to stents. Taking a look at stents, they are a physical object being put into your artery to widen it, our arteries which are the size of a drinking straw begin to deteriorate as we get older, this is when stents begin to not look so good. Although currently, there is no better option, synthetic biology could change this. I want to look into how we can potentially unclog arteries using SynBio, and eliminate the physical stent variable completely.
As we learned above proteins are essential for life, specifically, the essential proteins are not able to be produced in our bodies so we must get them from food. For those living in developed countries, this is no issue, we do not have to wonder where our next meal will come from. For those in poverty-stricken areas, I want to look into how we can solve the severe deprivation of these essential nutrients using SynBio, so that in the future we can produce these proteins on our own, so that at least in times of starvation we do not have to worry about becoming malnourished.
In Synthetic Biology we have looked at how proteins themselves have evolved to carry out tasks in the body, how cells adapt and edit themselves to a certain point depending on the situation, we have taken this into our own hands, and call this synthetic biology, and it is changing how we view both life and technology!
