Everything you need to know about the field of biocomputing and the future it has.
Imagine that you are sitting at your computer in 2035, and instead of your computer chip being made out of silicon, it is made out of living cells and DNA. In this world, every piece of data you created could be stored inside a cell. Well, this may become the reality, as scientists work to develop a way to use biological components to store data and carry out complex tasks.
So… How Did Biocomputing Come to Be?
First, in 1994, a scientist named Leonard Adleman proved that DNA may have future use in computing by solving the “traveling salesman” problem. In the “traveling salesman” problem, a salesman has to go to n number of cities, but he can only go to each city once. This goal of this problem is to find the shortest route for the salesman to take while hitting each city only once. For a computer, this could take years, decades, or even longer to solve the problem depending on how many cities there are. Using DNA though, as Adleman proved, is much quicker. The way that the DNA works is quite simple. As you can see in the diagram, each strand of DNA represents a city. When tow strands are put together, they create the paths between the cities. By analyzing the combinations of these paths, the shortest one can be selected. Since the DNA can run multiple possible paths at once, it takes much less time. This was the first step in a revolution of biotechnology.
Since the computation of biological substances was first discovered in 1994, a major problem has occurred in the tech industry, data storage. Humans have been creating more data, like Instagram posts and LinkedIn articles, than we can store. Currently, most data is stored on Silicon chips or tapes. The issue with Silicon chips is that they are finite and eventually will no longer be suitable to store the amount of data being created. The problem with these tapes is that they degrade quickly, and need to be repainted every 10 years. A new idea for data storage has come into light recently; DNA.
Using DNA for Data Storage
To understand how DNA is used for data storage, you need to first understand the composition of DNA. DNA is made up of four components or nucleotides; Adenine, Guanine, Cytosine, and Thymine, or A, G, C, T. Different combinations of these nucleotides make up your DNA. DNA is a double helix, meaning that it has two sides, sort of like a ladder. The sides of the ladder our created by a phosphate backbone. On these opposite sides, Adenine can only connect to Thymine and Guanine can only connect to Cytosine. Another important thing to know is that the code that makes up data is called binary code and consists of 0’s and 1’s.
The first step in being able to turn DNA into a data storage tool is converting the 0’s and 1’s to A, G, C, and T’s. This can be done through a new computing language, based on formal language theory. This language assigns each letter a numerical value of 0’s and 1’s. For example, A is 00 and T is 11. Once the binary code of 0’s and 1’s has been converted to A, G, C, and T’s, the DNA is then sequenced into the pattern. Sequences DNA involves reading the pattern of A, G, C, and T’s on the strand on DNA. The DNA that has been sequenced is then put into a test tube with water and the DNA and stored.
The reason that DNA works so well for biocomputing is that DNA is; dense, large in supply, small in size, and can last for millennia. We will also be able to sequence DNA for as long as we are around, meaning that humans far into the future will have access to data created now. This is important because some of our most important discoveries, for example, the Rosetta stone, come from our past, and it is important to preserve our current data for future generations.
Boolean Logic and Biocomputing
Boolean logic is the center of computing, which makes it a critical part of biocomputing. Boolean logic is a form of algebra focused around the words, “And,” “Or,” and, “Not.” In biocomputing, Boolean logic is encoded into the genetic material of the cell, which creates logic gates, the key to biocomputing. A logic gate is a component of computing that carries out a Boolean logic function. For example, in the diagram, you can see that for the light switches to turn on the light bulb both light switches must be on. This is an example of an “And” switch, as it takes both to be on for the gate to carry out the function.
In biocomputing, by designing the cell through inserting specialized genetic material, we can create the logic gates inside of the cells. With the use of logic gates, cells can carry out computational functions, such as the “traveling salesman” problem.
Using Molecules for Biocomputing
Although DNA is great for storing data, by using molecules, we could even perform tasks that a computer typically would. Many molecules in our body are made of proteins, which can tell our body how to perform certain functions and carry out tasks. Theoretically, we could harness the metabolic power of active cells to re-engineer the machinery in the cell. By changing the way the cell works, we can design the cells to solve specific computational tasks. For example in the diagram, you can see that the molecule is inputting other resources, such as Glycerol. This input, along with the other inputs of the task, changes the way that the molecule processes the task and then produces the output. Even though this would be a quick solution to creating a biocomputer, it is still very experimental and there has been very limited research done into it. If you want to learn more about how the metabolic of a molecule could be used in biocomputing, look here: https://www.frontiersin.org/articles/10.3389/fbioe.2019.00040/full
The Language of Biocomputing: SBOL
Just like how you and me have a language to communicate, scientists have a language to communicate designs and ideas in biocomputing. It is very important to have a standard of communication, such as SBOL, because it is important that scientists are able to share their findings to advance the field. SBOL stands for synthetic biology open language. SBOL is comprised of genetic vocabulary, called SBOL data, and schematic glyphs, which are pictures that represent the genetic designs, called SBOL visuals. Through the combination of SBOL data and SBOL visuals, scientists are able to effectively communicate within the field of biocomputing.
How can we use this in the future?
It might seem hard to see how a computer chip made from biological materials might impact you, but biocomputing has some crazy, real applications. One example would be using biocomputing to “solve” cancer. Researchers at Microsoft are currently doing research on how biocomputing can help give us a real-time model on how cancer cells are growing, expanding our knowledge of these cells and how they work. The hope is that by understanding these cells, we will be able to figure out how to stop them. Another future use would be to optimize energy usage. When we use traditional methods of computation, such as AI(artificial intelligence), we use tons of Gigawatts of energy, which is not good for the environment. If we were able to fit all of our computation and data storage into tiny cells and DNA, then we could save a lot of energy, that would not only help the planet but also save money. These aren’t the only example either, biocomputing can be used in many fields and do great things in the world.
Final Thoughts
Biological computing has a lot of potential for the future. Not only could it replace computers, but it could help us save very important data for future generations, and possibly do even more as we learn about its extensive applications. The future is bright for biocomputing and the people involved.
Vocabulary
DNA: Double helix molecule that protects and encodes genetic information inside the body; Deoxyribonucleic acid
Nucleotides: 4 molecules that are the building blocks of Nucleic acid
Binary Code: Computer processor instructions made up of 0’s and 1's
DNA sequencing: The process of determining the order of nucleotides in a DNA strand
Biocomputing: The design and use of computer systems made of natural or synthetic biological components
DNA synthesis: The creation of DNA; naturally or synthetically
Boolean Logic: A form of algebra that is centered around the words; “And,” “Or,” and, “Not”
SBOL: Synthetic Biology Open Language
