ClassX Video Lessons Subjects Artificial Intelligence This Synthetic DNA Factory Is Building New Forms of Life
In a cutting-edge laboratory, a team of biologists, software engineers, and automated robots are working together to accelerate the processes of nature. Their focus is on synthetic DNA, which they are remixing and programming into microorganisms. These microorganisms are being transformed into mini-factories capable of producing new foods, fuels, and medicines. Each piece of DNA is meticulously barcoded and cataloged in what is known as the world’s largest genetically engineered strain bank. This innovative biological assembly line is at the forefront of synthetic biology, a rapidly growing field that is attracting significant investment and attention.
Biology is an integral part of our daily lives, influencing everything from personal care products to the clothes we wear, the houses we live in, and even the gasoline we use. Understanding and engineering biology gives us the power to impact every aspect of our existence. While nature has had billions of years to perfect its designs through trial and error, humans have only begun to decode the source code of life in the last 50 years. Every living organism, from humans to exotic birds to simple amoebas, is built from a unique set of instructions encoded in DNA, which consists of just four letters. This DNA determines an organism’s appearance, behavior, and growth.
Recent technological advancements have made it possible to read, write, cut, and paste DNA more quickly and affordably than ever before. This allows scientists to create new sets of instructions that go beyond natural designs. Synthetic biology is defined not by the tools used, but by the intent behind them. While most biologists aim to understand nature, synthetic biology focuses on engineering nature to achieve specific goals, such as synthesizing vitamins, detecting environmental changes, or creating novel food products.
For example, if you’ve tried an Impossible Whopper at Burger King, you’ve tasted an engineered food product. The “meat flavor” comes from heme, an iron-containing molecule derived from a special soybean protein isolated from fermented yeast. The goal here is to elicit a function and create a product or cellular machine.
Thinking of cells as programmable machines merges biology, engineering, and computing. It views the building blocks of life—cells, tissues, and so on—as parts that can be reassembled, programmed, and standardized, similar to transistors and logic gates in a computer chip. Just as a computer operates on binary code, biology can be understood in a similar way, where DNA serves as the code that can be manipulated to encode organisms.
This concept may remind you of genetically modified organisms (GMOs), and indeed, synthetic biology utilizes genetic engineering as one of its tools. However, instead of merely tweaking a specific gene in a plant to enhance drought resistance, synthetic biology can create entirely new genetic codes that do not exist in nature.
At Ginkgo Bioworks, a synthetic biology start-up, team members hold unconventional titles like organism engineer and head of design, allowing them to focus on design and innovation while automated systems handle much of the laboratory work. They have worked with over 50 different organisms in the past year, each with unique capabilities for producing proteins, fatty molecules, drugs, and vitamins.
The engineering process at Ginkgo follows a classic cycle: design, build, and test. A team of computational biologists and data scientists designs experiments and DNA sequences to support various organism engineering programs. High-throughput DNA synthesis allows them to design DNA on a computer and have machines create it, significantly enhancing their ability to write and create DNA.
With the capacity to design libraries of thousands of genes, they can screen these in bulk to identify the best candidates for building optimal pathways. Once a pathway is established, they refine the strains using protein engineers and data scientists, employing machine learning and artificial intelligence to enhance efficiency.
The foundry operates as an automated laboratory, integrating various technologies to generate DNA, introduce it into strains, and grow them for testing at industrial scales. Each piece of DNA and every reagent is meticulously cataloged, generating vast amounts of data that are stored in a database created by software engineers. Currently, they are conducting millions of operations each month.
Despite the operational efficiency and rapid prototyping, biology remains a complex and unpredictable science, often requiring teams to revisit and revise their approaches. The process of experimentation is seen as an opportunity for learning and growth, with the understanding that the more they test, the greater their chances of success.
The vision of synthetic biology is to view it as a symbiotic manufacturing technology, reprogramming organisms to address various challenges. This approach has the potential to solve numerous problems, from sustainable production of flavors and fragrances to developing organisms that can fix nitrogen and enhance agricultural practices.
However, with these advancements come inherent risks. There is still much to learn about fundamental biology, and while nothing has left the lab yet for Ginkgo, scientists are actively experimenting with life’s building blocks. Questions remain about the implications of introducing synthetic organisms and products into the environment, as well as the potential for misuse.
As the field progresses, it will require collaboration among policy experts, scientists, and government leaders to navigate the challenges and ensure responsible development of synthetic biology, one gene tweak at a time.
Imagine you are part of a synthetic biology team. Design a hypothetical organism with a specific function, such as producing a new type of biofuel or synthesizing a vitamin. Consider the DNA sequences you would need and how you would program the organism to achieve your goal. Present your design to the class, explaining the potential benefits and challenges.
Research Ginkgo Bioworks and analyze their approach to synthetic biology. Discuss how their design-build-test cycle is applied in real-world scenarios. Evaluate the role of automation and data science in their processes. Present your findings in a group discussion, highlighting the innovative aspects and potential ethical considerations.
Participate in a debate on the ethical implications of synthetic biology. Divide into two groups: one supporting the advancement of synthetic biology for its potential benefits, and the other highlighting the risks and ethical concerns. Prepare arguments and counterarguments, and engage in a structured debate to explore different perspectives.
Attend a workshop where you will learn about the latest DNA manipulation techniques, such as CRISPR and high-throughput DNA synthesis. Engage in hands-on activities or simulations to understand how these techniques are used in synthetic biology. Reflect on how these tools can be applied to solve real-world problems.
Identify a product or process in your daily life that could be improved through synthetic biology. Develop a project proposal outlining how synthetic biology could enhance this product or process. Consider the scientific, economic, and ethical aspects, and present your proposal to the class for feedback.
Inside this advanced foundry, biologists, software engineers, and a fleet of automated robots are collaborating to enhance the speed of nature. They are working with synthetic DNA, remixing it, and programming microorganisms to transform these living samples into mini-factories that could potentially produce new foods, fuels, and medicines. Every piece of DNA here is barcoded and cataloged in what is considered the world’s largest genetically engineered strain bank. This biological assembly line is at the forefront of an emerging field that is attracting significant investment and attention: synthetic biology.
Biology is all around us. It influences personal care products, the clothes we wear, the houses we live in, gasoline, and medicine. Since biology is integral to so many aspects of life, having the ability to engineer biology gives us the power to impact every facet of our existence. Nature has had billions of years of trial and error to engineer biology and select its best designs, but we only began to understand the source code of life about 50 years ago. Every living organism, from humans to exotic birds to simple amoebas, is constructed from a unique set of instructions encoded in DNA, which consists of just four letters. DNA determines what an organism does, its appearance, behavior, and growth.
Recent technological advancements have enabled us to read, write, cut, and paste DNA more quickly and affordably than ever before, allowing us to create new sets of instructions that go beyond natural designs. Synthetic biology is defined not by the tools used, but by the intent behind them. While most biologists aim to understand nature, synthetic biology focuses on engineering nature to achieve specific goals, such as synthesizing vitamins, detecting environmental changes, or creating novel food products.
For instance, if you’ve tried an Impossible Whopper at Burger King, you’ve tasted an engineered food product. The “meat flavor” comes from heme, an iron-containing molecule derived from a special soybean protein isolated from fermented yeast. The goal here is to elicit a function and create a product or cellular machine.
Thinking of cells as programmable machines merges biology, engineering, and computing. It views the building blocks of life—cells, tissues, and so on—as parts that can be reassembled, programmed, and standardized, similar to transistors and logic gates in a computer chip. Just as a computer operates on binary code, biology can be understood in a similar way, where DNA serves as the code that can be manipulated to encode organisms.
This concept may remind you of genetically modified organisms (GMOs), and indeed, synthetic biology utilizes genetic engineering as one of its tools. However, instead of merely tweaking a specific gene in a plant to enhance drought resistance, synthetic biology can create entirely new genetic codes that do not exist in nature.
At Ginkgo Bioworks, a synthetic biology start-up, team members hold unconventional titles like organism engineer and head of design, allowing them to focus on design and innovation while automated systems handle much of the laboratory work. They have worked with over 50 different organisms in the past year, each with unique capabilities for producing proteins, fatty molecules, drugs, and vitamins.
The engineering process at Ginkgo follows a classic cycle: design, build, and test. A team of computational biologists and data scientists designs experiments and DNA sequences to support various organism engineering programs. High-throughput DNA synthesis allows them to design DNA on a computer and have machines create it, significantly enhancing their ability to write and create DNA.
With the capacity to design libraries of thousands of genes, they can screen these in bulk to identify the best candidates for building optimal pathways. Once a pathway is established, they refine the strains using protein engineers and data scientists, employing machine learning and artificial intelligence to enhance efficiency.
The foundry operates as an automated laboratory, integrating various technologies to generate DNA, introduce it into strains, and grow them for testing at industrial scales. Each piece of DNA and every reagent is meticulously cataloged, generating vast amounts of data that are stored in a database created by software engineers. Currently, they are conducting millions of operations each month.
Despite the operational efficiency and rapid prototyping, biology remains a complex and unpredictable science, often requiring teams to revisit and revise their approaches. The process of experimentation is seen as an opportunity for learning and growth, with the understanding that the more they test, the greater their chances of success.
The vision of synthetic biology is to view it as a symbiotic manufacturing technology, reprogramming organisms to address various challenges. This approach has the potential to solve numerous problems, from sustainable production of flavors and fragrances to developing organisms that can fix nitrogen and enhance agricultural practices.
However, with these advancements come inherent risks. There is still much to learn about fundamental biology, and while nothing has left the lab yet for Ginkgo, scientists are actively experimenting with life’s building blocks. Questions remain about the implications of introducing synthetic organisms and products into the environment, as well as the potential for misuse.
As the field progresses, it will require collaboration among policy experts, scientists, and government leaders to navigate the challenges and ensure responsible development of synthetic biology, one gene tweak at a time.
Synthetic – Relating to substances or materials made by chemical synthesis, especially to imitate a natural product – In synthetic biology, scientists create synthetic organisms by designing and constructing new biological parts and systems.
Biology – The scientific study of life and living organisms, including their structure, function, growth, evolution, and distribution – Advances in computational biology have enabled researchers to simulate complex biological processes using artificial intelligence.
DNA – Deoxyribonucleic acid, a molecule that carries the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms – Machine learning algorithms are now being used to analyze DNA sequences to predict genetic disorders.
Organisms – Individual living entities that can react to stimuli, reproduce, grow, and maintain homeostasis – Artificial intelligence is being used to model the behavior of microorganisms in various environments.
Engineering – The application of scientific and mathematical principles to design and build structures, machines, and systems – Genetic engineering involves the direct manipulation of an organism’s genes using biotechnology.
Automation – The use of technology to perform tasks without human intervention – Automation in laboratories has increased the efficiency of biological experiments by using robotic systems to handle repetitive tasks.
Proteins – Large, complex molecules that play many critical roles in the body, made up of one or more chains of amino acids – Deep learning models have been developed to predict the three-dimensional structures of proteins from their amino acid sequences.
Data – Facts and statistics collected together for reference or analysis – The integration of big data analytics in biology has revolutionized the way researchers understand complex biological systems.
Artificial – Made or produced by human beings rather than occurring naturally, typically as a copy of something natural – Artificial neural networks are inspired by the structure and function of the human brain.
Intelligence – The ability to acquire and apply knowledge and skills – Artificial intelligence is transforming the field of biology by providing new tools for data analysis and interpretation.
