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    From Lab to Life: Exploring Synthetic Biology with Drew Endy, John Cumbers, and Jennifer Holmgren

    Wed Jul 12 2023
    Synthetic BiologyBiologyEngineeringComputer ScienceDNA ManipulationMedicine ProductionCrop ModificationSustainable ManufacturingWetwareCircular EconomyPerformance MaterialsDecentralized ScienceWaste Carbon Utilization

    Description

    This episode explores the field of synthetic biology, which combines biology, engineering, and computer science to design and construct new biological systems. Synthetic biology allows us to manipulate and reprogram the DNA of living organisms, opening up limitless possibilities for applications in medicine production, crop modification, sustainable manufacturing, and more. The episode covers topics such as wetware, DNA synthesis, reprogramming cells, circular economy, performance materials, decentralized science, and utilizing waste carbon for sustainable production. It also highlights the potential of synthetic biology to revolutionize various industries and create a better future built with biology.

    Insights

    Synthetic biology combines biology, engineering, and computer science to design and construct new biological systems.

    This interdisciplinary field offers limitless possibilities for manipulating and reprogramming DNA to create new functions or traits in living organisms.

    Advancements in synthetic biology have made it easier to compose living systems and led to the emergence of new applications.

    By using technology like computers, code, and AI, synthetic biologists can create building blocks for composing living systems and develop a solid foundation for working with biology to solve problems.

    Synthetic biology allows for the creation of natural products without relying on traditional methods like harvesting plants or using poppy fields.

    By reprogramming cells, synthetic biologists can produce various plant natural products without relying on specific geographical locations or illegal markets.

    Synthetic biology has the potential to revolutionize manufacturing, climate change, equity, and the economy.

    By working with nature instead of against it, synthetic biology enables more efficient and sustainable processes, such as using microbes to fix cement and concrete or regrowing body parts through cell reprogramming.

    Decentralized science and synthetic biology can create a better future built with biology.

    By addressing broken systems in funding, publication, commercialization, and peer review, decentralized science aims to make scientific advancements more accessible and equitable. Synthetic biology plays a key role in this future by offering solutions to global challenges like climate change and sustainability.

    Chapters

    1. Synthetic Biology
    2. Advancements in Synthetic Biology
    3. Wetware and DNA Synthesis
    4. DNA Print Synthesis and Reprogramming Cells
    5. Synthetic Biology Applications and Future Possibilities
    6. Transitioning to Sustainable Manufacturing
    7. Synthetic Biology in Architecture and Material Science
    8. Unlocking the Potential of Synthetic Biology
    9. Fermentation and Synthetic Biology
    10. Synthetic Biology and Performance Materials
    11. The Potential of Synthetic Biology
    12. Reprogramming Cells and Circular Economy
    13. Creating Sustainable Ecosystems with Synthetic Biology
    14. Decentralized Science and Synthetic Biology
    15. Utilizing Waste Carbon for Sustainable Production
    16. Ethanol Production and Circular Economy
    17. Fermentation and Sustainable Manufacturing
    Summary
    Transcript

    Synthetic Biology

    00:05 - 07:29

    • Synthetic biology combines biology, engineering, and computer science to design and construct new biological systems.
    • With synthetic biology, we can manipulate and reprogram the DNA of living organisms to create new functions or traits.
    • The products of synthetic biology are limitless, as DNA is a Turing complete computational platform.
    • Synthetic biology has applications in medicine production, crop modification, and more.
    • It offers a more efficient and resource-intensive manufacturing process compared to traditional methods.
    • In the future, synthetic biology could enable the growth of cities and everything inside them.
    • Drew Endy is a leader in synthetic biology and will discuss wetware, read/write functions for DNA, and the potential for growing buildings, planes, cars.
    • John Kumbers will provide technical details on fermentation, programming multicellular organisms, and nature's efficiency in comparison to human manufacturing.
    • Jennifer Holmgran from Lonz Attack will talk about their efforts in capturing carbon emissions and converting them into usable materials like jackets.

    Advancements in Synthetic Biology

    07:00 - 13:55

    • MetaMask has introduced MetaMask Portfolio, a holistic view of your crypto portfolio across all chains
    • MetaMask Portfolio reports the aggregate value of assets in MetaMask wallets and imported wallets
    • MetaMask Portfolio allows users to buy, swap, bridge, and stake crypto assets
    • Drew Endy is considered one of the fathers of modern synthetic biology
    • Synthetic biology involves improving our ability to compose living systems by putting biology together
    • Biotechnology has traditionally been used as a last resort for solving problems that can't be addressed with other technologies
    • Synthetic biology aims to develop a solid foundation for working with living systems to solve problems
    • Advancements in synthetic biology have made it easier to compose living systems and led to the emergence of new applications
    • Synthetic biology uses technology like computers, code, and AI to create building blocks for composing living systems
    • The frontier of synthetic biology is still being explored and there is much progress yet to be made
    • Biology is a general purpose technology that can be partnered with for various purposes
    • The fundamental unit of life is the cell, which is not fully understood operationally
    • Ambiguity at the cellular level means that building with biology requires Edisonian trial and error methods

    Wetware and DNA Synthesis

    13:26 - 20:48

    • Design build work is preferred over design build test.
    • Cells are like computers, but we lack knowledge of 30% of their components.
    • Computing operates at the intersection of JUUL's and VINTS, while cells operate in the domain of Jules Bitts and Adams.
    • A cell is a self-mixing milieu that is alive and can make a physical copy of itself within minutes.
    • Wetware has the potential to be orders of magnitude more powerful than current technology.
    • Biology allows for reproducing machines and the ability to read and write DNA.
    • DNA sequencing translates atoms into bits, allowing for manipulation and computation upon genetic code.
    • DNA synthesis reconstructs DNA polymers from specified sequences.

    DNA Print Synthesis and Reprogramming Cells

    20:23 - 27:34

    • DNA print synthesis allows us to reconstruct a polymer of DNA by specifying a sequence and dispensing chemicals in a particular order.
    • DNA sequencing and DNA synthesis make genetic material and genetic information interconvertible.
    • Synthetic biology combines the superpower of the internet with the power of compute, enabling growth, reproduction, and local manufacturing.
    • The read and write layer involves reading DNA, uploading it in digital form, and writing DNA to manifest in actual DNA creation.
    • A DNA printer is like a 1D printer that programs the molecular machinery of cells, leading to three-dimensional manufacturing.
    • Cells can be reprogrammed to perform various functions, such as producing chemicals normally found in plants.
    • Plants have developed defenses against insects and mammals through the production of unique chemicals.
    • Inspiration for chemistry can be derived from plant substances, which can be obtained by reprogramming yeast metabolism instead of growing plants.
    • Reprogramming yeast metabolism allows for the production of various plant natural products without relying on specific geographical locations or illegal markets.

    Synthetic Biology Applications and Future Possibilities

    27:07 - 34:26

    • Synthetic biology allows for the creation of natural products without relying on traditional methods like harvesting plants or using poppy fields.
    • Programming cells at a molecular scale is becoming a reality, although it is not yet routine.
    • The current go-to-market model for synthetic biology involves centralized capital and industrial fermentation.
    • To reach more people and provide essential medicines to everyone, synthetic biology needs to transition from an industrialized model to one that enables brewing of medicines in rural areas.
    • The goal of the biological revolution is to enable 10 billion people to flourish on the planet by 2050 while preserving biodiversity.
    • Biology represents the intersection of energy (Joules), information (Bits), and matter (Atoms).
    • Photosynthesis provides enough energy for bio manufacturing, with approximately four and a half times more energy than civilization consumes.
    • Solar panel manufacturing has reached a return on energy (ROE) above one, indicating a transition to electricity generation abundance.

    Transitioning to Sustainable Manufacturing

    33:58 - 41:20

    • Transitioning to electricity generation abundance
    • Using electricity to fix carbon from the atmosphere
    • Bioengineering organisms to eat formate
    • Improving the efficiency of converting electricity to formate
    • Expanding biological manufacturing through electro-biosynthesis
    • Solving the challenges in synthetic biology for advancements in medicine, longevity, and biosecurity
    • The need to overcome low-level ambiguity in synthetic biology
    • Looking ahead to leveraging synthetic biology in the future
    • Staging of development and deployment of biological tools
    • The potential of mastering technology in the future

    Synthetic Biology in Architecture and Material Science

    41:03 - 48:08

    • The Lithuanian synthetic biology movie called Vesper is a dark exploration of a future with biotechnology.
    • The movie highlights the idea of using biology embedded within us and our environment to provide information about our health.
    • Artist Phil Ross pioneered micro-texture by building buildings using mushrooms.
    • There is potential to grow houses and trees quickly by grinding up natural materials and reforming them with organisms like wood fungus.
    • Phil Ross built T-houses out of mushrooms that could be used to make tea.
    • Biology operates at the nano scale but can grow macroscopic objects, such as bridges made from rubber tree roots or suspension cables made from spider thread.
    • The focus should be on dealing with current issues responsibly before exploring more imaginative possibilities in synthetic biology.

    Unlocking the Potential of Synthetic Biology

    47:41 - 54:32

    • Synthetic biology removes three constraints on all life on Earth: lineage, reproduction, and availability.
    • Unlocking synthetic biology allows us to construct fully understood cells and explore the diversity of life beyond Earth.
    • Biology is Turing complete and operates in the realm of atoms, without limitations.
    • Jon Kumbers fell down the rabbit hole of synthetic biology through his interest in longevity and space settlement.
    • Sin Bio Beta is an innovation hub that brings together synthetic biology entrepreneurs and investors.
    • The lay of the land for the synthetic biology rabbit hole started about 50 years ago with Genentech's founding and the development of recombinant DNA technology.

    Fermentation and Synthetic Biology

    54:05 - 1:01:39

    • Fermentation is a key part of synthetic biology and allows for the reprogramming of microorganisms to produce different substances.
    • Synthetic biology involves reading, writing, and editing DNA to create cells that can produce desired products.
    • The production platform created through synthetic biology can be used to make various products such as insulin, materials, chemicals, polymers, and food products.
    • Fermentation is the process of converting one molecule into another using oxygen in the environment.
    • By reprogramming fermentation processes, we can produce substances more efficiently and at lower costs compared to traditional methods.
    • Genetic engineering and fermentation have been used to create anti-malarial drugs by brewing them in yeast cells instead of extracting them from plants.
    • Synthetic biology allows for the creation of new compounds by finding diverse sources in nature or engineering genes into cells.

    Synthetic Biology and Performance Materials

    1:01:16 - 1:08:47

    • Checkerspot is using synthetic biology to create new performance materials from molecules found in nature.
    • They have made cross-country skis with improved properties by editing natural molecules.
    • Synthetic biology combines the best of nature's problem-solving abilities with human technology.
    • The future of biology involves programming multi-cellular systems and creating sophisticated biological devices.
    • Synthetic biology allows us to understand and harness the chaotic yet efficient nature of organic systems.
    • Synthetic biology is a movement that emerged about 20 years ago, combining engineering principles with biology.

    The Potential of Synthetic Biology

    1:08:22 - 1:15:43

    • Synthetic biology is a movement to make biology easier to engineer.
    • The goal is to program biology as easily as we can program a computer.
    • The field is still in its early stages, but there is a burning passion among synthetic biologists to get there.
    • Synthetic biology has the potential to revolutionize manufacturing, climate change, equity, and the economy.
    • Nature can do some things really well, like growing wood, which has important applications for humanity.
    • Applying synthetic biology to more complex systems than just cells can change the landscape of the world we live in.
    • One example is using microbes to fix cement and concrete, which reduces CO2 emissions compared to traditional cement production.
    • Synthetic biology allows us to work with nature rather than against it, resulting in more efficient and sustainable processes.
    • There is also potential for regrowing body parts through reprogramming cells.

    Reprogramming Cells and Circular Economy

    1:15:15 - 1:22:00

    • The potential to reprogram cells in the body to regrow limbs and teeth
    • Biology's ability to grow large structures like pterodactyls, T-rexes, and sequoia trees
    • The concept of growing buildings and furniture using synthetic biology
    • The current state of biology compared to the punch card phase of computing
    • Significant investments in the synthetic biology industry
    • The idea of reprogramming DNA to grow specific objects or structures
    • Programmed pattern formation as an area of research
    • The example of a jacket made from a polymer produced by LanzaTech through fermentation
    • LanzaTech's process of using waste CO2 from steel mills to produce various molecules
    • Creating circular ecosystems by utilizing CO2 in the atmosphere for production

    Creating Sustainable Ecosystems with Synthetic Biology

    1:21:39 - 1:28:27

    • Synthetic biology and computing manufacturing platforms can create cyclical ecosystems by customizing both inputs and outputs.
    • Biology is programmable, as seen in the circadian rhythm and the binding of dopamine to receptors.
    • Setting goals in life is important due to the oscillation of dopamine binding and release.
    • In 2000, a synthetic oscillator was created inside an E. coli cell, marking the era of synthetic biology.
    • Synthetic biology will become integrated into everyday life, replacing petrochemicals with biological alternatives.
    • The workshop focused on creating future network states built with biology for sustainable economies and reducing climate change impact.
    • The decentralized science community aims to address broken systems in funding, publication, commercialization, and peer review.

    Decentralized Science and Synthetic Biology

    1:28:05 - 1:34:54

    • Decentralized science community aims to fix broken systems in funding, publication, and commercialization of science
    • Blockchain technology can be used to achieve equitable distribution of benefits in decentralized science
    • The network state can address core issues in democracy
    • Synthetic biology has the potential to fix broken tools in democracy
    • Combination of decentralized science, network state, and synthetic biology can create a better future built with biology
    • Conference on decentralized science and synthetic biology happening on May 23rd-25th at Oakland Marriott
    • Introduction courses available for newcomers interested in decentralized science and synthetic biology
    • Uniswap Labs released Uniswap mobile wallet for iOS, making it easier to trade tokens on the go
    • Toku helps companies manage token issuance compliance in a complex regulatory environment
    • Jennifer Holmgren discusses the problem of one-way flow of carbon from the ground into the air
    • Need for a circular economy that reuses waste carbon instead of extracting more from the ground
    • Universality of the problem requires deep solutions that go down to the root level
    • Most people are unaware that pollution and goods come from fossil carbon

    Utilizing Waste Carbon for Sustainable Production

    1:34:39 - 1:41:53

    • Most people don't know that pollution comes from fossil carbon.
    • New technologies can use waste carbon to make products.
    • Biology is selective and handles inhomogeneity well, making it suited for a new carbon economy.
    • Biology can help transition from a one-way flow of carbon to a circular flow.
    • Living organisms adjust and handle chaos, making biology suitable for accounting for the changing nature of waste feedstocks.
    • Lonsateck ferments gases like carbon dioxide and waste gases from industrial mills to produce ethanol efficiently.
    • The first application of Lonsateck's technology is in large-scale factories where the waste gases are already present.
    • Lonsateck pays for the gas at its energy value and often licenses their technology to partners who build and own the plants.
    • The ethanol produced by Lonsateck is used as an intermediate to make sustainable aviation fuel and materials.

    Ethanol Production and Circular Economy

    1:41:33 - 1:48:35

    • Ethanol is a basic building block that can be used to make sustainable aviation fuel and various materials.
    • Ethylene, derived from ethanol, is the largest used chemical today and is used in the production of foam, polyester, and plastic.
    • The goal is to replace ethylene derived from fossil fuels with ethylene derived from recycled carbon.
    • The process involves converting ethanol to ethylene, which becomes a key raw material for many products.
    • The idea is to utilize all the carbon already above ground and recycle it instead of emitting it into the atmosphere.
    • The technology can be applied to various waste materials like municipal solid waste, shoes, tires, and agricultural residue.
    • Scaling up the technology will reduce costs and make it more accessible for widespread adoption.
    • There are no major obstacles in terms of regulations or resistance from nation states or incumbents.
    • Distributed systems like this have proven successful in other industries like farm-to-table supply chains.

    Fermentation and Sustainable Manufacturing

    1:48:08 - 1:51:09

    • Fermentation is a simple biological process that has taken a long time to discover and optimize.
    • The process involves optimizing bacteria to produce the desired product, developing a bioreactor, and creating an efficient process around it.
    • Scaling gas fermentation was initially believed to be impossible, but with years of work and collaboration between biology and engineering experts, it has been achieved.
    • In the future, a utopia can be created by using various technologies to recycle everything and eliminate waste.
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