FT014 - What is Synthetic Biology?

Summary

Synthetic biology is an engineering approach to DNA, where scientists apply design principles to create new biological systems or tools. Unlike traditional genetic engineering, which was more of an artisanal process, synthetic biology leverages modern tech like CRISPR, automation, and AI to standardize and quantify biological experiments. The field emphasizes an engineering mindset, focusing on design, build, test, and learn loops, and fosters a community of 'nerds' passionate about integrating engineering with biology.

Takeaways

• 🧬 Synthetic biology is the application of engineering design principles to DNA, aiming to understand and construct new biological systems.
• 🔍 Synthetic biologists are scientists, developers, or inventors who focus on reading, writing, and editing DNA using engineering approaches.
• 📚 The term 'genetic engineering' originated in the 1970s and was limited by the technology of the time, often relying on cutting and pasting existing genes.
• 🛠️ Modern synthetic biology differs from early genetic engineering by incorporating standardization, quantification, automation, and simulation.
• 📈 The advancement in DNA sequencing, synthesis, and laboratory automation has enabled a more systematic approach to genetic manipulation.
• 💡 Synthetic biology is not just an extension of genetic engineering but a distinct field that emphasizes engineering principles and design processes.
• 🔄 The 'design, build, test, learn' loop is a core iterative process used by synthetic biologists, reflecting an engineering mindset.
• 🌐 The synthetic biology community is defined by its shared approach to applying engineering design to DNA, fostering collaboration and innovation.
• 🧰 The current tech stack in synthetic biology includes advanced tools like CRISPR, omics technologies, and generative AI for DNA design.
• 🌟 Synthetic biology is a dynamic field that continues to evolve with the development of new tools and the growth of its community.

Q & A

What is synthetic biology?

Synthetic biology is the engineering design process applied to DNA, where scientists use design principles to construct new biological systems that are interesting or useful, or create new technologies and tools for reading, writing, or editing DNA.

How does synthetic biology differ from genetic engineering?

While genetic engineering involves the manipulation of genes, synthetic biology goes further by applying engineering principles to design and build new biological systems, focusing on standardization, quantification, automation, and simulation.

What role do synthetic biologists play in the field of biology?

Synthetic biologists act as scientists seeking design principles for biology, developers constructing new biological systems, or inventors creating new technologies and tools for genetic manipulation.

Why did the term 'genetic engineering' become popular in the 1970s?

The term 'genetic engineering' became popular in the 1970s as the first DNA technologies were emerging, marking a productive era for biotech with the creation of transgenic mice and recombinant human insulin.

What limitations did early genetic engineering face?

Early genetic engineering was limited by a lack of tools for working with DNA, such as sequencing technology, DNA synthesis capabilities, measurement tools, and laboratory automation, making it more of an artisanal craft process.

How has the advancement of technology transformed genetic engineering into synthetic biology?

Advancements in DNA sequencing, synthesis, gene editing tools like CRISPR, omics technologies, laboratory automation, and AI for DNA design have enabled the standardization, quantification, and automation of biological systems, leading to the emergence of synthetic biology.

What is the significance of the 'design, build, test, learn' loop in synthetic biology?

The 'design, build, test, learn' loop is an iterative process used in synthetic biology that reflects the engineering forward approach, focusing on enabling technology, measurement, and the design process.

What is a 'chassis' in the context of synthetic biology?

In synthetic biology, a 'chassis' refers to an engineered yeast strain or other biological system that serves as a base upon which genetic circuits or other biological components are built.

What is a 'genetic circuit' in synthetic biology?

A 'genetic circuit' in synthetic biology is a piece of functional DNA that has been designed to perform a specific task or function within a biological system.

Why is the term 'synthetic biology' important for the community?

The term 'synthetic biology' is important as it helps to bring together a community of people who share the goal of applying engineering design processes to DNA and seek to find others with similar interests and approaches.

How does synthetic biology relate to computer code?

Synthetic biologists often debate the similarities between genetic code and computer code, reflecting the field's focus on using engineering principles, including computational tools, to design and manipulate biological systems.

Outlines

00:00

🧬 Synthetic Biology: Engineering DNA

This paragraph introduces synthetic biology as an engineering design process applied to DNA, distinguishing it from traditional genetic engineering. It describes synthetic biologists as scientists, developers, or inventors who apply design principles to construct new biological systems or create tools for DNA manipulation. The paragraph provides historical context, explaining how genetic engineering emerged in the 1970s with limited tools and how advancements in DNA sequencing, synthesis, and automation have paved the way for synthetic biology. The narrative emphasizes the engineering mindset of synthetic biologists and their use of standard parts, quantitative measurements, and computational tools to approach biological problems.

05:00

🤖 The Synthetic Biology Community and Its Practices

The second paragraph delves into the community aspect of synthetic biology, highlighting the importance of the term in uniting individuals who apply engineering principles to DNA. It discusses how synthetic biology is defined by the community's practices, including the use of a tech stack for DNA manipulation, an engineering-forward mindset, and the iterative design-build-test-learn process. The paragraph also touches on the 'genetic circuit' and 'chassis' terminology used by synthetic biologists, indicating their interdisciplinary approach that often draws parallels between genetic code and computer code. The summary invites those who resonate with these concepts to join the synthetic biology community, suggesting a shared enthusiasm for innovation in this field.

Keywords

💡Synthetic Biology

Synthetic biology is an interdisciplinary field that combines science and engineering to design and construct new biological parts, devices, and systems or to redesign existing, natural biological systems. It is central to the video's theme as it represents the modern approach to engineering DNA, moving beyond the limitations of early genetic engineering. The script describes synthetic biology as the application of engineering design principles to DNA, emphasizing the creation of new biological systems and the development of tools for DNA manipulation.

💡Genetic Engineering

Genetic engineering refers to the direct manipulation of an organism's genes using biotechnology. The term became popular in the 1970s and is associated with the early days of DNA technology. In the script, genetic engineering is contrasted with synthetic biology, highlighting the more artisanal and less systematic approach of the past, which lacked the standardization and automation present in synthetic biology.

💡DNA

DNA, or deoxyribonucleic acid, is the molecule that carries the genetic instructions for the development, functioning, and reproduction of all known living organisms. The script frequently mentions DNA as the fundamental material that synthetic biologists work with, whether it's for sequencing, synthesis, or editing using tools like CRISPR.

💡Engineering Design

Engineering design is a process where engineers devise solutions to problems using creativity and scientific methods. In the context of the video, engineering design is applied to biology, indicating a systematic and principled approach to creating and modifying biological systems. Synthetic biologists use these principles to construct new systems and develop technologies for DNA manipulation.

💡Biological Function

Biological function refers to the role or purpose of a particular biological component, such as a gene or a protein, within an organism. The script mentions that synthetic biologists seek to understand the rules governing how DNA creates biological function, which is essential for designing new biological systems.

💡Design Principles

Design principles are fundamental guidelines or rules that are used to create effective and efficient designs in various fields. In synthetic biology, as discussed in the script, these principles guide the creation of new biological systems, emphasizing the need for standardization, quantification, and automation in the engineering process.

💡CRISPR

CRISPR, which stands for Clustered Regularly Interspaced Short Palindromic Repeats, is a revolutionary gene-editing tool that allows scientists to modify an organism's DNA. The script mentions CRISPR as part of the tech stack of tools available to synthetic biologists, highlighting its importance in the reading, writing, and editing of DNA.

💡Omics Technologies

Omics technologies refer to a collection of fields in biology that end with '-omics,' such as genomics, proteomics, and metabolomics, which involve the study of the complete sets of genes, proteins, or metabolites in an organism, respectively. The script includes omics technologies as part of the current toolset in synthetic biology, emphasizing their role in understanding and manipulating biological systems at a comprehensive level.

💡Laboratory Automation

Laboratory automation involves the use of technology to perform repetitive laboratory tasks, reducing the need for manual labor and increasing efficiency and accuracy. The script mentions laboratory automation as a key development that has enabled synthetic biologists to standardize protocols and scale up their work, moving away from the more manual, artisanal methods of early genetic engineering.

💡Generative AI

Generative AI refers to artificial intelligence systems that can create new content, such as designs or code, based on existing data. In the script, generative AI for DNA design is mentioned as part of the tech stack in synthetic biology, indicating its role in the automated and innovative design of new biological systems.

💡Community

The term 'community' in the script refers to the group of people who share a common interest or goal. In the context of synthetic biology, the community is made up of individuals who embrace the engineering design process in working with DNA. The script emphasizes the importance of this community in driving the field forward and providing a collective identity for those involved in synthetic biology.

Highlights

Synthetic biology is defined as the engineering design process applied to DNA.

A synthetic biologist seeks design principles for biology, focusing on how DNA creates biological function.

Synthetic biologists are developers who construct new biological systems based on design principles.

They are inventors creating new technologies and tools for DNA manipulation.

The common goal of synthetic biologists is engineering DNA.

Genetic engineering and synthetic biology are often confused but have distinct historical and social contexts.

Genetic engineering emerged in the 1970s with limited tools and was more of an artisanal craft process.

Synthetic biology differentiates itself by embracing modern engineering features like standardization and automation.

The term 'synthetic biology' gained traction around the year 2000 as a more intentional engineering approach to biology.

Synthetic biology is sometimes described as 'genetic engineering on steroids', emphasizing its advanced nature.

A simple definition of synthetic biology is that it puts the engineering in genetic engineering.

The field of synthetic biology is characterized by a tech stack of tools, a way of thinking, and a community of people.

The current state of synthetic biology is closely linked to advancements in DNA sequencing, synthesis, and editing technologies.

The synthetic biology mindset is engineering-forward, with a focus on technology, measurement, and the design process.

Synthetic biologists use an iterative design-build-test-learn loop for engineering R&D.

The term 'synthetic biology' is essential for bringing together a community of people who apply engineering to DNA.

Synthetic biology is a community-driven field, existing as long as people are interested in engineering design for DNA.

Transcripts

What is synthetic biology?

How is it different from genetic engineering?

Today we're talking about why synbio is a thing

and why it might be your thing.

So come with me, fellow nerds, as I get lost in the weeds

over semantics and we work out a definition

for synthetic biology.

Let's get right to it.

Synthetic biology is the engineering design

process applied to DNA.

A synthetic biologist is a scientist who seeks out

design principles for biology.

The rules that govern how DNA creates biological function.

Or a synthetic biologist is a developer

who uses those design principles

to construct new biological systems

that are interesting or useful.

Or a synthetic biologist is an inventor

who creates new technologies

and tools for reading, writing or editing DNA.

For everything synthetic biologists do,

engineering DNA is the common goal.

Now, I hear some of you out there saying “Engineering DNA?

Jake I thought we already had a term for that,

because that sure sounds like genetic engineering.”

And look, that's fair.

I'm not here to be the word police.

But I do think looking at the different uses of these terms

can give some historical

and social perspective about what we're all trying to do here.

So let's take a quick journey through time.

The phrase “genetic engineering” became popular in the 1970s

just as the very first DNA technologies were coming online.

It was an extremely productive era for biotech.

Picture the very first transgenic mouse.

Picture recombinant human insulin.

Those early pioneers had a very limited set of tools

for working with DNA.

Sequencing was still new tech,

so they were usually working blind.

DNA synthesis was barely possible,

so they had to cut and paste existing genes.

Measurement tools were pretty rough and involve things like

eyeballing the sizes of spots on a blot.

Laboratory automation didn't exist

so they did everything by hand.

Software? Forget about it.

In other words,

early genetic engineering didn't have most of the features

we associate with modern engineering:

standardization, quantification, automation, simulation.

It was more like an artisanal craft process,

relying on human intuition and trial and error.

There wasn't any single breakthrough

that transformed biology into an engineering discipline.

By the nineties, you could sequence DNA routinely.

By the 2000s, you could synthesize whatever you needed,

at least for shorter pieces of DNA.

Laboratory automation meant that you could

standardize protocols and scale them up.

Mass spectrometry, fluorescence imaging,

and other measurement technologies

made biological experiments more quantitative.

Software tools let you model

and simulate more biological complexity.

Sometime around the year 2000, a critical mass of people

had noticed a pattern.

Borrowing approaches from engineering and using them on

biological problems was often a good idea.

So they said, let's do that on purpose.

Let's build biology around standard parts,

quantitative measurements,

computational tools, and scalable automation.

And that's the story of how “synthetic biology” became a thing.

The way that synthetic biologists

passionately embrace engineering

sometimes leads people to the understanding that synbio is like

genetic engineering only moreso.

“Synthetic biology it's genetic engineering

on steroids” is one you might have heard.

That's from an article in Science magazine in 2012.

And I have to say, I don't love it.

I mean, do I look like I use steroids?

But I get it.

I respect the simplicity.

My version of a simple definition for synbio might go like this:

“Synthetic biology puts the engineering in genetic engineering.”

My extended definition for synbio is what happens

when three things come together: a tech stack of tools,

a way of thinking and a community of people.

The state of synthetic biology at any given moment is closely

linked to the tools we have for reading, writing and editing DNA.

Today, that tech stack includes DNA sequencing

synthesis, gene editors like CRISPR, omics technologies,

laboratory automation, and generative AI for DNA design.

The synthetic biology way of thinking is engineering forward

with a focus on enabling technology

measurement and the design process.

If you've ever heard a biologist talk about the design, build, test,

learn loop, the iterative process used for engineering R&D,

that person was probably a synthetic biologist.

They were engineering a yeast strain

and they called it a good “chassis”?

That's a synthetic biologist.

They designed a piece of functional DNA

and they called it a “genetic circuit”?

Synthetic biologists.

They were debating the similarities

between genetic code and computer code.

Oh yeah, we do that a lot.

In other words, we're huge nerds.

And that brings me to our community of people.

The most important reason why

we need the term “synthetic biology”

is that it helps bring people together.

Fundamentally, symbio is what the symbio community does.

The term will exist for as long as people

want to bring the engineering design process to DNA,

and want to find other people who think the same way.

If that sounds like a good idea to you, then welcome to the club.

I'm excited to hear about your favorite chassis

for building genetic circuits.