Synthetic Biology in a Nutshell

What happens when biology meets engineering

What is it though?

If you were looking for a clear, precise, and official definition of synthetic biology, I need to tell you the truth. As of now, there is none.

Synbio = the expansion of biotechnology as a multidisciplinary field that seeks to create new biological parts, devices, and systems, or redesign already existing ones, so that they produce a substance, or gain a new ability by combining engineering principles with biology

Biotechnology

Multidisciplinary

Some of the various disciplines involved are biotechnology, systems biology, biophysics, chemical and biological engineering, electrical and computer engineering, control engineering, and evolutionary biology.

Approaches

Synthetic Biology Levels of Abstraction
  1. Bottom-up approach: from the micro to the macro scale. DNA → Parts → Devices…

Standardizing Life

The reason why we think biology is not a precise science is that everything seems to happen randomly, without any precise instructions: without logic.

Electronics

Don’t feel intimidated by the diagram on the left. Logic is something that can be easily understood by anyone, logically 🥴.

  • Wash the dishes OR clean your bedroom, she’ll give you some money to go out with your friends: you can do either of them to receive the “prize”
  • Prepare your lunch XOR watch TV all afternoon, you can sleepover at your best friend’s house: you’ve been working hard so far, so you must have one false (watch TV) for you to get the reward ;)
  • Stop studying for your test NAND/NOR eat some candy, you can go on a trip with your friends!: your mom tells you to stop working so hard. You need a rest, so if you don’t do any chores, you can get a reward
  • NOT brush your teeth today, she’ll give you a dollar: this sounds like a dystopian story where the opposite happens, right?

Biological Part

This is supposed to be an article in which you learn the Principles of synthetic biology in a nutshell. So to go faster, we won’t go through computational circuits. Instead, we’ll dive into genetic circuits right away. Exciting, right?

Synbio symbols

Devices

Devices are more complex assemblies of parts. In fact, they’re a collection set of parts, that implement a human-defined function.

Systems

Biological parts can be joined with each other to form devices, and devices can be joined to form: genetic circuits, plasmids, or vectors. These are concepts that we can use to refer to these systems. Some important concepts are:

This is what a common vector looks like

Genetic LEGOs

These are the most standardized parts that we can find in synthetic biology. A BioBrick can be assembled with any other BioBrick to create a new BioBrick. It is based on restriction enzymes, but these restriction enzymes are always the same: you only need EcoRI, XbaI, SpeI, and PstI.

  1. Check your DNA sequence for the presence of BioBrick restriction sites. Even if you find them, with a little engineering, you will still be able to create your specific BioBrick.
  2. If your gene is small enough, you can order *primers with the BioBricks end sequences and use PCR to generate the desired BioBrick part. If your gene is too large for regular PCR, it is recommended to get your gene synthesized
Surface-level explanation
A more detailed explanation

Languages

You can tell the field has been developing quite a lot when you know that we now have more than one programming language, just to design biological circuits.

Creating biological models

As mentioned above, this discipline consists of the fusion between biology and engineering. Thus, in this part of the article we’ll focus on the creation of mathematic models that reflect how our biological systems function.

  1. Diagram all the protein interactions of this pathway
  2. Describe the speed of the reactions using mass action kinetics (where differential equations come in)
Chemical Reaction
Modeling that chemical reaction with an Ordinary Differential Equation

Synbio’s Central Dogma

Biology can be standardized after all! One of the main outcomes of this standardization is the cycle that every knowledgable person in the field follows:

Design → Build → Test → (Analyze/Learn)

Remember the biological models and programming languages, and levels of abstraction? That’s designing! The cloning methods and biobricks? That’s building. The process of actually inserting those biobricks into living things would be considered as testing, and after doing all of that, we should have learned something new, and analyzed our results.

It’s very likely that you’ll continue seeing diagrams like this to represent the DBTA cycle :)

Applications

If I explained myself well, we should already have a good understanding of the principles of synthetic biology: levels of abstraction are and what each of them means, the functions encapsulated by essential biological parts, programming biological languages, what creating a biological model means.

Bio-computing

Bio-sensors

A biosensor refers to an engineered organism, usually a bacterium, that is capable of reporting some ambient phenomena such as the presence of heavy metals or toxins. By using the principles we’ve just talked about, synthetic biologists can design circuits that include the genes for such bio-sensors.

XNA

In May of 2014, researchers announced that they had successfully introduced two new artificial nucleotides into bacterial DNA!

Drug Delivery platforms

Synthetic biologists can now reprogram bacteria to sense and respond to a particular cancer state. The advantages of using bacteria? It can deliver the drug directly into the tumor, minimizing off-target effects.

Synthetic life

Synbio 🦄s?

If you’ve read until here, you likely agree with me: the applications of synthetic biology are definitely mind-blowing. Not only because they sound advanced and futuristic, but also because we’re making real progress in making them true.

Ginkgo Bioworks

The name of a tree? Well, Ginkgo is also a synthetic biology company valued at more than $4 Billion 🤯. They are “The Organism Company”, a synthetic biology platform in which they aim to build the future of biology by standardizing processes and using the power of tech as well.

Ginkgo’s foundries 🙌

Twist Bioscience

They supply DNA for research and commercial applications of genetic engineering. They are now developing digital data storage applications and DNA origami-based biomaterials and nanostructures. Twist is valued at $2.7 billion!

Anyone Can Cook!

What if I told you that YOU can be a bio-hacker?

Can you imagine a world in which we can all program life, as easily as we now program websites? That would be a world free of disease and global warming, full of centenarians who look and feel like teenagers, and bio-computers!

DIY-Bio Movement

Do-It-Yourself biology is a growing biotechnological-social movement in which individuals, communities, and small organizations study biology and life sciences, using the same methods as traditional research institutions.

Check out Josiah’s YouTube channel, where we posts videos teaching people how to culture chicken cells, modify bacteria and even create a DIY cover vaccine!

iGEM

You don’t have to believe Josiah or me. You can trust iGEM: the international Genetically Engineered Machine competition, an event born in the MIT, in which people from around the world, ranging from high school students to postdocs solve world-class problems using synthetic biology.

The “Giant Jamboree” at MIT. iGEM’s closing event

Community Labs

Another great way to start to do biohacking, without the need for prior experience or much monetary resources. Interestingly, community labs have been here for some time already.

Biohackers at Genspace, NY

Bioinformatics

I wish I knew this when I first discovered the world of biotech. Bioinformatics is the greatest way to learn about synbio/biotech without needing anything but your computer and a wifi connection.

Successful Biohacking Projects

So all of this sounds like a utopia: anyone can cook! However, that doesn’t mean that anyone can be a chef, does it? What have biohackers actually achieved up to date?

Biosafety

What can be the risks associated with people creating their own coronavirus vaccines, or simply making bacteria glow? How can we prevent that biohackers become bioterrorists? Some worst-case scenarios would include:

  • The purposeful design and release of an intentionally harmful organism or system
  • A future over-reliance on our ability to design and maintain engineered biological systems in an otherwise natural world
  • Working to educate and train a responsible generation of biological engineers and scientists
  • Learning what is possible (at what cost) using simple test systems
  • Biocontainment by: biological kill switches, disabling of the organism to replicate or pass modified or synthetic genes to offspring, use of xenobiological organisms or genetic material (XNA, see above)

What will you GROW?

If there’s one thing that I’d expect you to stay with after reading this guide, is that you build something. Actually, that you GROW something ;)

let’s give more life to life!

Ambitious teenager building innovative projects with Synthetic Biology and Artificial Intelligence

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