Synthetic Biology 101 — Past, Present, and Future

Aryan Khimani
6 min readMar 13, 2023

The world is such a complex place if you just take a couple of seconds and look outside. Looking at the trees, insects, and then even looking at yourself, all your cells have such mesmerizing characteristics and properties which all come together to keep you alive. Now imagine we can take those very cells and edit their properties to make them into whatever your wildest imagination can come up with. From turning oak trees permanently and naturally red. To making an entire organ from scratch, this is all possible with synthetic biology. But what is synthetic biology exactly?

Ground Zero

So to start we need to define synthetic biology because without a proper meaning to use as a base you will get lost reading this article.

Synthetic biology as of right now still doesn’t truly have a set definition. but for your understanding it’s a field of science that involves redesigning organisms for useful purposes by engineering them to have new abilities. That simply means giving scientists the ability to edit life itself.

The beginning of synthetic biology started with a landmark publication by Francois Jacob and Jacques Monod in 1961. The paper itself was about their study of the lac operon in E. coli, which led them to discover a regulatory circuit. Creating the vision of one day in the future being able to assemble new regulatory systems from scratch. Nevertheless, it was a flimsy idea, who knew one thought this could be possible.

Time Travel Time

From its origin in 1961, the idea began to slowly gain more and more traction, finally getting a breakthrough after developing molecular cloning and PCR in the 1970s and 1980s. Making genetic manipulation widespread in microbiology research, allowing a process in which scientists get the means to engineer artificial gene regulation. However, many research approaches were still restricted to cloning and recombinant gene expression. Basically, synthetic biology was not yet equipped with the knowledge or tools to create entire biological networks that we can do now.

Then came the mid-1990s, bringing a new era of automated DNA sequencing and improved computational tools enabling the science community to sequence microbial genomes. As the advancement in time and technology we started to discover new techniques for many biological systems and functions. This rapid growth in molecular biology generated new fields of biology. Bringing biologists and computer scientists together in a combined pursuit to synthetically engineer cellular systems.

With the explosion in knowledge and likelihood of that flimsy piece of paper that babbled about hypothetically creating our own biological engineered organism becoming a possibility brought even more popularity to the field

Now entering the 20th century, it brought new light to synthetic biologists with the creation of simple gene regulatory circuits. Might not seem impressive at first, but was a notable breakthrough, as it could carry out functions in a similar manner to electrical circuits. Turning biology into computer science, as simple genetic circuits could be described using simple mathematical models. Bringing elements of computer science, circuitry, and math to life science.

This is the genetic makeup of a E. coli bacteria

This all began with turning E. coli into the perfect molecular biology test subject. This works as we already have an in-depth understanding of its biology. That makes it easy for us to genetically manipulate vast quantities for wet lab experiments.

Fun Fact: During the first month of the new millennium (January 2000), the first reports of genetic circuits that had been engineered to carry out designed functions were published.

During the mid-2000s, synthetic biology began another wave of popularity. The first international conference for Synthetic Biology, was held in the summer of 2004 at the Massachusetts Institute of Technology (MIT) Bringing together researchers from biology, chemistry, physics, engineering and computer science, the meeting was widely lauded for its positive impact on the field, helping to create a community of scientists working towards the singular goal of creating/designing biological systems

With the dawn of mid-2000 century, an important breakthrough took place in the form of a RNA-based systems for synthetic circuit design in E. coli. Other novel inventions in circuit designs continued to appear, such as an AND logic gate.

With the amount of progress made in the field also came the obstacles keeping them from progressing further. To start, we still lacked efficient methods to assemble individual genetic parts into biological circuits, causing us to do many tedious tasks for simple tasks.

The second issue was the lack of an established organization system for characterizing genetic parts based on their functionality. Creating splinters in their current method as a massive amount of time and effort spent on redesigning something that has maybe been already made.

Present 2022

In the present day, with the fullest exposure to the internet and new discoveries making it even easier to make biological circuits, it brought an unprecedented amount of people to the field. Synthetic biology wasn’t just growing in popularity, but both in pace and quality of product. From being able to use an extensive variety of biobricks that can perform complex functions without fail.

Despite that all progress, the greatest breakthrough in the field in recent years was the addition of CRISPR…

What is CRISPR?

For those who don’t know what CRISPR is, it can essentially edit the genome of any living thing! Therefore, to put it more simply, it’s a ctrl+f and Delete protein. One of the most common CRISPR proteins is Cas9.

How does it work?

At the end of the day, a protein means it doesn’t have eyes. So for Cas9 to be able to find the target sequence, we need to give it a guide or in this case a guide RNA (gRNA). Most gRNAs have three main features; the first two are crRNA and tracrRNA, which the lab turns into a Single Guide RNA (sgRNA). The third feature is in the gRNA sequence itself; it is a specific extension at the end of the gRNA which we call the PAM. It has a 2–6 base-pairs length that needs to match with the DNA or else the Cas9 Protein won’t make a Double-Strand Break (DSB) required for its function.

Applications of Synthetic Biology

The applications of synthetic biology are limitless, as it gives us the keys to controlling life itself. We can synthetically create any living organism, produce, or even things straight out of the imagination. Some examples would be hamburger meat that can be made completely synthetic, biosensor/rapid tests for variety of dangerous circumstances and so many more that will blow your mind away.

It’s just one google search away…



Aryan Khimani

I’m 16-years old who is very passionate about using Gene Editing and Machine Learning to disrupt the world of biomedicine, using my knowledge of Python, AI, ML