The Circle of Synthetic Life
In this course we’ll go step-by-step through the process of a creating a simple GMO. We start with a normal, boring, regular old E. coli bacterium. Then we introduce a small circle of DNA called a plasmid, carrying the genes of our choice. We grow the transformed cells, which carry our plasmid DNA and replicate it alongside their own genome. Finally we harvest the cells to collect and purify the plasmid DNA inside. We end up back with the same plasmid again, except now we have lots more plasmid DNA ready for future modifications. Along the way we will get familiar with DNA sequence editor software, allowing us to read the exact DNA sequence and features of the plasmid that we are transforming. We are also going hard into math with a robustly quantitative model of growing cells. Ready?
Unit 1: A Passion for Plasmids
A plasmid is a simple, small, self-contained circle of DNA. Synthetic biologists love plasmids because they are easy to move into cells and out of them again. In Unit 1, we review the important functional features of plasmids. Then we use DNA sequence editor software to take a closer look at how these features are connected to specific DNA sequences. We’ll use plasmids and sequence editor software literally millions of times in this course; they are both extremely common tools in all kinds of synthetic biology and biotechnology. So feel free to let yourself fall in love, geek out, and learn everything about them.
Plasmids are really actually this exciting for real.
Unit 2: DIY DNA Factories
Some people are satisfied with just a few plasmids. We call those people “not synthetic biologists.” In a synbio lab, we usually want to have tons of plasmid DNA on hand, because most procedures for modifying DNA require that we start with lots of DNA. In unit 2, we go through some laboratory protocols that we use to make more plasmid DNA. Our friends the E. coli are happy to help with this, taking up foreign plasmid DNA and then replicating it as if it were their own genome.
With a good attitude, this dog will go far.
Let me be real with you for a minute. In this unit, like always in this course, we show real laboratory protocols in real time. We thought about showing simplified teaching protocols that are easier to follow. But then we were like “the students are smart enough to handle the real thing.”
To help you get the most out of these videos, we offer these tips.
- Don’t worry about specific details like time, temperature and quantity. These things will change anyway for different versions of the protocol.
- Do ask yourself about the overall purpose of each step of the protocol. How does this change things and why?
- Put the videos at 1.5x speed if it is a boring part that you already understand.
- Pause and google stuff if you see something new. We won’t be offended if you learn something from a different website.
Our overall goal here is just to get familiar with the big picture and feel at home in the lab. If you understand the purpose of the protocol and recognize the equipment, then you are doin’ fine.
Unit 3: Bacteria Divide and Multiply
Bacteria are very good at growing. Billions of years of evolution have shaped them into perfect little growing machines. In synthetic biology, we harness the power of bacterial growth to absolute maximum effect.
In unit 3, we will learn to precisely measure growth and to model it quantitatively it. Often, we will want to capture bacteria exactly when their growth rate reaches a maximum, because this is when they are the most healthy and active. Other times, we will need to predict how much bacteria will grow over time under given culture conditions.
Differential equations are the correct mathematical tool for modeling systems that change over time, like a flask of growing bacteria. This unit is the first time that we introduce differential equations. If you’ve had a year of calculus, the equations that we use should be easy for you. If you are a total math n00b, then you may find this unit intimidating.
Everything is fine.
Here is our advice for someone coming at these models for the first time: Don’t worry about trying to solve the equations. That’s not really what these equations are for. Instead, focus on what each term in the equation represents in the real world. C is the number of cells. T is time. G is the growth rate, and so on. The equations in our models are meant to express relationships between real world things. When you understand a system precisely, you will be able to translate back and forth between mathematical language and a verbal description.
You may want to brush up on the basics of calculus or differential equations.
Unit 4: GMOs OMG 👍 😱 👎
We have no illusions: if you are taking this course, you probably consider yourself to be pro-GMO. We hope there are also a few GMO opponents out there, and for sure there are plenty of you who have no strong opinions yet.
Synthetic Biology One will try hard to maintain an objective and nonjudgemental voice when it comes to the politics of GMOs. We will never say “We are the scientific authority and only experts like us have the right to say what is safe and good.”
But we will take one specific position on the GMO debate: We assert that the debate has more than two sides. Declaring yourself for or against GMOs will not help you when real GMO policy involves dozens of important questions connecting ethics, economics and science. Being a real synthetic biologist means having a long-form opinion on many issues, not just “yay” or “boo.”
To justify our position, we will present various opinions that we’ve curated from around the web. You will see that they agree and disagree on a variety of points in a variety of ways. In the videos, we read everyone’s statement in the same voice and try to make all opinions sound equally authoritative. The purpose of this is to focus on the details of the opinion itself, rather than our natural instinct to agree or disagree.
Once you’ve seen many opinions and broken them down into pieces, you may be able to re-assemble them into your own personal, comprehensive, nuanced, GMO policy position. Then we’ll all go on the internet and tell the trolls why they are morons. It will be a lovely time!