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My biology research is applied! What does that mean?

A lot of scientists do research do discover something that is happening in nature and that was previously not known. In biology, this will be true for all the famous scientists you know; think of Darwin – he found out how evolution works, Crick, Watson, and Franklin – they disocvered the structure of DNA.

But if you think about other disciplines, like physics, and you’ll realize that the closer in history you look, the more they went from discovering things, to inventing things! Take Isaac Newton, everyone knows him as an incredibly important physicist from the 17th century who discovered the law of gravity – but do you know anything he invented? Then take Michael Faraday, who lived a century later; he discovered principles of electromagnetism. But he didn’t leave it at that, he used his knowledge to apply it to an invention: the electric motor! Again 100 years later lived Nikola Tesla, and although his study was physics – you don’t know him for his discoveries anymore. You know him only because of his inventions (too many to list, among others radio, the induction motor, and alternating current). Physicists developed from discoverers to engineers.

The same is happening in biology at the moment, we are currently where physics was in the 19th century: most scientists are still trying to discover something, because there is still so much that we don’t know. But some biologists stopped trying to find out things, and instead start trying to use the knowledge to invent things. Similarly to physics, we also call ourselves engineers.

Instead of mechanical machines, I engineer biological machines – enzymes. In every cell, enzymes are doing the most important tasks, they do chemical transformations. For example, humans need to breath air, because they require oxygen. The oxygen is used to make energy, and in that process oxygen is transformed into water. This is a chemical reaction, and it is only possible because an enzyme helps it happening – it catalyses the reaction. Another example is food – we eat, because we need to make the building blocks that make up our body. But we can’t just take a piece of a hamburger and attach it to our biceps, first, we need to break the hamburger down into small parts – its individual molecules. Next, we shuffle around some atoms, stitch the molecules together in a different fashion, and only then do we have a new muscle cell. All of this is catalysed by enzymes – the breaking down of the food down, the atom shuffling, and the molecule stitching.

Scientists like me realized that this these reactions are not only essential for us to survive, they are also sometimes incredibly useful for something that humans like to produce. The chemical industry built huge plants to also transform one type of molecule (such as the ones gained from crude oil) into something we want (such as plastic), and the pharmaceutical industry produces drugs in that way. They all use chemical catalysts, for example heavy metals, which are often really hazardous and create a lot of waste that polluts the environment.

My aim is to stop people from using chemicals that are bad for the environment, I want them to use enzymes instead. They are natural, which makes them both sustainable as well as degradable. Also, they work much more efficient, because nature has evolved them for millions of years to work extremely well. The only problem is, they are not so easy to produce in big amounts and often don’t like to work in the conditions that the industry prefers: a big reactor tank, with high pressure and temperature for example.

For that reason, I engineer the enzymes. That means, I exchange some of the parts that make up the enzyme (its amino acids), and see if they work better. This requires quite some experience, first, you need to know how to change the amino acid (you change its gene), then how to produce an enzyme (we let bacteria grow and convince them to make the enzyme for us), then you need to isolate it (we use a trick that makes them stick to a material that lets us fish them out), and then you need to test its function (for which we need complicated analytical machines that, for example, meausure the mass of the molcule that the enzyme produced). But we have many other tricks up our sleeves, for example, we can determine the three-dimensional structure of our enzyme (using something called x-ray crystallography), and then we can look at the structure in the computer and think what parts are the best to exchange.

Right now, I’m trying to engineer DNA polymerases. These enzymes copy DNA, and the reason we engineer them, is because we want them to copy other molecules as well. DNA is a very useful material, that’s why all the cells on the planet use it, but that also means that every cell on the planet can degrade it. Certain types of DNA are more and more used as drugs to treat diseases, but because the body can break it down so quickly, patients have to take a lot of the drug to make it effective. If we change the chemistry of the DNA a little, the body will take much longer in breaking the drug down. That is why we want to convince DNA polymerases to work on DNA-like molecules, to make these special drugs in an easier way.