Becoming Fluent in the Language of Life
During university, I was the only person in my student flat who could speak just one language. Welsh, Chinese, French and Vietnamese all featured prominently during most friends’ visits and calls home, except mine. Feeling linguistically deficient and hoping to spend the summer abroad, I became determined to try my hand at French.
My experience will be familiar to many who have tried picking up a language as an adult. The basics seemed straightforward enough, and I worked hard until I felt confident I could hold my own in a French conversation with my housemate Claire. I survived the initial pleasantries well enough (ca va bien merci, et toi?), and understood the general gist of what Claire was saying to me. Then she paused expectantly. The time had come for me to reply, but I just couldn’t form the words. Clearly I had much more work to do.
French may be the language of love, but what about the language of life? If the dictionary and grammar rules are stored and encoded in DNA, the words themselves are the proteins which diligently work inside every cell of every life-form. Scientists understand proteins about as well as I did about French when I initiated my conversation with Claire.
Proteins are large molecules that make up a quarter of the contents of a cell, and they have thousands of different roles to play. The more we learn about proteins, the better we can explain how we develop in the womb, get energy from food, detect bacterial invaders and respond to drug treatments when we fall ill. Proteins also have their uses on supermarket shelves, such as in biological washing powders and for breaking down the lactose in dairy products for those who cannot tolerate it.
Yet as I discovered my student flat, the gap between comprehension and creation is not small. The same appears true for protein research; after decades of researching the natural varieties, only now is the prospect of designing brand new ones looking feasible. Ross Anderson and his lab at the University of Bristol are among the first researchers to explore this possibility. “We are now at the stage where we wish to use the knowledge we have gained from the past hundred or so years and develop simple naturally-inspired proteins which we can use”, Ross explains.
Proteins are made by chaining together small molecular units called amino acids, carefully arranged like letters in a paragraph. There are only twenty varieties of amino acid, but the complexity and diversity of proteins arise from their arrangement. Put the right letters in the right place and you get a sentence or even a sonnet. Get it wrong and you risk an embarrassing typo or unintelligible gibberish.
Ross’s lab is trying to piece together the rules that distinguish sense from nonsense by trying and testing new proteins from scratch. “By building proteins from the ground up we are really beginning to understand the versatility of these twenty amino acids and how nature has crafted an immense variety of functional components from them,” he says.
So far they have been successful in designing working drafts of new proteins which, which they call maquettes. French for “scale model”, the original maquettes are useful tools for sculptors as rough guides during the design of grand sculptures. Maquettes are inspired by their natural counterparts but are much more straightforward and useful because they don’t come with evolutionary baggage.
The proteins in our cells evolved in a messy, inconstant world. Thanks to changing environments and blind chance over billions of years, it’s often impossible to tease apart precisely why natural proteins turn out the way they do. Meanwhile the manmade maquettes show clear development as researchers draft and redraft ever-improving versions, and it’s much easier to see the effect of each adjustment.
The maquettes are showing tremendous potential as tools. After designing a maquette which binds and stores oxygen, Ross’s team only needed to make a few small changes to convert it into one which can harvest light for energy. In the right bacterial system, this could become living solar power. Further into the future, new proteins could be put to work producing cheap and sustainable fuel or pharmaceuticals, substances which presently must be either extracted from the Earth’s ever-depleting resources, or synthesised using harsh chemicals and expensive treatments.
Such goals may be many years away, but as Ross puts it “once a certain level of sophistication is reached with protein construction, our imaginations will be our limit. It’s an exciting time to be in this field”. We’ve been listening and learning from the language of life for so long, it might be about time we start talking back.
This post was my (non-shortlisted) entry for the 2014 Wellcome Trust Science Writing Prize Competition in association with the Guardian and the Observer. Housemate’s name has been changed (because it’s actually the same as my own and that might have gotten confusing…)
Header image credits: Word cloud (“life” in various languages) generated by me using WordItOut. Surrounding proteins (actin filaments for the edges and glutamine synthetase at the corners) from this educational poster created by the amazing PDB.