Engineering life, one gene at a time

Jan 18, 2016 Blog 0

Synthetic biology offers possibilities of writing new DNA sequences and building biological components that are drawing even artists and designers to it. The field, however, is riven with ethical questions

The White Queen’s reply to Alice’s “one can’t believe impossible things” is one of the more popular quotes from the 19th century classic, Through the Looking-Glass. With imperious hauteur, she tells Alice, “I daresay you haven’t had much practice…Why, sometimes I’ve believed as many as six impossible things before breakfast.”

Today, it’s easy to imagine 10 impossible things before breakfast, and chances are that the impossible is well on its way to becoming possible by supper. Imagine microbes engineered to glow like a string of fairy lights, or reprogrammed to destroy malignant tumours. It’s almost as if the limits of what is possible and probable have become a function of our imagination.

And a large part of this can be attributed to synthetic biology or the application of the principles of engineering in biology where scientists not only read or decode DNA, but also write new sequences from scratch and build biological components to either imitate nature or create something totally new. Think of bacteria as hard discs with storage capacities that can be programmed to do things.

Bio-engineering at play

Anjali Thomas
The term synthetic biology has been around for more than a decade, and is a mix of multiple facets of science. As Dr. Mukund Thattai from the National Centre for Biological Sciences (NCBS), Bengaluru, points out, chemical engineers existed before synthetic biology. So did genetic engineers and metabolic engineers.

“Now these communities come together and they see themselves as making large-scale manipulations of existing organisms in different ways rather than manipulating one gene at a time,” says Dr. Thattai, who got involved with synthetic biology during his Ph.D. at the Massachusetts Institute of Technology (MIT). His lab at NCBS uses ideas from engineering to study how complex cells are put together from simple parts.

In recent years, synthetic biology has attracted artists and designers. While she was a research student at MIT Media Lab, Julie Legault, who has a background in design, built a “playful” bio-engineering kit called Amino biolab, which allows anyone to experiment with synthetic biology at home. The first iteration of the desktop laboratory, which Ms. Legault describes as an “easy-bake oven for the 21st century”, has all the necessary hardware to engineer and grow cells.

“It works with refillable DNA programmes that contain transformation liquids, a strain of safe E. coli bacteria and the food it needs to grow,” she says. Detailed instructions show a user how to put the DNA programme into the bacteria, cultivate it [there are sensors to monitor how fast the E. coli is growing], and make it glow like a firefly, for example. It creates a growing living nightlight,” says Ms. Legault, who is not a scientist, but was drawn to bio-engineering and felt the need to “demystify” it. She plans to launch different DNA programmes or ‘apps’ that will let buyers tinker with bacteria to create new smells, perhaps brew beer and so on.

At $499-699, the kit is far too expensive for most Indians; through economies of scale, she hopes to bring the price down to a few hundreds. But for science to have an impact, it has to be more egalitarian. And Bengaluru artist Yashas Shetty is trying to do just that.

Back to the future

Far away from Boston, his studio at the Srishti Institute of Art, Design and Technology in Bengaluru is the antithesis of the pristine chaos of the MIT Media Lab where Ms. Legault built the prototype of her biolab.

The best way for a non-scientist to understand science is to get to deconstruct it, says Mr. Shetty, an artist-in-residence and faculty member at (Art)ScienceBLR, Srishti’s public laboratory. A rudimentary PCR DNA amplification machine with green tubes, bulbs and fans lies on his workbench next to a transparent box filled with what appears to be bits and pieces of wire and circuits. It’s a microscope made from an inverted webcam. He’s also assembled a centrifuge from a blender and incubators from a bulb and two discarded computer fans.

In 2009, Mr. Shetty started experimenting with synthetic biology and something called BioBricks, standardised DNA sequences that can be used to design synthetic biology circuits where the biological parts of a cell are designed to perform functions akin to electronic circuits. At the time, he was an artist-in-residence at NCBS. “I was an artist in a science institute. Synthetic biology allowed me to be Frankenstein. I felt I could build things, create life,” he says, the excitement of his recollection tinged with regret.

BioBricks, created by synthetic biologists including Drew Endy and Tom Knight, are like Lego blocks that can be assembled or taken apart to manipulate existing or create new biological systems. Some of the standardised parts include a promoter (that initiates the transcription of a particular gene), coding sequences (it’s the part of the gene’s DNA or RNA that codes for protein), terminator sequences, and so on.

“BioBricks were always meant to be sort of a thought experiment. A conceptual exercise, where we are imagining a world which isn’t here yet. It was never meant to be the actual way synthetic biology was done. And the genius of Drew and Tom Knight and others was that they ran the iGEM (International Genetically Engineered Machine) competition,” says Dr. Thattai, who has, over the years, taken many teams to iGEM. It’s open to undergraduates, high school students… and in Mr. Shetty’s case, students of design.

“When we first approached MIT and iGEM, they were gobsmacked,” says Mr. Shetty. Here was a bunch of design students asking to be a part of genetically engineered competition. “They got in touch with Mukund who assured them that we knew what we were doing.” A set of standard biological parts or BioBricks were promptly shipped to them, and they had to use these parts or create new parts to build biological systems in living cells.

The ethical dimension

For the 2009 iGEM, under the guidance of Mr. Shetty and Dr. Thattai, a team of undergraduate art and design students got a bacterium to emit the smell of rain hitting fresh earth. They won a bronze medal for the project.

But Mr. Shetty was disturbed by the experience. He felt that the ethics of synthetic biology were not being discussed with as much vigour as the applications themselves. To prove his point, the next year his team submitted a thought-provoking experiment: they successfully fed transparent worms called C. elegans bacteria that were engineered to disable some of their neurological functions.

He has since moved away from synthetic biology, but in many ways the experiment with BioBricks has made the ethical debate all the more real for people who are not scientists. It allows society to have conversations that would otherwise have been in the realm of the abstract. “So now, let’s start talking about the ethics, regulation, the crazy possibilities. If I had started that conversation before, you would have plugged it with any other kind of fanciful extrapolation. That’s another great social role of having this community built up,” says Dr. Thattai.

It’s bringing artists and scientists out in the same arena, and perhaps it’s a tenuous bridge linking two cultures: science and art.

anjali.thomas@thehindu.co.in The Hindu