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Nanocrafter: Playing a Game of Synthetic Biology (Repost)

This post was originally published on January 22 at the CitizenSci Blog and is reposted with permission from the author under the Creative Commons License.

Carolyn Graybeal trained as a neuroscientist and, in addition the intricacies of the human brain, she is interested in science education and how current teaching practices influence society’s understanding of science.

Image courtesy of Nanocrafter
Image courtesy of Nanocrafter

On its surface, it looks like just another science puzzle game. In reality, the game is part of a broader goal to enable non-scientists to contribute to synthetic biology research.

‘It’ is Nanocrafter, a project created by researchers and game developers at the Center for Game Science at the University of Washington. They are the same team behind the citizen science project FoldIt.

“Most citizen science games are designed to gather data for a specific research question. Players may need to be good at pattern recognition, abstract reasoning, or other cognitive skills. Our focus at Nanocrafter is different,” says Nanocrafter Project Lead Jonathan Barone. “The project isn’t intended to address any existing research. Rather, we are interested in developing a user community that is familiar enough with the principles and parameters of synthetic biology to generate new ideas, identify new questions and create their own solutions.”

Synthetic biology is an engineering discipline within a biological context. The field uses techniques and principles from a number of different disciplines to create biological devices and understand biological systems. Synthetic biologists use biological components like DNA, RNA or proteins as their building materials. For example, scientists can insert DNA or proteins composites into a bacterial host to increase or refine a biological pathways involved in drug synthesis. In other cases, the molecules are used in ways that are unrelated to their normal biological function. A DNA fragment can be constructed as abiosensor, fluorescing in the presence of a pathogen.  Or in a particularly wild example, DNA can be used to store data like a computer hard drive.

But these are complex tasks. Before users start working on these kind of problems, they must master the basics.

The Nanocrafter game teaches users about basic DNA biochemistry and how to manipulate DNA reactions, eventually enabling the player to create logic circuits or mechanized structures. Their video provides examples. In the game, players organize colored puzzle pieces to react in specific ways. The behavior of the puzzle pieces mimics the principles of DNA nucleotide-nucleotide pairing, nucleotide chaining and double helix formation. In the game, only certain puzzle pieces can pair up and pieces only form chains and double strands in a precise hierarchy of reactions.  This might seem overwhelming but the game eases player into the rules, step by step.

“Once users master the principles, they can try our biweekly challenges. Challenges might replicate existing research or be a problem the Nanocrafter team thought up,” explains Barone. “While replicating published data is always useful, it is when users create their own solutions that we start to see really interesting and exciting stuff.  If we can demonstrate that player submissions are theoretically sound, we can present them to scientists to try in their labs.”

Of course if that is too much structure, users can always play in the ‘sandbox’. The sandbox is a completely open ended format with no rules or defined goals. One player created a ‘flagellum’ from DNA, which ‘though not scientifically interesting (or even possible)’ says Barone, speaks to the creativity and fun people seem to have with Nanocrafter.   User designed solutions to past challenges include strands that assemble into a three-way junction or strands that form long repeating polymers.

Though they have a community of over one thousand individual users, posted challenges only get half dozen responses. Moving forward, the Nanocrafter team wants to increase their user base and are hoping to increase the computational and modeling capabilities of their online interface.

If logic, creativity and a little DNA pique your interest, be sure to check out Nanocrafter.

 

Discussion
  1. Along with advances in technology today, as well as the arrival of risk commensurate with that progress. The last few years video games, both offline and online, is growing rapidly. Demand not only the children in big cities, but also adults and in small towns and even villages.

    Playing games at first not be patalogis or interfere with daily activities, but if the addiction can interfere with child development. In 2013, one of the psychiatric hospital in Jakarta, has treated more than 11 patients of children and adolescents are addicted to the game. 5 of them in intensive care because of a serious psychiatric disorder.

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