Crowdsourcing Science: Engaging the Public to Help Solve Complex Puzzles in the Laboratory
Crowdsourcing Science: Engaging the Public to Help Solve Complex Puzzles in the Laboratory
by Jonas Calsbeek
Sometimes scientists need help answering complex questions, and more people contributing can lead to faster answers to those questions. Advances in technology over the last few decades have connected humans globally more than any time in history, and now this technology is connecting citizens with scientists, too. Several websites and initiatives allow the public to participate in real science, like counting fish on a live camera feed, running simulations of protein folding, or mapping neurons in the brain from the comfort of their own computers. There are many ways for the public to engage with science, and the following are a few of these remote opportunities that anyone can join.
Zooniverse: A Platform for Citizen Science
Zooniverse is a massive platform for research that allows anyone and everyone to participate in science by building their own research project or working for projects that have already been created. Once a project is created, it is made available so that others can sign up to volunteer and help.
Examples of projects currently available include transcribing written correspondence between anti-slavery activists from the 19th century, counting baby herring that are swimming out to sea on camera, or deciding which variable star is seen at the center of the galaxy.
Users of this platform can filter projects by discipline to find research relevant to their skills or interests and communicate with other volunteers via a forum known as Zooniverse Talk. Check out their website to learn more about current projects and the publications that have resulted from their work.
Homepage: https://www.zooniverse.org/
Embedded Video: https://youtu.be/F-B8gXJyMHc
Publications: https://www.zooniverse.org/about/publications
Folding@Home: Harnessing Processing Power
During the lockdown resulting from COVID-19, I learned about an interesting project called Folding@Home, that asked the public to contribute in studying the spike glycoprotein that the coronavirus uses to enter human cells. This project was in collaboration with the “COVID Moonshot,” an initiative aimed at developing a new anti-viral therapy for COVID-19 at a low cost, and without patents.
After signing up to help with their project, software on a computer at home allows the user to decide when and how much computing power to contribute to various ongoing projects studying cancer and other diseases involving proteins. The newest version of their software allows the user to prioritize assisting specifically in COVID-19 projects above others. By combining all of the volunteers’ processing power, the modeling of protein folding can be performed much faster, and in larger quantities.
Folding@Home broke records earlier this year for total computer processing power, when they exceeded the exaFLOP barrier (one quintillion floating-point operations per second) due to the number of citizen scientists participating at one time. To put this in perspective, you would need to perform one calculation per second for around 31,688,765,000 years to match the processing power that an exaFLOP computer performs in one second. Check out their website to learn about how this work is producing publications and contributing to therapeutic development for cancer, infectious diseases, and neurological disorders.
Homepage: https://foldingathome.org/
COVID Moonshot: https://covid.postera.ai/covid
Publications: https://foldingathome.org/papers-results/
Foldit: Game-based Protein Folding and Design
Foldit is another protein folding site that allows the public to participate, but this time using a gaming format to incentivize the folding of protein residues in a competitive manner. Because proteins are so complex and vary in size, they can fold in the body in many ways, complicating existing computer simulations to model how they might behave in nature.
This is where human intuition can be harnessed through crowdsourcing to improve protein folding simulations, providing a better understanding how a protein will actually fold in a biological setting. This information not only provides researchers with new potential drug targets for different diseases, but the software also allows players to design their own novel proteins that can be developed as future pharmaceutical drugs.
After protein structures are correctly predicted or designed, researchers can take these leads into experimental trials to determine if there is biological plausibility to the finding. Interestingly, players are credited for their contribution in many publications with authorship under the name “Foldit Players.” Check out the TedxVancouver Talk, or their website to learn more about how to get involved with the game.
Homepage: https://fold.it/portal/
Embedded Video: https://youtu.be/uBA0vKURH3Y
Publications: https://fold.it/portal/info/about#folditpub
Borderlands Science: Sequencing Microbial DNA
One unique approach to crowdsourced science uses a strategy within a current video game, Borderlands 3, using a minigame that makes microbial genotype sequencing fun. The Microsetta Initiative collected thousands of fecal samples and ran DNA sequencing on the microbial content, producing vast datasets containing millions of sequences. While computers are good at some jobs, they are not great at mapping DNA sequences, and upstream errors cause downstream problems in analysis.
Humans are more efficient with this sort of task, and the gaming platform provides an interesting way to combine the size of the Borderlands community with these challenging problems. Borderlands Science took the millions of sequences collected and broke them up into smaller “bite-size” puzzles for players to solve. By placing correctly colored blocks within an empty grid, you can help map the DNA sequences and correct errors from previous computer-based analysis at the same time.
In order to play, a player can use the Borderlands Science machine (on Sanctuary 3) in the Borderlands 3 video game to get started. Completing puzzles will provide critical data to the scientists, and the player will earn currency to spend on their character in the Borderlands 3 game. The main goal of this project is to produce an entire library of microbial data to influence human healthcare, exercise, and diet recommendations.
Homepage: https://borderlands.com/en-US/news/2020-04-07-borderlands-science/
Embedded Video: https://youtu.be/L_mH6Ak_Ny0
Microsetta Initiative: https://microsetta.ucsd.edu/
Eyewire: A Game to Map the Brain
Eyewire is another great example of how the combination of gaming and crowdsourcing can be exploited to help solve scientific challenges, like mapping the human brain. When you arrive to their website, you need to create a username and sign up via email to begin the game. Once inside the game, you will click the “Start Playing” button to begin the 5-step tutorial which introduces players to how the game works.
Basically, the human brain has been spatially divided into 3D cubes, and neurons from the human brain are being mapped by players one at a time, inside these cubes. The left side of the screen displays an empty 3D cube where neurons are mapped, while the right half of the screen contains the source image that is used to align the neuron within the cube.
Once a player has mapped a neuron and synapses inside the cube, the result can be submitted for quality checking, and the player is awarded points for how much time it took, how much volume they added, or how similar their contribution was to other players for that cube. Check out their homepage or the tutorial video to learn more about how to play.
Homepage: https://eyewire.org/explore
Embedded Video: https://youtu.be/zMmjGExpDP8
These projects and websites are just a few great examples of current efforts by researchers to engage the public with scientific exploration. As laboratory technology advances, so does the ability to generate massive datasets that need to be processed and analyzed by computers, and ultimately validated by humans. Connecting these datasets with eager volunteers from the public can expedite and improve the analysis, and many of these data will be open source to benefit the public. As our society adjusts to the consequences of COVID-19, these projects and websites offer ways to remain engaged in science no matter what field you are in or where you are quarantined.