Coop’s Scoop: Mind over Mainframe – next #CitSciChat discusses citizen science games

By Caren Cooper February 24th, 2015 at 9:29 am | Comment

The next time you get into an argument with your laptop or shake a fist at your computer, try to refrain from calling it “a stupid machine.” That would be gloating. We really are more intelligent than our computers. Case in point, the human mind can solve some puzzles better than computers. On this principle, using game elements in citizen science, called gamification, is a popular approach in biology. That’s the topic of the next #CitSciChat on Twitter.

The next time you want to argue against a group, think twice. Groups can be more intelligent than individuals. On this principle, some game elements often involve creating teams that compete against each other. Within group cooperation, in the context of competition across teams, is a powerful motivator.

The fields most gamified in citizen science – molecular, cell, and synthetic biology – are key to understanding, treating, and curing diseases. Studies of proteins, amino acids, RNA, and DNA can happen in silico (in computer models) and in vitro (in laboratory experiments), but are often too difficult in vivo (in a living cell). Now these serious topics of research are being carried out in gamo. (have I coined a term, in Latin no less?)

For example, figuring out DNA configurations presented researchers with problems that were computationally too intensive for a single computer. At first, molecular biologists looked for a solution with a type of citizen science called distributed computing. Volunteers help research by donating their unused CPU (Central Processing Unit) and GPU (Graphics Processing Unit) cycles on their personal computers to causes like Rosetta@Home and Folding@Home.

screensaver of Rosetta@home

screensaver of Rosetta@home

Unexpectedly, when distributed computing volunteers saw the screensaver of Rosetta@Home, as it illustrated the computer stepping closer and closer to a solution of each protein-folding puzzle, they wanted to guide the computer. Volunteers came to the conclusion that they could solve these 3-D puzzles better than their computers. Researchers and game designers believed in the abilities of their volunteers and declared, “Game on.”

At the cellular level, human minds are important again. One doesn’t have to be a trained pathologist to identify cancer cells and help find biomarkers in these cells. Cancer Research UK takes games very seriously. In their newest game, Reverse the Odds, players identify bladder cancer cells before and after different treatments, which will help future patients know whether their best odds are with surgery or chemotherapy.

Why are people better than computers at protein-folding puzzles? Why is the human mind better than computer algorithms at figuring out how DNA regions align? Why is the trial and error approach of people better than formal techniques and alogrithms of bioengineering RNA? Why are teams smarter than individuals? Why is gamification so popular that, when the online game Phylo launched in 2010, the computer servers crashed, unable to handle the volume of thousands of simultaneous players? Why are there over 37,000 people working (meaning playing) at RNA design puzzle in an open, online laboratory called EteRNA?

For answers to these questions and more, join us for the next citizen science Twitter chat by following the hashtag #CitSciChat. The #CitSciChat are co-sponsored by SciStarter and the North Carolina Museum of Natural Sciences. Anyone is welcome to join with questions, answers, comments, and ideas. Don’t be shy and don’t forget to include the hashtag #CitSciChat so that others in the conversation don’t miss your Tweets. I will Storify each session and post the recap on this blog.

The #CitSciChat guest panelists this Wednesday, February 25 at 7pm GMT (26th in Australia) include:

Phylo, nanocrafter and FoldIt were featured in a recent SciStarter newsletter, check out the rest of the projects here and sign up for the newsletter on the SciStarter homepage to get to know about more.

Citizen science chats take place on Twitter at #CitSciChat the last Wednesday (Thursday in Australia) of every month, unless otherwise noted. To involve people across the globe, chats take place 7-8pm GMT, which is 2-3pm ET in USA and Thursday 6-7am ET in Australia. Each session will focus on a different theme. To suggest a project or theme for an upcoming chat, send me a tweet @CoopSciScoop!

Like your citizen science with a side of fun? Check out these gaming projects!

By Arvind Suresh (Editor) February 23rd, 2015 at 1:00 am | Comment

Citizen science makes serious contributions to our understanding of the world, but that doesn’t mean we can’t have some fun doing it!

Here are five projects that combine science and gameplay to create an exciting experience for everyone.

Cheers!
The SciStarter Team

Read the rest of this entry »

Categories: Apps,Gaming

Nanocrafter: Playing a Game of Synthetic Biology

By Carolyn Graybeal February 22nd, 2015 at 6:00 am | Comment

 

Nanocrafter image

Image Credit: 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 a biosensor, 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.

 

Reports from the Hackfest at the Citizen Science Association conference

By Darlene Cavalier February 18th, 2015 at 1:58 pm | Comment

Thanks to everyone who participated in the Citizen Science Hackfest on 2/11 at the Citizen Science Association’s conference in San Jose, CA! This hands-on and discussion-driven meet-up was a wonderful opportunity for participants to  dream up AND build creative tools to improve the field of citizen science! .

Once we settled into our digs (conveniently situated between the bar and food!) and after our ears adjusted to the noise around us, Arvind Suresh (SciStarter’s managing editor) kicked things off with introductions and each project owner pitched their ideas.
hackfest introductions

 

Steve Gano, our director of product development at SciStarter, organized the pitches into themes.

citizen science hackfest project ideas

We divided the projects into four groups:

1) Platform Interoperability. This team worked on what is needed to better support online data management for citizen science projects . There’s so much work to be explored here. Contact Greg Newman (Gregory.Newman at ColoState dot Edu) if you’d like to join the ongoing dialogue.

 

platforms

platform interoperability citizen science

2) Participant experience: finding projects, submitting and sharing individual points of data. We brainstormed ways to help researchers (biologists, in particular)  subscribe to fresh data alerts for their species and regions of interest from many (wildlife observation) citizen science platforms, and enable observers on those platforms to be notified if their observation was sent to someone. We also discussed the development of a simple, accurate representation of a project’s geographic area of interest which is important not only for validating the contributed data, but also for finding and recruiting potential participants who live or visit the area of interest and may be able to contribute. We’ve decided to continue these discussions and if you’d like to join us, email info@scistarter.com to indicate your interest. 

hackfest finding citizen science projects

 

3) Prototyping a data collection app.  S. Andrew Sheppard and Teal Wyckoff worked on Species Tracker, a concept for a mobile app for biodiversity monitoring, inspired by the WyoBio project.  They used the wq framework to create a simple prototype that allows anyone to upload photos and GPS coordinates together with species information.  The prototype and source code are available online at species.wq.io.

prototype citizen science

4) Updating Wikipedia definition of Citizen Science: Between 80-90% of Wikipedia editors are male, so Dr. Caren Cooper, particularly wanted to encourage women to participate. One concern raised at the hackfest was that there’s not much oversight on who can edit someone else’s contribution so it’s a frustrating experience when someone puts time and energy into a thoughtful definition only to have it wiped out and replaced by more self-serving definitions. Contact Caren Cooper at Caren.Cooper at naturalsciences dot org to get involved in this effort.

wikipedia citizen science

 

As these projects progress, we’ll post updates here.

Special thanks to @MarDixon for providing early guidance and support! She’s a pro at this…and she’s my sister!

And the winners of the #spacemicrobes Microbial Playoffs are…

By Arvind Suresh (Editor) February 11th, 2015 at 9:00 am | Comment 1

bacteria plate

Editor’s Note: This is a guest post by David Coil a Project Scientist in the lab of Jonathan Eisen at UC Davis and a member of the Project MERCURRI team. 

We’ve finished analyzing all the data from the “Microbial Playoffs” part of Project MERCCURI(described here).   Each microbe that was chosen to fly to the International Space Station (list of candidate microbes here) was plated out 6 times on the plates that were analyzed in space.   We looked at three categories; Best Huddle, Best Tip-Off, and Best Sprint.    Here are the winners for each of the three categories:

 

Best Huddle (The microbe that grew to the highest density, really packing into their space)

 

best huddleYuri’s Night, Los Angeles: The microbe “Kocuria rhizophila” was collected on a camera at a Yuri’s Night Party with Buzz Aldrin in Los Angeles. Here are some photos of the team swabbing Buzz Aldrin’s shoe. For an image of the microbe and more information, see the trading card at the Space Microbes web site.
San Antonio Spurs: The microbe “Kocuria kristinae” was collected on the court after a San Antonio Spurs game. Here are some photos of the team swabbing the court and a blog post about the experience. For an image of the microbe and more information, see the trading card at the Space Microbes web site.
Davis, CA: The microbe “Leucobacter chironomi” was collected in a residential toilet in Davis, CA. For an image of the microbe and more information, see the trading card at the Space Microbes web site.

 

Best Tip-Off (The microbe that got off to the fastest growing start straight out of the freezer)

 

best tip offPop Warner Chittenango: The microbe “Bacillus pumilus” was collected on a Porta-Potty handle by Pop Warner Chittenango Bears cheerleaders. For an image of the microbe and more information, see the trading card at the Space Microbes web site.

Academy of Natural Sciences, Philadelphia: Bacillus stratosphericus: found in a butterfly water dish at the Academy of Natural Sciences. Here is a photo of the kids that participated in the swabbing. For an image of the microbe and more information, see the trading card at the Space Microbes web site.
Smithsonian Air & Space Museum: The microbe “Pantoea eucrina” was collected on the Mercury Orbitor at the Smithsonian Museum of Air and Space. Here are some photos of the team swabbing at the Museum. For an image of the microbe and more information, see the trading card at the Space Microbes web site.

 

Best Sprint (The microbe that grew the fastest in any single 24-hour period in space)

 

best sprintParkway Middle School: The microbe “Bacillus horikoshii” was collected on a lobby banister at Parkway Middle School as part of a Broward County STEM teacher’s event. For an image of the microbe and more information, see the trading card at the Space Microbes web site.

Pop Warner Chittenango: The microbe “Bacillus pumilus” was collected on a Porta-Potty handle by Pop Warner Chittenango Bears cheerleaders. For an image of the microbe and more information, see the trading card at the Space Microbes web site.
Mars Exploration Rover (JPL): Paenibacillus elgii: On a Mars Exploration Rover before launch (2004) at the Jet Propulsion Laboratory (JPL- NASA, Pasadena, CA) For an image of the microbe and more information, see the trading card at the Space Microbes web site.
Shown here are the top three microbes from each category, a full ranking of all the candidates will soon be published at www.spacemicrobes.org

Categories: Citizen Science