Archive for the ‘Biology’ Category

Nanocrafter: Playing a Game of Synthetic Biology

By 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.

 

Citizen Science for Your Genes and Proteins

By February 9th, 2015 at 9:10 pm | Comment

dna

Photo: genome.gov

DNA, proteins, and chromosomes are too small to be seen with the naked eye, but there are plenty of citizen science projects that make the building blocks of life accessible to us all.

Here are some great projects that need your help to advance our understanding of what we’re made of and where we come from.

 

Read the rest of this entry »

What is killing California’s trees, and what can you do about it?

By January 12th, 2015 at 9:00 am | Comment

(Eskalen Lab. UC-Riverside, Reproduced with permission)

Trees infested by the polyphagus shothole borer in California (Eskalen Lab. UC-Riverside, Reproduced with permission)

Editor’s note: This post originally appeared on the author’s blog. Project SCARAB is one of more than 800 great citizen science projects on SciStarter. Use our project finder to find one that you can participate in!

The great thing about living in a major port city such as Los Angeles is having access to ideas and goods from the around the world. However, the port of LA, and by extension every trade conduit branching off from there, takes the chance on cargo containers carrying an invasive species. In 2003 one such species, the polyphagus shothole borer (PSHB), was spotted in Whittier, a suburb of Los Angeles. In the intervening decade it has quickly spread to many of the trees in southern California. Read the rest of this entry »

SciStarter’s Top Fourteen Citizen Science Projects of 2014!

By January 5th, 2015 at 7:00 am | Comment

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As we ring in the New Year, we’re celebrating the 14 Top Projects of 2014! These are the projects that received the most visits on the SciStarter website. Resolve to do more citizen science in 2015!
We’ll help you with that goal. Happy New Year!

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Photo: Mike Hankey
1.  American Meteor Society – Meteor Observing
Report meteors and meteor showers online or with an easy smartphone app and help scientists determine their astronomical origins. Get started!

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Photo: NASA
2.  Perfect Pitch Test
If you have perfect pitch, this project needs you! Just take a brief survey and a quick pitch-naming test to help determine if perfect pitch differs for different timbres. Get started!

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Photo: NOAA
3.  Digital Fishers
Only have a minute to spare? Use it to analyze short video clips of amazing deep sea life. Get started!

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Photo: EyeWire
4.  EyeWire
With EyeWire, you can play a captivating image-mapping game that helps maps the retina’s neural connections. Get started!

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Photo: LLNL
5.  American Gut
Our guts contain trillions of microbes. Sample and identify the organisms in your gut with this cool project. Get started!

KONICA MINOLTA DIGITAL CAMERA
Photo: Dennis Ward, Project BudBurst
6.  Project BudBurst
Do you enjoy following the trees and plants in your yard as they leaf out, flower, and produce fruit? Record your observations and submit them to BudBurst. Get started!

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Photo: NASA
7.  Loss of the Night
Stargazers take note- Identify and report all the stars you see at night in order to measure light pollution. Get started!

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Photo: NASA
8.  SatCam
Use your smartphone to record sky and ground conditions near you, and SatCam will send you satellite images for the same area. Get started!

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Photo: NPS

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Photo: Victor Loewen
10.  Celebrate Urban Birds
Observe the birds outside your window and report the presence of 16 common species. How many will yousee? Get started!

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Photo: DDQ
11.  Dark Sky Meter 
Use your phone to measure the brightness of the night sky and contribute to a live map of global light pollution. Get started!

1312.  World Water Monitoring Challenge
Curious about your local water quality?  This project provides a simple kit for you to test water temperature, pH, and more. Get started!

1413.  Ignore That!
Help scientists study the human mind by playing a 5-minute game that determines how distractable you really are. Get started!

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Photo: NASA
14.  GLOBE at Night
This is a great project for children and adults who enjoy looking up at the night sky and want to track light pollution. Get started!

Citizen Scientists Keep Watch for New Epidemics

By December 2nd, 2014 at 7:53 pm | Comment

Iain Wanless / Flickr. Dying crows were one early sign of West Nile Virus entering North America

Iain Wanless / Flickr. Dying crows were one early sign of West Nile Virus entering North America

In 1999, crows began dropping dead in the United States. A crow here, a crow there – nobody thought much of it at the time, says Joshua Dein, a veterinary scientist working with the University of Wisconsin-Madison. But this was the precursor to outbreaks of the West Nile Virus in North America. Since scientists knew the virus infected crows at a near 100% mortality rate, Dein says it is possible public health officials could have been forewarned about the oncoming virus had someone been monitoring the crow situation.

But this is a goal easier said than done. Early detection of disease events that affect wildlife is often difficult to achieve because sometimes the evidence is diffuse and hard to collect. “When you have hundred dead ducks in one place that usually gets attention. You usually when you get ones or twos – not so much,” Dein says. Read the rest of this entry »