Thursday, January 30, 2014

Gamers-turned Scientists

I wonder if soon you will find this video game on your Xbox. Yes, in my micro-world at science publishing, Crowdsourcing research is being tossed around as an idea on how to get those much needed funding in a climate that's experiencing a long dry spell. But this took my breath away. In which world does Biochemistry and Gaming go together and get funded too?  Sure, I've already written about having fun in the lab, and making a biotic game out of paramecium here, and there's also FoldIt mostly for biochemists who want to play with protein folding on their spare time, but EteRNA is different. It allows people who do not have PhD or science background for that matter try their hands at solving complex ribonucleic acid (RNA) structures. Who would have thought that RNA will be the next hot videogame??



http://www.strangerdimensions.com/2012/08/28/eterna-played-by-humans-scored-by-nature/
http://www.strangerdimensions.com/2012/08/28/eterna-played-by-humans-scored-by-nature/
 
Coming from the same group that developed FoldIt, EteRNA was developed by an Assistant Professor of Computer Science at Carnegie Mellon University to challenge gamers in solving complex scientific problems. Ah! My husband, a CMU alumni, will surely be proud of this one. And yes, that's the same university that gave you Spock 2.0, Zachary Quinto. This university just oozes of geek charm.  What can I say?

What is EteRNA about? I especially like this tag line "Your efforts will help reveal new principles for designing RNA-based switches and nanomachines -- new systems for seeking and eventually controlling living cells and disease-causing viruses. By interacting with thousands of players and learning from real experimental feedback, you will be pioneering a completely new way to do science. Join the global laboratory!" And this:

What good stuff am I contributing by playing?

Besides purely biochemical advances, EteRNA is a radical experiment in citizen involvement in cutting-edge laboratory science.
In my mind, EteRNA achieve opposite what most games usually do.  I always think of games as a medium that transport you to another dimension; to create that fantastic world, even in an era of your choosing.  Eterna does the opposite - it brings gamers from the virtual world to reality.  What they do with this game is actually applied science.  The result - players, young and old, discover new rules in RNA folding that the scientific community did not know before. Of course, there's no royalty, but hey, high score is what gamers go for right? And as a bonus, they are now co-authors of a paper published in a top tier publication, PNAS. How many authors in all? 37,542 authors, only 10 of whom are scientist.  Congratulations to all 37,542 of you!

Thursday, January 23, 2014

Science of snow and a fond farewell


 

White

whispers,

    f

       l  o

            a

         t

           s,

clumps,

traces its wet finger

on branches and stumps.

White dazzles day

and turns night

inside out.

 


By: Joyce Sidman

 

Having grown in the Pacific islands just north of the equator, I've always had a great fascination with snow. When I was little, I secretly wished for even just a snow globe for my holiday present, but those were also uncommon in a tropical country. While lots of folks in the northwestern hemisphere, Arlington area included, would complain or panic about the predicted coming of snow, tropical islanders can only dream of what it would feel like - to see, to touch, to taste - this white wonder. So much so that when Mt. Pinatubo erupted in 1991, and the light grey ash began to fall, I, along with confused children in Manila, momentarily thought that it was snowing! It is only if you have not seen snow, that you will understand the yearning to see it. The closest you’ll ever get is through your imaginings, or if you have one, a television.


These past weeks, I am thinking about snow more than ever. Perhaps that childhood fascination lingers that is why I feel less daunted about our impending move to Minnesota than I ought to be. I love the idea of working from home while watching the snowflakes lazily float silently to the ground. I guess that snow fatigue would set in at some point, conceivably while shoveling in -40 F weather. But perhaps it would take a few years still. All I know is I’m moving somewhere magical, because snow is magic, right?
 

Because science makes magic real, I couldn’t help but ask “Where lies the magic in snowflakes?” Contrary to what people may think, snowflakes are more than just frozen rain. To form, the water droplets have to be at a temperature less than freezing, but snowflakes are actually made up of 180 billion molecules of water! And just like any crystal, each and every snowflake needs a seed for nucleation. A water droplet condenses on a speck of dust impurity, and as it freezes, other droplets condense, and the crystal grows. The crystal gets heavy, and starts to fall to Earth.

Did you ever notice or wonder why most snowflakes are hexagonal in shape? It's because of the way water molecules fit together. The water molecules crystallize around the dust particle in a hexagonal lattice, which is stable between -100 °C and 0 °C. These hexagons can stack in sheet called 'facets', which can be slow-growing if it is smooth, and faster if it is rough, consequently defining the shape of the crystal. Those that fall to the ground can range in size from 0.2 mm to 5 mm. Any smaller will be too light; any bigger will be too fragile that they willl remain afloat.

 
No two snowflakes are identical, so we are told. Now, who would be crazy genius enough to test this hypothesis? Apparently, one man was. Wilson A. Bentley loved snow so very much that in 1880, he decided to study snowflakes up close, and purchased a microscope to view its delicate structure. Hooking up a camera to it, he was the very first person to photograph a single snow crystal in 1885. In his lifetime, he would permanently capture the structures of more than 5000 snowflakes on film showing over 80 different shapes like needles, columns, and hexagons, but ultimately showing that no two snowflakes are alike, and the rest is history. Thank you, "Snowflake" Bentley!
 



But WHY are no two snowflakes identical? Actually, close to nucleation process, they can be, but not when they grow. Even the smallest temperature and humidity difference will affect their shape. As they grow, they are blown inside the clouds, experiencing different conditions and growing at different rates in their micro-environment, determining what type of flake will form. In high clouds, where it is coolest, snowflakes assume six-sided columns; in low clouds, they can assume flat six-sided hexagonal plates, short columns, thin needles and stars. While it is not proven (yet) that no two mature snowflakes are identical, given the 180 billion water molecule composition of a single flake, it would be very hard to create two mature flakes that are the exactly the same. They are enchanting individually and as Caroll’s white quilt.
 

www.weatherwise.org
Nakaya diagram
 

As I was thinking about the science and magic of snow, I read the headline: “A snowstorm occurred in Jerusalem.” While not foreign, the accumulation of snow is rare in Jerusalem as well. It caused a lot of flight delays and kvetching, but also provided fun for the children. Then I realized that we’re really no different than snowflakes. Singularly, we are beautiful, and as a group, a Jewish community, we can enchantingly change the world in a day. We each have our journey; we each are fragile, and transitory, but can bond together to make something that can last a bit longer and transform together.
 

This line from an article Times of Israel caught my eye:

 

The secret of the snow of Jerusalem is also the secret of the Jewish people and the Jewish State of Israel. We are a People and a state built upon a history that defies logic, full of events that simply weren’t supposed to happen...

With that said, I would like to take this opportunity to bid all our DC friends a fond farewell, and until we meet again. We will miss being a part of the magic that is Etz Hayim, our syngogue. We weren’t supposed to fall in love with the people here, but we did. Our synagogue was our second home in Virginia, where we left our tensions by the door steps; to be greeted with warm smiles and hugs inside, where our children learned, played, laughed and sang their hearts out, and took a lot of coaxing to go home. Thank you, above all, for letting us grow with you.

Snowy, white winter in Minnesota, here we come.

*modified; published in Etz Hayim Chronicle February issue



Then come the wild weather,
         come sleet or come snow,
                   we will stand by each other,
                          however it blow. - Simon Dach