Thursday, October 16, 2014

All Power To The Hive Mind: Harnessing the collective reasoning of a gaming population to solve nature's toughest puzzles. By Matthew Billman.

In a time where fear of government surveillance, abuse of big data, and malicious social networking sites runs rampant, it is easy to forget just how awesome (and genuinely beneficial) hi-tech can be. Much of technology's promise arises not from how much work it can take off our hands, but by how much work it can help us get done; less Rosie the Robot, more T.A.L.O.S. And the fact of the matter is, there are many more innovations being made today in that vein than in any other. This is a very good thing.

One such innovation you might have missed: FoldIt, the protein folding game. Developed by 
the University of Washington Center for Game Science in conjunction with the UW Department of Biochemistry, FoldIt presents its users with at 3-Dimensional model of a partially folded protein, and then lets the user try to fold it the rest of the way. The more energetically favorable the final model is, the more points they score. That new model is re-circulated among the community, and the process repeats. And repeats. Until finally –  at least by FoldIt standards – the protein's tertiary structure is "solved."

While FoldIt began in 2008 as little more than a joke amongst UW BioChem grads, the competitive bent of human nature soon reared its beautiful head: as of 2012, there were 240,000 players registered on the site. 

This is all well and good. But does it WORK? In four words: yes, very much so. In 2011, the structure of the Mason-Pfizer monkey virus protease was solved in a matter of days, a task scientists had been unable to accomplish conventionally for fifteen years (http://bit.ly/Zr1pDi).  In 2012, the FoldIt community was able to redesign a Diels-Alderase used commonly in synthetic chemistry by adding 13 amino acids to the backbone, increasing it's reactivity by more than 18 times (the article in Nature: http://bit.ly/1wbTkx6; in Scientific American: http://bit.ly/1sXQhLb). And now, the community has turned its attentions to Ebola: the first Ebola protein puzzle was uploaded six months ago, and work is ongoing.

Computers are better than us in a lot of ways: they're unparalleled in their execution of incredibly complex algorithms at blazing speeds, churning out results much more accurate than humans could ever hope to produce. But humans are creative. Humans are spontaneous. We have intuition, and a brain evolved over millions of years that is arguably the most complex organism in the entire universe. Though in the time it takes us to formulate a single thought a computer might execute a billion operations, each of our thoughts are unfathomably more complex. By harnessing the technology of social networking and gaming to bring together hundreds of thousands of the world's greatest minds to work on a single problem, we integrate computing's massive breadth of thought with humanity's already massive depth of thought – working together, a synergistic meta-android of the mind, our productivity scales exponentially.

Working together, we achieve the impossible. Welcome to the future.

Further reading:

http://en.wikipedia.org/wiki/Foldit

http://fold.it/portal/

http://cosmiclog.nbcnews.com/_news/2011/11/07/8684955-gamers-create-scientific-recipes

Sunday, January 15, 2012

From lollipox to measles parties: we’re talking about a whole new kind of crazy


So if the lollipox and the rise of chickenpox parties weren’t bad enough, here’s a kicker…Now on the rise: measles parties? My gosh, from what we’ve learned about measles and it’s complications, this is a highly contagious and serious disease for which we have an effective vaccination. So why are some parents insisting on purposely exposing their children to such danger.

According to an article this week, measles parties are on the rise. Organizers of such events usually take the stance that measles is a “harmless childhood disease” and tend to be opponents of immunization. They often believe that naturally induced infection has greater benefit for the patient than vaccinations.

Unfortunately, as we have learned in class, actually being infected with wild type measles virus carries with it significant health risks. For example, complications of measles include otitis and lung infections as well as post infectious measles encephalitis and subacute sclerosing panencephalitis (a 100% deadly disease).

Measles can be a severe, debilitating and even deadly disease. On top of that, while people think they are exposing their child to measles, without a doctor present, a measles party could unintentionally spread other diseases. Lastly, due to the highly contagious nature, intentionally spreading the disease could likely have severe effects on infection rates of people outside of the measles parties. All in all, this sounds like a terrible recipe for disaster.

Now consider this: Conversation Parties and HIV. I’ll look into this next week but google it. CRAZY!

--Elena Jordan

http://www.iol.co.za/lifestyle/family/kids/measles-parties-a-hazardous-route-to-immunity-1.1211175

Thursday, March 17, 2011

Using Magnets to Image Influenza’s M2 Protein: Implications for Drug Design


Researchers from Florida State and BYU recently used a 900 megahertz magnet to image the M2 protein of influenza A. The magnet offers an inside view of the virus similar to the images seen with magnetic resonance imaging (MRI). Because the M2 protein exists in a water-repellent cell membrane, it cannot be imaged using MRI because MRI scans spin hydrogen water molecules. To image M2 researchers used a technique called solid-state nuclear magnetic resonance spectroscopy that spins molecules other than hydrogen and makes it possible to image proteins outside of a watery medium.

By focusing on nitrogen atoms, researchers found that M2 is activated in an acidic environment. Histidine carries protons from the host cell into the virus and tryptophan acts as a gate to let the protons through. Apparently, the passage of protons through M2 eventually allows the virus to reproduce.

Recently, major M2 inhibitors such as Amantadine and Rimantidine have suffered in their effectiveness because of viral mutation (i.e. M2 has changed shape). In 2006, the CDC even recommended against the use of these common drugs. Because this atomic mechanism is novel, researchers hope that it can be used to develop new antivirals against influenza. Its uniqueness makes researchers believe that any drug that utilizes the pathway will be extremely effective for a long time because it appears essential to viral replication.

-Owen Marecic

Wednesday, March 16, 2011

Norovirus vaccine candidate effective in Mice


Scientists at Ohio State University have successfully tested a new vaccine against norovirus in mice. According to the study, the vaccine induced high levels of antibodies, white blood cells, and other parts of the immune response. This particular vaccine is not amplified using cell culture, but is amplified using a vector-based technique similar to the one being tried with HIV and Hepatitis C vaccine trials. This vaccine uses vesicular stomatitis virus (VSV) as the vector and vehicle of delivery of recombinant virion fragments to confer immunity. This novel technique seems promising for combating norovirus.

While this seems like a promising vaccine, norovirus does not cause a significant amount of mortality, though it does cause some morbidity. It usually lasts for just a day or two and then passes on. Is it worth creating a vaccine against this virus if it doesn’t cause mortality? 

 -Tim

http://www.sciencedaily.com/releases/2011/03/110315130056.htm

Monday, March 14, 2011

HPV and cervical cancer in South Africa


A recent report published by the WHO about Human Pappiloma Virus is South Africa highlighted the huge risk for women.  The report claimed that 16.84 million women are at risk for developing cervical cancer caused by HPV.   In South Africa about six thousand women are diagnosed with cervical cancer every year.  The real incidence may be much higher since these are merely the diagnosed cases.  Cervical cancer is the second most common cause of cancer in South Africa.  In South Africa, approximately 21% of women are infected with HPV.  The large HIV epidemic is thought to have increased the spread of HPV through immunocompromsed individuals.  Although there is a vaccine for HPV, it is not widely available in South Africa.  This article brings up ethical questions about where money should be spent in resource limited settings.  Should South Africa fund HPV vaccines when they still have a huge need for ARVs?

Hannah Harrison

http://www.timeslive.co.za/local/article966244.ece/Two-thirds-of-SA-women-at-risk-for-cervical-cancer

Gilead’s success slows HIV drug research


Gilead’s success in providing an effective once a day drug for HIV has limited the development of new HIV drugs.  There are fewer drugs in the pipeline now because the market for drugs that need to be taken multiple times a day is much smaller when there is a once a day option.  This poses a problems with the high mutation rate of HIV and the great potential for resistance.  Last year, Atripla, a three drug combination of truvada and Sustiva captured about 40% of the HIV drug market.  The San Francisco Chronicle reported that there were about 100 drugs in various stages of testing in 2006 but there were only 60 drugs in testing in 2010.  Unfortunately, the great success of recent HIV drugs is leading to declines in research because the market is smaller and the competition is fierce. 

Hannah Harrison
http://www.sfgate.com/cgi-bin/article.cgi?f=/g/a/2011/03/13/bloomberg1376-LHPT9W07SXKX01-6NLHS2MMBPB2I1OSLRHQSGK3RK.DTL&type=printable

Mosquitoes carrying dengue fever




As many of you probably recall, Bob mentioned the appearance of Aedes mosquitoes in Florida.  The potentially fatal disease that many Key West Floridians have been exposed has shown “flu-like” symptoms, but has been more acutely identified as Dengue. At least 46 cases have been reported. This the first substantial outbreak in the continental U.S.. However, because of the harm is threatens to cause, health officials have begun to implement prevention efforts.  Aedes mosquitoes populations are now being tracked and people in the surrounding areas are being educated both about the mosquitoes and the disease. For example, most mosquitoes appear at night and remain outdoors. Thus, screens, staying inside from dusk to dawn, and wearing repellent are all useful techniques. However, aedes mosquitoes tend to live indoors or near the house and bite during the day. Because of the more proximal nature of the aedes mosquitoes, health officials are warning everyone to be particularly vigilant about stagnant water near their homes. One benefit of the aedes mosquitoes’ habits, however, is that they do not travel far during their lifetime. Thus, controlling their populations and their spread should be easier than that of regular mosquitoes.


http://www.miamiherald.com/2010/07/31/1755271/mosquitoes-carrying-dengue-fever.html#ixzz1FTvzkegr




alysha