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A few years ago, I blogged about an ingenious crowdsourced game called Fold.It. The concept was pretty simple:

• Use human intuition to help solve complicated three-dimensional protein folding challenges which is oftentimes as effective but significantly faster & cheaper than computational algorithms
• Pool together lots of human volunteers
• Turn the whole experience into a game to get more volunteers to spend more time

The result was a nifty little game which contributed findings which have made it, to date, into a number of peer-reviewed publications (see PNAS paper here and Nature Structure & Molecular Biology paper here)!

Well some researchers at McGill University in Canada want to take a page out of this playbook with a game they built called Phylo (HT: MedGadget) to help deal with another challenging issue in bioinformatics: multiple sequence alignment. In a nutshell, to better understand DNA and how it impacts life, we need to see how stretches of DNA line up with one another. Now, computers are extremely good at taking care of this problem for short stretches of DNA and for “roughly” aligning longer stretches of DNA – but its fairly difficult and costly to do it accurately for long stretches using computer algorithms.

People, however, are curiously intuitive about patterns and shapes. So, the researchers turned the multiple sequence alignment problem into a puzzle game they’ve called Phylo (see image below) where the goal is to line up multiple colored blocks. Players tackle the individual puzzles (in a browser or even on their mobile phone) and the researchers aggregate all of this into improved sequence alignments which help them better understand the underlying genetics of disease.

And how has it been doing? According to the McGill University press release:

So far, it has been working very well. Since the game was launched in November 2010, the researchers have received more than 350,000 solutions to alignment sequence problems. “Phylo has contributed to improving our understanding of the regulation of 521 genes involved in a variety of diseases. It also confirms that difficult computational problems can be embedded in a casual game that can easily be played by people without any scientific training,” Waldispuhl said. “What we’re doing here is different from classical citizen science approaches. We aren’t substituting humans for computers or asking them to compete with the machines. They are working together. It’s a synergy of humans and machines that helps to solve one of the most fundamental biological problems.”

With the new games and platforms, the researchers are hoping to encourage even more gamers to join the fun and contribute to a better understanding of genetically-based diseases at the same time.

Try it out – I have to admit I’m not especially good with puzzle games, so I haven’t been doing particularly well, but the researchers have done a pretty good job with the design of the game (esp. relative to many other academic-inspired gaming programs that I’ve seen) – and who knows, you might be a key contributor to the next big drug treatment!

Singapore is a fascinating country – despite the lack of what most in the West would recognize as democratic freedom, it consistently ranks well in terms of lack of corruption and high and growing standard of living for its people.

It is also one of the boldest when it comes to instituting policies and reforms: they were the first to implement a congestion tax to help manage traffic. Unlike most countries, Singapore is open to competition and investment from foreigners in strategic areas like telecommunications, power generation, and financial services. Singapore has also been extremely active in attempting to build up its capabilities as a center for life sciences excellence.

So it shouldn’t surprise me that they are among the first countries to actively utilize social media applications like Facebook and Twitter to help deal with a public health risk like Dengue Fever (from The Jakarta Globe):

The city-state’s National Environment Agency (NEA) plans to roll out … providing information on the latest dengue clusters or areas that have been earmarked as high-risk – on these new media platforms within the next three months … Through Facebook and Twitter, the public will also be able to post feedback or provide tip-offs. For example, if Singaporeans notice an increase in the number of mosquitoes in your neighbourhood or find potential breeding sites, they can alert NEA officers by posting on the agency’s Facebook page or tweeting the NEA account. “We need to put more information out in the public space, so more people can be informed and take action,” said Derek Ho, director of the environmental health department at NEA. “Leveraging on new media channels such as Facebook and Twitter is a good way to do that.”

A refreshing understanding of the uses of social media by a government agency – more interesting than that, though, is the work Singapore’s NEA is doing to build image recognition capabilities into smartphone apps like the NEA’s iPhone app to help field workers (and potentially the public) track and identify mosquitos and mosquito larvae!

The NEA is also in the process of developing a mosquito-recognition program that can identify the species of mosquito from a photograph of its pupae or larvae. With such software, and with the help of a mini microscope that attaches to the camera on a personal digital assistant or cellphone, NEA officers will be able to take photographs of larvae or pupae found in mosquito-breeding sites and instantly find out if they belong to the Aedes species, which spreads dengue … When it is ready, the agency hopes to be able to integrate it with the NEA iPhone application, so that the public or grassroots members conducting checks around the neighbourhood can use the technology as well.
Early identification will allow the NEA to act more swiftly to curb the spread of dengue in potential high-risk zones.

Very cool demonstration of the power of smartphones and of a government that is motivated to try out new technologies to tackle serious problems.

We’ve commented before about the ability of telemedicine solutions to bring cutting edge technology and quality of care to emerging economies. One example is some of the recent work that the Camera Culture Group from MIT’s Media Lab has done by building a clever optometry solution into an accessory and an application for Android-powered smartphones (HT: Engadget).

The concept is very cool. Many optometrists today use autorefractors, machines which scans the images formed on the back of a patient’s retina to get a rough, but automated, measure on the quality of your vision. Optometrists will then use phoropters to get to a precise enough measure of your eyes as to be able to prescribe lenses for contacts/glasses.

The problem with this approach is that autorefractors and phoropters are too expensive and too time consuming for widespread use in many places around the world. The NETRA solution that the Camera Culture Group came up with was to build an accessory and an application which force a user to make a pair of lines overlap using controls on the phone. Doing this repeatedly lets the application do a calculation similar to what is done by an autorefractor to calculate the quality of the user’s vision in a process which is much faster (several minutes) and cheaper than a standard eye exam (more details in the video and images below)

The project website shows a very compelling table which compares the relative prices and accuracies of optometry solutions in existence today.

It’ll be interesting to see where this technology can go once displays similar to Apple’s Retina Display become cheaper and more prevalent. This example definitely shows the power of telemedicine approaches and is hopefully a harbinger for more equally compelling and innovative solutions for the needs of scientists and doctors around the world.

(Images and video from NETRA website)

A recent NBER paper (gated) by Benjamin Jones from Northwestern conducts a systematic review of trends in scientific research and made a couple of conclusions that won’t come as a surprise to anyone in science (HT: Inside Higher Ed):

As science advances and knowledge accumulates, ensuing generations of innovators spend longer in training and become more narrowly expert, shifting key innovations (i) later in the life cycle and (ii) from solo researchers toward teams

As evidence to this, the average age at which a scientist made a discovery which later qualified for a Nobel prize has increased by 6 years over the course of the 20th century. When looking at publications, the researchers found that the average author list on a publication grew, on average, by 15-20% per decade!

We’ve discussed before the “decline of the Lone Ranger model of science”, but Jones’ paper focuses on looking at the policy implications for such a change. He concludes that the government (and, probably, the academic and private institutions which support researchers) need to adapt policy to reflect this new reality by:

• Tailoring funding and messaging to help keep young researchers interested despite the longer and more difficult training period
• Finding new ways to evaluate the worthiness of proposals as scientist’s expertise becomes more and more specialized
• Altering incentive structures as the team of collaborators replaces the Lone Ranger scientist model of discovery

These policy suggestions are definitely good ones, and are certainly necessary to adapt to a new scientific environment, but one dimension of this which Jones doesn’t discuss as much are the technological (the focus of this blog!) innovations which can help further research in this brave new world.

• Improving science communication with the public. We’ve made multiple mentions of this in the past, but they are no less true here. Active public communications management not only helps secure funding and raise public awareness of the good scientists can do, but it also helps attract the interest of future generations of researchers and policymakers.
• Embracing new collaboration tools. To really kick-start collaboration between scientists across geographies and specialties, we need tools that go beyond just email and fax machines. Tools like Google Wave, wikis, distributed version control, and social media forums like Friendfeed are an early taste of the sort of live collaboration that new web technology can bring about.
• Leveraging cloud computing and heterogeneous compute. One of the reasons discoveries are taking longer and are more expensive is that there is so much more data to collect and to analyze than before. One technological innovation which we’ve talked about at lengths here is the ability of graphics cards/GPUs to make supercomputer-level processing power more readily accessible to research labs. Another is the use of new cloud computing services like Amazon’s to rapidly increase the computational resources that a lab/company has access to. Neither are panaceas for all the data analysis issues which scientists face, but they are definitely ways to make things easier for research groups who have stringent IT budgets.
• Using crowdsourcing to speed innovation. Who says research has to take longer and be more expensive? Perhaps its time to pull on new technological levers which let scientists borrow on the resources and brains of a wider group of people. While new platforms like ChemBioConnect, distributed computing systems like Folding@Home, and volunteer crowdsourcing initiatives like Fold.IT are far from perfect, they hint at a future where researchers can call on resources beyond what their personal computers and brains are capable of.
• Building new research attribution models. When I say new attribution models, I’m referring to two things. The first is embodied by new standards like ORCID which make it easier to understand which person is the author/researcher in question (something which will become more and more important as more people with the same initials/names enter the sciences). The second, and more substantive, is finding new ways to understand who contributed what to a particular study. In today’s digital age, I find it laughable that we still rely on simple author list order to determine the relative roles and positions of the researchers listed on a publication. Employing metadata and other graphical cues can help scientists achieve the recognition they deserve, as well as provide appropriate incentives for teams of researchers to contribute.
• Contributing negative and after-publication results to open repository. While I can understand the hesitation for most research groups to pursue a pure open access strategy, those concerns should not hold with negative or post-publication experimental data. While opening up access to data from failed/negative experiments does little to hurt a lab’s ability to publish first, it can be a dramatic boon for other research groups (especially new labs or labs with interdisciplinary focuses) who can not only use the data for their own analyses and experimental designs, but avoid committing resources to experiments which have already been conducted. If it can work for biotechs and pharma companies, then there’s no reason it should be any different for non-commercial groups.

These suggestions only scratch the surface of what new technologies and policies can do to help scientists in a world where scientific training takes longer and where scientific discoveries need to be more collaborative. If anyone else has any other suggestions, feel free to leave them in the comments!

One of the best ways for scientists to reach out to the general public is through video. This past Friday, I got a chance to experience this firsthand at the IMAX theater at Boston’s New England Aquarium. A while back, I had caught the trailer for Hubble 3D at an IMAX movie and, given my love for all things Hubble, I had wanted to catch a showing. Seeing that the Hubble special was only ~40 minutes long, I decided to also buy a ticket for Under the Sea 3D as well.

And, as my Tweets that day pointed out, I was blown away:

There are some today who think high-def/3D is usually a gimmick by movie studios and digital display sellers, but that was definitely not true for either of these films. The 3D really enhanced the impact of the visuals. It let the audience, many of whom are unlikely to ever conduct spacewalks or scuba-dive where the Under the Sea 3D crew went to really feel what it was like to see undersea life. And, in the case of some of the deep space Hubble 3D shots, it gave the audience a very cool new look at objects so far away that its almost inconceivable that human beings will ever actually get to visit them.

Couple that with strong performances on interesting material by Leonardo DiCaprio in Hubble 3D and Jim Carrey in Under the Sea 3D and you get a strong combination which, if I’m any judge, not only gives the audience a juicy taste of why science is cool, but why its important to continue to study it.

I have definitely been sold on these, and I not only plan to check out more of these as they come out (I’ve got my eye on Sea Rex 3D), but would recommend this to anyone who has an hour to spend or would like to check out a visually stunning way to learn something new.

We’ve posted before on the Federation of American Scientist’s Immune Attack computer game as a great example of the use of games in science education. But, science “edutainment” isn’t limited just to computer games. Fans of Wizard’s Magic the Gathering and Konami’s Yu-Gi-Oh trading card games will immediately recognize The Healing Blade, a trading card game designed in the spirit of Magic and Yu-Gi-Oh but designed around the battle between antibiotics and bacteria (HT: AMEDNEWS)

The game was designed by two self-admitted “mega-geek” physicians, Dr. Arun Mathews and Dr. Francis Kong, who met in medical school and created the company Nerdcore Learning to promote The Healing Blade and other medicine-related “edutainment” paraphernalia. As to why they created the concept, Dr. Mathews notes:

I was struck upon the complexity and yet innate nature of gaming within the choice I would make for putting some of my sick patients on particular antibiotics … Essentially, in a similar way, when you are playing a complex multi-tiered video game, we are making similar choices by obtaining data from our cultures [and] making risk-management decisions.

Truer words were never spoken.

Amazingly, while Mathews and Kong had only intended to bring 30 copies of the game to launch at the American Medical Students Association annual meeting, a printing error turned that into over 100 copies, 90% of which sold! Mathews describes the sight:

We had this gaggle of students just sitting down, spreading out on a bunch of tables, all playing the game. That is one memory that will take a while to fade, because it was such a neat thing to see students getting super excited about infectious disease and therapies.

As an unabashed former-Magic-and-Yu-gi-oh player, I can definitely see the appeal. There is something very compelling about the mix of chance and strategy in trading card gameplay. Sadly, at the time of the writing of this blog post, The Healing Blade’s online purchase form shows that the game is sold out. So, in the meantime, I will have to leave you with some pictures of some very nice-looking game card art:

(Images and video from Healing Blade website)

Despite all the cool and meaningful innovations we’ve discussed on this blog, few come as close in terms of impact on a scientific field as the Hubble Space Telescope. And this weekend, you can help celebrate it’s birthday!

Officially launched on April 24, 1990 (can you believe that was 20 years ago!?), it has provided one of humanity’s best looks into deep space and has, among other things:

• Helped refine the field’s understanding of Hubble’s Law and the Hubble Constant
• Showed that the expansion of the universe was not decelerating, but accelerating, suggesting the existence of dark energy
• Helped to establish the existence of massive black holes at the center of galaxies and their relationships
• Provided sharp images of the impact of comet Shoemaker-Levy 9 into Jupiter
• Collect data on extrasolar planets and protoplanetary discs
• Furthered the study of Wolf-Rayet Stars, suspected to be the precursors of Gamma-ray bursts, the most powerful energy bursts known in the universe
• The mindblowing look 13 billion years into the past known as the Hubble Deep Field

And, potentially, most important of all: the gorgeous pictures of deep space (from Space Telescope Science Institute’s HubbleSite website).

Happy 20th birthday, Hubble!

(Image credits – Hubble Site via Space Telescope Science Institute)

Here at Bench Press we’re always interested in new initiatives that harness the advantages of the internet. We’ve covered various powerful distributive computing initiatives as well as breakthrough collaborative endeavors in scientific research. So I was intrigued when I saw buzz on Twitter about the Obama administration’s attempt to crowd source suggestions for scientific policy.

Through the American Association for the Advancement of Science (AAAS) and associated non-profit Expert Labs, the Obama administration wants to hear what grand challenges scientists envision taking on.

Expert Labs has a nice video explaining the reasoning behind this grand experiment in policy crowd sourcing.

After a quick search on Twitter I’m a bit curious as to how Expert Labs plans to parse all the data they’re going to get from this call to arms, but I’m optimistic that some interesting insights can be gleaned as to the opinions of Americans on the directions science should be headed in. More data never hurt right? If you’re interested in submitting an idea follow the directions here, you’ve got until April 15th!

We posted before about the rhymes of Stanford University biologist Tom McFadden who creates very inspired raps about science to help his undergraduate students prepare for exams. A friend of mine showed me one of his latest creations, a remake of Fifty Cent and The Game’s song Hate It or Love It about metabolism.

What especially caught my eye, however, was another video in McFadden’s collection: “Clouds Make it Rain”. It’s a re-make of the Fat Joe song “Make it Rain”, but what made it special was that instead of the usual undergraduate-level “flow”, this was focused on and starred a classroom of fifth graders! According to the YouTube caption, McFadden worked with a classroom at East Palo Alto Chartered School with a program of field trips, lab experiments, and short presentations to study the water cycle and its impact on insect life.

East Palo Alto is notorious for being a difficult neighborhood, especially for children. This project’s use of hip hop and other integrated learning experiences strikes me as an ideal way to better connect science to the children’s lives and to make the learning more fun and memorable. Judging from the quality of the music video and the enthusiasm of the kids in it, I think this counts as a strong success.

Well done!

A few weeks ago, we posted a number of reasons why we believe the Pharmaceutical industry needs to pursue greater openness to accelerate innovation and reduce the cost and time of drug development. A few weeks after that, almost as if by magic, pharmaceutical giant GlaxoSmithKline made a very encouraging announcement which is hopefully a first step in the direction of openness and a promising boost to global health initiatives around the world working on Malaria:

GSK has screened its pharmaceutical compound library of more than 2 million molecules for any that may inhibit the malaria parasite P.falciparum, the deadliest form of malaria, which is found primarily in sub-Saharan Africa. This exercise took five scientists a year to complete, and has yielded more than 13,500 compounds that could lead to the development of new and innovative treatments for malaria, which kills at least one million children every year in Africa.

GSK will make these findings, including the chemical structures and associated assay data, freely available to the public via leading scientific websites. The release of these data will mark the first time that a pharmaceutical company has made public the structures of so many of its compounds in the hope that they could lead to new medicines for malaria.

Building upon its commitments to create a “knowledge pool” for neglected tropical diseases, GSK
today announced that governance of the “knowledge pool” will be taken over by an independent third party, BIO Ventures for Global Health (BVGH). GSK and BVGH have also signed a Memorandum of Understanding with the Emory Institute for Drug Discovery (EIDD) to join the pool and further open up knowledge, chemical libraries, and other assets in the search for new medicines for neglected tropical diseases. A second collaboration has also been established with South Africa firm iThemba Pharmaceuticals. This work will help research and discovery into new medicines to treat tuberculosis.

In addition to opening up its library of malaria hits to the public and creating a third-party administered “knowledge pool”, GSK is even promising to give 60 scientists access to its advanced facilities in Spain and a funding pool of $8 million to help fund malaria research.

While GSK is reaping (well-deserved) kudo’s for this, we believe (perhaps, more correctly, hope) that GSK is also using this to figure out if greater openness can help their underlying business and how best to do it. As a Nature editorial on the subject opines:

The move advances the pharmaceutical industry’s slow but steady shift towards more open sharing of data. At least for early-stage, precompetitive research, drug companies are finding it useful to lower the firewalls around their intellectual property and pool their resources. Making data public brings fresh eyes and minds to the problem, and has the potential to accelerate the discovery process.

Let’s hope this marks the beginning of a very productive move towards greater information sharing.

(GSK Press Release) (Image credit) (Nature editorial)