Archive for October, 2009
Developing genomic tools for emerging diseases
Here at Bench Press we’re fans of PLoS because they strive to expand access to the world’s scientific and medical literature with their open access stance as well as other experimental endeavors such as PLoS Currents: Influenza. That’s why when I checked in on PLoS Biology I was intrigued by a new collection titled Genomics of Emerging Infectious Diseases.
The collection is a series of essays, perspectives, and reviews discussing the potential genomics research holds in understanding emerging infectious diseases. While I haven’t had a chance to read through very much of the collection yet, one perspective written by Rajesh Gupta, Mark H. Michalski, and Frank R. Rijsberman suggests an interesting plan for infectious disease research. They suggest beginning an Infectious Disease Genomics Project (IDGP), much like the Human Genome Project.
The IDGP would be:
a coordinated, large-scale, international effort focused on the genomes of pathogens, vectors, hosts, and reservoirs and linked to end-point surveillance and response systems. Such a project could coordinate activities in four specific areas: generating data, linking data, analyzing data, and applying data.
The figure above illustrates some of the specific things the authors envision the IDGP being able to coordinate. Ideally the IDGP provides:
- A “roadmap” for researchers to follow in sequencing and monitoring emerging pathogens that allow researchers worldwide to aid in global efforts while continuing critical research on local diseases.
- Advanced data management in an easy to use, open-source, real-time interface. With an emphasis on linking as much data with relevant details (e.g. literature references).
- A centralized analytical toolbox with dynamic databases allowing for collaboration worldwide in addition to improved access for researchers in resource-limited settings.
- Ability to incorporate emerging technologies and provide access (e.g. new assay methods, next generation sequencers).
Personally I find the IDGP very intriguing simply from the standpoint of developing a framework for worldwide scientific collaboration. If this were successful it could provide a model for future projects. On a practical level, providing a network of this sort for scientists to rely on could at least increase the speed at which emerging diseases are detected. Increasing the speed of detection is always a good thing when dealing with novel pathogens with pandemic potential. It’ll be interesting to see what the scientific community thinks about beginning an IDGP.
Readers any thoughts?
Pocket Ultrasound
When I heard that GE’s CEO and Chairman Jeffrey Immelt was going to be at this year’s Web 2.0 Summit, I expected an “old business” CEO weakly touting all the ways that his company was embracing social media. I did not expect him to come to demonstrate a portable ultrasound device ‘with the works’:
GE’s new Vscan pocket ultrasound device is reminiscent of the mobile phone-powered portable ultrasound and light microscope that we’ve covered before, but while those mobile phone attachments felt more like demonstrations of mobile phone/medical technology mashup curiosities, the Vscan feels like its in an entirely separate category:
pushed by a major healthcare technology company- fits in the palm of your hand
- thumb operated UI to adjust gain or look at a color-doppler scan
- high quality display
- real-time imaging capability
- preset modes to fit what doctors are most likely to use
- support for WiFi transmission of information
- ability to annotate with voice recorder
- Immelt: “could be the Stethoscope of the 21st century”
Medical technology blog Medgadget captured a fascinating preview on YouTube:
In his presentation at the Web 2.0 Summit, Immelt captures what I perceive to be the real significance behind the VScan:
“This has the same power and image quality of an ultrasound from 2-3 years ago that cost $250,000! This is Moore’s Law in action. To get this image scale in 1995, you had a product that weighed several hundred pounds!”
On a medical level, this opens up new doors for physicians to study illnesses and treat patients in a wider range of regions, but even beyond that, it underscores the ability of technological innovation to
increase the ability of doctors, scientists, consumers, and patients all over the world to access the latest in scientific and medical technology.
The Lone Ranger
I suspect that most people who enter the sciences are inspired by tales of the great scientists of yesteryear: bold luminaries who, through brilliance and ingenuity, helped uncovered the laws which govern the universe. For me, one of the most inspiring stories was that of Albert Einstein who, as a mere clerk in a Swiss patent office, published four papers which shook the foundations of physics in the span of one year! After all, who becomes a scientist who doesn’t have the dream of making a discovery or two so great that you become recognized as Person of the Century?
But, is this conception of science as a world where scientific Davids slay the Goliaths of orthodoxy and ignorance too romantic to be accurate? Is science still a field driven by brilliant individuals? This is a question which was top of mind for those attending the meeting of the International Astronomical Union, held in Rio de Janeiro from Aug 3-14, 2009 (HT: The Economist).
While theoreticians and well-funded groups in certain fields may still be able to comfortably push the “lone ranger” model of scientific research, in many areas (especially astronomy), the scientific frontier is being increasingly dominated by massive endeavors which consume enormous amounts of resources. After all, if your brilliant idea requires long, uninterrupted access to the Hubble Space telescope (i.e. the Hubble Deep field), you either get in line and save up, or you try to convince the rest of the astronomical community that your idea is worth pursuing (over their own, other, projects). This need to allocate very limited resources to a wide range of demands in astronomy has led to what The Economist refers to as “managerialism”:
The present is a “golden age” [for astronomy]. The rate of discoveries has been increasing, along with the means to keep up with the details. That has, in turn, led to bigger and more expensive telescopes, and the introduction of management techniques intended to ensure the smooth running of large projects. But it is that managerialism that is beginning to worry some of the more thoughtful members of the union. They fear that although it brings short-term benefits, it may, in the long run, crush individual flair.
This same clash between the desire to foster scientific Davids, but the need to build scientific Goliaths in order to use the latest and greatest (and most expensive) equipment is probably not unique to astronomy. After all, advances in technology have made possible new types of visualization (i.e. Imaging Mass Spectrometry to visualize how and where molecules move within a cell), new collections of vast amounts of data (i.e. the Diseasome), and even new ways of analyzing these new vast collections of data (i.e. the Millennium Simulation).
So is the “lone ranger” scientist doomed to have to one day ride off into the sunset? I don’t think so.
As we’ve discussed many times here at Bench Press, there are still plenty of innovative and relatively low-cost things that enthusiasts and scientists can do to push scientific inquiry. While there is no doubt that a lot of good can and will come out of big projects requiring costly equipment (I’m looking at you, LHC!), I think we’re far from the point where all experiments and models require multi-billion dollar investments.
Furthermore, while more expensive technology has made it more expensive to do experiments at the cutting edge, the advance of technology has made many other forms of inquiry much cheaper. For instance, technology has now made it possible for more and more people to collaborate and have access to data and the computational tools needed to analyze and report on it. If you had told Watson and Crick back in 1953, that every researcher would one day be able to as easily search a public database of nearly every gene and DNA/RNA sequence known for a match as they could read a book, they probably would’ve thought you were insane. And yet, today, I can not only randomly and arbitrarily search as many sequences as I want by using the NIH’s BLAST tool, I can quickly and cheaply deploy my own computing cluster using Amazon EC2 or, for specific types of computational workloads, even a graphics card/GPU!
I also think that, on some level, the fears about growing managerialism come from people who dramatically underestimate the value of collaboration between multiple scientists who can bring multiple specialties to the table, and the new ease of collaboration enabled by tools like Google Wave and Friendfeed.
In any event, even the field of astronomy seems to be trying to swing the pendulum back in favor of the Davids and Lone Rangers of the world:
Dr White suggests astronomers should ensure small science can flourish alongside its larger counterpart by, for example, ensuring that telescopes designed to look for big fish can also be used for projects that might be considered as small fry.
Another way to encourage gifted individuals might be to reform the way time on telescopes is allocated. The IAU’s new president, Robert Williams of the Space Telescope Science Institute in Baltimore, Maryland, is a supporter of this idea. He reckons decisions about who gets what observing time should be made by the directors of observatories, answerable to a governing body, rather than by groups of the great and good, as tends to happen now.
Williams is a particularly good authority on this – as he was one of those responsible for allotting the time necessary for Hubble’s Deep Field to be captured.
Viva la Lone Ranger!
Good news for 2036
Previously we’ve covered the extensive tracking and modeling of near-earth objects NASA undertakes as well as efforts to pass along data to the public via the internet. In Ben’s post about modeling near-earth objects he wrote about a specific asteroid designated 99942 Apophis. Discovered in 2004, it has been closely scrutinized by astronomers worldwide as it’s size and potential for collision with Earth have sparked interest.
Meet Apophis. Discovered in 2004, it will likely set a record for harmless near earth pass in 2029.
Earlier data pointed to the asteroid potentially passing through a troublesome gravitational keyhole which increased the threat to Earth in 2036, however new data from previously unreleased images from a University of Hawaii telescope near the summit of Mauna Kea have allowed NASA scientists to improve their models. New models show a reduced risk of collision in 2036 from 1 in 45,000 to 1 in 250,000.
From the NASA press release:
“The refined orbital determination further reinforces that Apophis is an asteroid we can look to as an opportunity for exciting science and not something that should be feared,” said Don Yeomans, manager of the Near-Earth Object Program Office at JPL.
Modeling asteroids and allowing humanity a chance to risk assess is only one example of the power of computer modeling. However, this example also illustrates one important caveat about modeling. One’s model is only as good as the data utilized in generating and analyzing it. Let’s hope that future data on Apophis continues to produce good news.
Who’s Counting?
Movies glorifying card counting may become a thing of the past.
If you’re like me, and you’ve seen the movie 21, you probably think counting cards in Blackjack is the coolest skill you could ever pick up around a casino. However, counting cards may become a near impossibility if University of Dundee graduate Kris Zutis has his way with things. At the age of 22, Zutis has already developed a system which studies visual feeds from cameras to detect card counters for his final-year project in college. Detailed in his research paper ‘Who’s Counting?: Real-Time Blackjack Monitoring for Card Counting Detection,’ Zutis’ program has captured world-wide attention, and Zutis himself has already been invited to computer vision conferences to lecture about his work.
Kris Zutis’ program first uses various visual recognition techniques to collect various bits of information such as contour analysis to detect what cards have been flipped and stereo imaging to measure the height of chip stacks to determine how much has been bet. After the data is collected, the program analyzes a player’s betting patterns and monitors what cards have been seen already. If a player’s actions are suspicious given the known information, the system can alert the casino of its findings.
The system shows considerable promise for commercialisation, and could become an invaluable asset for casinos. Other devices exist to try and combat car counting that use expensive RFID chips. Kris’s method offers significant cost cutting opportunities for casinos while more effectively identifying car counters and detecting dealer errors.
We’ve already seen examples of computer programs which utilize visual data to perform eye-tracking, determine attractiveness, and perform object recognition, and this new breakthrough is just another extension of what can be done with computer vision.
Near-space exploration for $150
In a day and age where scientific exploration seems to require very expensive apparatuses, its hard to remind people that they can do their own mini-scientific inquiries relatively cheaply, with cell phones rigged as smart-sextants, Foucault pendulums, a gaming setup, or a widely available program like Mathematica .
It’s in that spirit that I was very happy to learn about the efforts of two enterprising MIT students who, in what they appropriately called Project Icarus, were able to take high-altitude pictures from the “edge of space” with a setup that included a weather balloon filled with helium, a cheap digital camera (Canon A470), a pre-paid phone with GPS (Motorola i290), an antenna (to extend the range of the phone, some basic tracking/geography software like Google Earth and Accutracking, and a styrofoam beer cooler to insulate the setup such that, collectively, cost them only a mere $148!
The results? Over a 5 hour period, the setup went 17.5 miles up (to the “edge of space”), where the balloon popped, and fell to the earth over a 40 minute period and landed about 20 miles away from the launch site. And, as for the pictures, well, you can see them yourself in the students’ MIT directory or in the timelapse video they put together (below).
If that doesn’t inspire you to do a little exploration of your own, I don’t know what will!
Not to be outdone, British students launched teddy bears into near-space using a similar technique, but included temperature sensors (to measure the temperature extremes), insulating “spacesuits” (to protect the bears from freezing solid), and even a parachute to gently glide the bears down to Earth!
(Note: if you’re in the US and want to do something similar, please make sure to (a) contact the FAA, (b) use the University of Wyoming’s balloon trajectory estimator to make sure that your balloon won’t land in a densely populated region, and (c) make sure the balloon can land gently without injuring anyone or your equipment)
(Photo’s from 1337arts site) (Teddy Bear photo’s from DailyMail)