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If you’re an astronomy buff, February 14 means a lot more than just Valentines Day. It also marks the fateful day (HT: NASA Jet Propulsion Laboratory), in 1990, when the Voyager I spaceprobe took a “family portrait” of all the planets of our solar system that it could see as one last parting gift before it shut down its camera and continued its journey towards “interstellar space”:

The diagram above shows the 60 frames that Voyager I took. The pictures aren’t high-resolution beauties (as a result of needing to use optical tricks to correct for the amazing brightness of the sun and the light it scatters, and smearing from the long exposure times needed to capture Neptune and Uranus), but it is still amazing to think that this is the only family portrait mosaic of the solar system ever taken. Closeups on the 6 prominently visible planets are below (left to right and top to bottom are Venus, Earth, Jupiter, and Saturn, Uranus, Neptune):

More details are at the NASA JPL page, but I will leave you all with this bit from Carl Sagan:

This was the image that inspired Carl Sagan, the the Voyager imaging team member who had suggested taking this portrait, to call our home planet "a pale blue dot."

As he wrote in a book by that name, "That’s here. That’s home. That’s us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. … There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world."

Happy 20 year anniversary to the grandest family portrait humanity has ever taken, and happy Valentine’s Day to all.

(Image credits – NASA JPL)

It is unfortunate that much of what we need to do to the human body to treat it requires that we cut it open, as this creates a whole set of risks and complications for science and medicine. Thankfully, science and technology march on in the quest to reduce our dependence on invasive surgeries. An interesting Economist article takes a look into some of the more unconventional tools that are being explored as potential non-invasive replacements.

Let’s take a classic problem which often has a surgical solution: the removal of a cancerous tumor. How could we solve this without resorting to the use of a scalpel?

• Of course, there’s radiation – which, as we’ve discussed before, is potentially dangerous if the radiation dosage isn’t calculated sufficiently well.
• The use of ultrasound as a means to visualize what’s going on under the skin is commonly known. But a small startup in Washington called Mirabilis Medica came up with a means to use ultrasound not only to see a tumor or blood clot, but also to focus it and generate enough heat to destroy the tumor/blood clot (what they’ve called High-Intensity Focused Ultrasound or HIFU; explanatory diagram below).

• Professor Weihong Tan at the University of Florida published a paper in PNAS in early 2009 a means of using light as a way of non-invasively activating blood clotting. The system is described in the picture below, but relies on a means of inhibiting the activity of Thrombin (a protein that helps control blood clotting) with short stretches of DNA (which they’ve cutely termed “Thrombin-binding Aptamers” or TBA) that have been chemically modified to be able to change shape in the light (cis-trans isomerization under photon stimulation). The vision is to one day be able to inject a patient with these Thrombin-TBA “molecular clasps” and hit the patient with a light source, cutting off the blood flow to the tumor and all without needing invasive surgery!

These only scratch the surface of what new technologies and scientific advances might be capable of. Son et lumiere (sound and light) as surgical tools indeed!

(Image credit) (Image credit – Mirabilis Medica) (Image credit – PNAS publication)

With smartphones becoming more sophisticated and more popular, its only natural that there are a growing number of attempts to use them as a platform for scientific inquiry (pocket ultrasound, microscopy, and astronomy for example). This is especially useful in developing countries, where a relative lack of high-end computers and fixed broadband access make smartphones a very suitable alternative to the more expensive, bulkier solutions that are used in the developed world.

It should come as little surprise, then, that doctors in India are helping to pioneer a new “telemedicine” tool using the camera and processing capabilities of Apple’s popular iPhone to do remote diagnosis of Retinopathy of Prematurity (RoP), a condition which is more likely to afflict infants born underweight. While curable, RoP needs to be treated within days of detecting it as to prevent permanent damage to a child’s eyes, something which the iPhone’s camera, mobile broadband, and robustness of software and security platform allows pediatric eye surgeons to diagnose from remote locations, hundreds or even thousands of miles away.

But, the potential of smartphones to function as a tool for tele-medicine can probably go far beyond this. At least, that’s what i2i TeleSolutions, an Indian-based startup, is betting on. They provided part of the software solution for the RoP diagnosis tool, and are aiming to provide software and services to enable further telemedicine technology – mainly:

• Security – It is important that sensitive medical information is transmitted securely in a way such that only the appropriate medical professionals see the information.
• Data compression – As fast as 3G and the new LTE networks are (and will be), network coverage and data transfer rates will continue to be a limiting factor on the adoption of telemedicine. As such, a true telemedicine solution will require lossless compression techniques.
• IT support – Medical organizations are not especially well-suited for building sophisticated IT capabilities, nor do medical professionals necessarily have the time to learn an arcane user interface. For that reason, telemedicine solutions should aim to provide web-based access methods (in addition to any non-web based methods they may choose to push) to access and react to data.

i2i provides further details on the scope of their platform on their web page, but I think it represents a strong start for a solution. Going forward, I’d like to see them (and any competitors that emerge) provide support for:

• Additional types of data – i2i’s focus seems to be primarily on images, but the full range of capabilities on smartphones is massive – GPS, accelerometer, magnetometer, and even microscopy and other medical attachments – and I would hate to think that tele-medicine would be limited only to its imaging capability
• Deployment on more phones – The iPhone is unique in the maturity of the platform, but it would be nice to see similar applications on other operating systems like Android, Symbian, and Windows Mobile.
• Interactivity – The i2i platform appears to be very unidirectional: (1) take a picture, (2) send it to a remote surgeon. I think the true promise of telemedicine is something which allows for a greater level of flexibility and interactivity on both ends (to refine the view, or make a suggestion on some other place to scan, etc).
• Ability to tack on analytics – There is a significant amount of medical data that needs to be analyzed/processed before it can be acted upon. Building some sort of open protocol or extendability (a la Firefox or Salesforce or LinkedIn/Facebook model) would do a great deal towards enhancing the potential of a telemedicine platform

Anyone else have any other ideas?

Image depicting ant movements. Credit: University of Granada.

Its impressive how much humans can learn from biomimicry. Soldiers, for example, may soon owe their lives to the same pesky ants living in your own backyard. Researchers from the University of Grenada(UGR), under Antonio Miguel Mora García, Professor Juan Julián Merelo Guervós, and Professor Pedro Ángel Castillo Valdivieso, have taken inspiration from how ants find trajectories from their colonies to their food sources in order to develop a simulator that can devise the “safest” trajectory in a battlefield between any two points, given the necessary parameters.

Dubbed the “ant colony optimization (ACO),” this algorithm has already allowed Antonio to employ it to the videogame, Panzer General, with promising results. Currently, the University of Grenada has received participation from the Ministry of Defense to devise new strategies for them if its success continues.

The scientists of the UGR have developed a mini-simulator in order to define the settings (battlefields), locate the unit and their enemies, execute the algorithms and see the results. In addition, the software designed by them offers a few tools useful to analyze both the initial map and the results.

To prepare this system, Mora García started from the battlefields present in the videogame Panzer General, defining later the necessary properties and restrictions to make them faithful to reality.

While the ACO has immediate benefits to saving the lives of our soldiers, I’m also excited for its applications outside of the military. By extrapolating its uses, we could potentially use the ACO to optimize shipping orders, create shortest routes, plan airplane seating, etc, all by harnessing the creativity and intelligence of Mother Nature. So the next time you see an army of ants devouring your picnic basket, take some time to marvel at the beautiful tapestry of Nature before squashing all of them with your feet.

(Image Credit)

Dust can be a pain if you’re an astronomer. In the same way that clouds obscure a view of the night-sky, interstellar dust can distort an astronomer’s view (even if through the Hubble telescope) of interesting astronomical phenomena. This problem is compounded when you consider that stars and planets tend to form in dense interstellar dust clouds.

The distortions caused by spacedust are caused by radiative transfer – a process of light absorption and scattering which also explains why the sky is blue and why sunsets/sunrises look red. Astronomers have built highly sophisticated models to understand radiative transfer across a wide range of different dust backgrounds. These models have enabled researchers to build very cool simulations, such as this one of two galaxies colliding:

Interestingly, greater sophistication in our understanding of spacedust and a greater desire for precision and resolution in the modeling has meant that more and more of the computational processing of these radiative transfer models has been spent on calculating dust grain temperatures rather than the math behind the actual radiation transfer (a product of the fact that you need to calculate across many points in the “dust cloud”, across many types/sizes of dust particles, and because you need to iterate many times to find an equilibrium) – something on the order of 10¹¹-10¹² exponentials per simulation!

That traditional processors are not well suited for calculating exponentials and that there were simply so many calculations which needed to be done in parallel convinced researchers to turn to NVIDIA’s CUDA as a potential solution. As we’ve noted before with using raytracing as a means to accelerate radiotherapy dosage calculations, NVIDIA’s CUDA is a standard programming toolset which lets programmers more easily use the power of (NVIDIA) graphics cards for calculations. Because the calculations needed to do high-performance graphics for a game of Modern Warfare 2 are similar to the calculations that supercomputers crunch through, NVIDIA’s CUDA has been demonstrated to be able to accelerate calculation speed by orders of magnitude!

In the case of dust grain temperature calculation, the results were equally impressive. Not only were the researchers able to accelerate dust grain calculation using a NVIDIA Tesla C1060 (with 4 GB of memory) over an 8-core Intel Xeon E5420 processor (with 32 GB of RAM) alone by a factor of 55, they were able to do this despite:

• the fact that 17% of processing time on the GPU solution was dedicated to data transfer (something the CPU-only solution has to worry about less)
• the maximum theoretical capacity of the GPU was only 6 times greater than that of the CPU, highlighting a big difference between the CUDA philosophy (crank up performance) and the CPU compiler philosophy (abstract but flexible)

Amazingly, the researchers found that even if the CPU were to run an interpolation scheme (requires less processing power, but introduces a little more error and makes it harder to do more sophisticated calculations vs. the equilibrium calculations done here), the GPU solution is still faster by a factor of 16 times!

So: spacedust – 0. GPU – 1. Now let’s see if they can tackle the flexible dust temperature problem…

Paper: “Accelerating Dust Temperature Calculations with Graphics Processing Units”, submitted to New Astronomy; ArXiV link

A few weeks ago, I had the pleasure of visiting the lovely California Palace of the Legion of Honor. While I expected the art within to be stunning, I was also amazed at how beautiful the museum and its surroundings are. If you live nearby or are ever in the area, I would highly recommend a visit.

If you are making a visit before July 4, 2010, and have a scientific bent, you’ll have another reason to visit: an exhibit which the Legion of Honor has called “Very Postmortem: Mummies and Medicine” in honor of the return of Irethorrou, an Egyptian mummy over 2500 years old which had been on loan from the museum since 1944.

While anyone even remotely fascinated by the Ancient Egyptians will find the exhibit interesting, what I was most struck by was that a large part of the exhibit was dedicated to what could be found by using modern CT scans and X-rays on the mummies. These scans were able to probe not only what amulets/objects were encased with Irethorrou (and hence help out with the understanding of Ancient Egyptian culture), but they were even able to take a deeper medical look at Irethorrou’s organs, muscles, and bones – and all of this without requiring any direct handling of the mummies (and hence risking damage to them).

With this information, they were able to create a facial reconstruction of what Irethorrou might have actually looked like and even tell a short story of Irethorrou’s medical history! By partnering with with Fovia, a Palo Alto-based company specializing in high resolution volume rendering technology, the exhibit also portrays a rich three-dimensional high-def video “fly-by” of the CT scan’s findings.

The potential of using modern medical technology on “non-traditional” subjects is only beginning to be tapped. A recent Wall Street Journal article reports on a fascinating study which took CT scans of mummies from the National Museum of Antiquities in Cairo, Egypt. They revealed, surprisingly, that some of the mummies (especially the older ones) showed the same artherosclerotic plaques which doctors see today in patients with heart disease, completely questioning the notion that such plaques were correlated with modernizing and the Western, sedentary, fast-food-intensive lifestyle. Or, as researcher Gregory Thomas puts it, "Not only do we have atherosclerosis now, it was prevalent as long as 3,500 years ago. It is part of the human condition."

What that finding could mean in terms of understanding the causes of cardiovascular disease is up to history to decide, but what shouldn’t be in question is the power of modern medical technology to shed light on the lives and health of ancient peoples.

California Palace of the Legion of Honor (link)

(Image credit – Legion of Honor website)

Nowadays, digital attacks are talked about almost as much as swine flu, and for good reason. Information stealing and identity theft are two major reasons why people should be wary of possible hacking vulnerabilities in their computer. While hacking is a very serious and destructive threat to security, a team of researchers headed by MIT professor Martin Rinard hope to provide a security blanket to defend against these malicious attacks. Using their new utility, ClearView, Rinard and his team plan to provide an application which will self-patch vulnerable software and detect anomalies within a program’s execution.

By monitoring the normal execution of a program, ClearView establishes guidelines for how a program should run normally and correctly. Once a program’s normal behavior is established, the program is probed by ClearView and checked to see that its execution proceeds according to the standard guideline that was set for it. In Rinard’s paper, Rinard and his team issues a procedure that ClearView takes to identify possible vulnerabilities:

1. Learning: While a subject program is running, ClearView dynamically observes the program’s behavior and tries to identify certain rules which always hold true during its execution, called invariants. Invariants may include what locations in memory the program is likely to access or what values certain variables should hold. One attribute of ClearView is that the more executions a program runs, the better information ClearView has to prevent attacks.
2. Monitoring: Once ClearView establishes what invariants the program has, it proceeds to classify each execution of a program as either correct or incorrect.
3. Correlated Invariant Identification: Once a failure has been detected, ClearView proceeds to apply a series of patches which create “a set of correlated invariants.” These patches do not fix the error, but finds groups of invariants which categorize normal and invalid execution.
4. Candidate Repair Generation: Once these sets of invariants have been identified, ClearView applies another set of patches which re-establish the invariants that have been broken and hopefully fix the failure.
5. Candidate Repair Evaluation: After the patch has been generated and applied, ClearView analyzes the result of the patch and observes whether the patch seemed to work or not.

Rinard and his team tested ClearView’s capabilities by applying it on a group of computers to Firefox. Once ClearView established Firefox’s base behavior, a team of hackers attempted to infiltrate the web browser with minimal success.

ClearView was tested on a group of computers running Firefox and an independent team to launch an attack on the Web browser. The attack team used 10 different attacks to inject malicious code into Firefox. ClearView was successful in all 10 attacks by blocking the malicious code and shutting down the program before its intended attack took effect.

With more and more information being stored digitally, giving hackers more incentive to infiltrate computers, ClearView is clearly a step in the right direction. However, what impressed me the most about this breakthrough in computer security is how ClearView demonstrates how software can evolve and defend against malicious attacks, much like our own bodies defend against viruses. While sentient robots may be a long way off, this idea of software which performs better over time by simply observing its own execution may be a prelude to smarter programs which grow based on its user’s needs or cars which adjust to how a person drives. For now, however, I’d be perfectly fine with never needing to run my anti-virus software again.

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?

(Source – PLoS Biology: Can an Infectious Disease Genomics Project Predict and Prevent the Next Pandemic?)

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.

(Image credit – Immelt and Vscan from GE website)

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!

(Image credit – Einstein) (Image credit – the Lone Ranger)