Bench Press

We have always sought out new frontiers and this generation is no different. Today’s frontiers can’t be found on a map. They’re being explored in our classrooms and our laboratories, in our start-ups and our factories. And today’s pioneers are not traveling to some far flung place. These pioneers are all around us — the entrepreneurs and the inventors, the researchers, the engineers — helping to lead us into the future, just as they have in the past. This is the nation that has led the world for two centuries in the pursuit of discovery.

-President Barack Obama,  Energy Speech at MIT October 23, 2009

As a candidate for President and throughout President Obama’s first year he has established himself as a friend of the scientific community. He has made many statements like the one above poignantly establishing the importance of innovation and scientific discovery in our nation’s goals. However, supportive statements don’t pay the bills and as I’ve had reiterated to me several times during my conversations with various professors at graduate school interviews; funding is king. Ultimately, the best way for President Obama to demonstrate his support of the sciences is to show us the money. He started off on the right foot with the science funding handed out in the stimulus package last year. The chart below illustrates President Obama’s proposed budgetary changes.

Minus the small decrease in funding for the CDC, many scientific organizations could potentially see sizable increases in funding. As I’ll be starting my graduate work in biosciences next fall I’m extremely happy to see the proposed increases. I’m quite surprised to see a reduction in funds budgeted to the CDC after the recent swine flu outbreak. However, the overall increase in funding is a huge step forward compared to the prior administration. Hopefully Congress will pass a budget with increases similar to the President’s proposed budget. These funds could be used to improve the financial status of many labs across the country that were affected by declining funding availability. I’ve got my fingers crossed that President Obama will continue supporting the sciences in not just his speeches but in his actions as well.

(Chart – Wired.com)

The Open Science movement is driven by the idea that collaboration and openness are good for innovation and discovery. After all, the logic goes, who is more likely to discover a cure for cancer: five research groups with different sets of skills and specializations who don’t share any information with one another, or five identical groups who actively pool their knowledge?

Ironically, that reasoning seems to have completely skipped over the biotech/pharmaceutical industry who seem intent on pursuing the “divided we fall” approach despite the escalating costs of drug development. The application of openness itself is especially relevant here, as a significant piece of the $800 million – $1.2 billion price tag that goes with bringing one drug to market is the cost of failed R&D projects.

This problem is one that is not only a burden on the shareholders and executives at these companies, but also a burden on the healthcare systems of people around the world, which end up paying more and waiting longer for drugs to make it through a company’s pipeline.

About a month ago, the New York Times cast a spotlight on this problem:

Although many companies have committed to publishing the results of clinical trials, whether or not they succeed, drug makers don’t typically publish information about projects that fail at an earlier stage. A result is that companies waste many millions going down experimental paths that their competitors have already found to be dead ends.

M.I.T. is proposing dead-end drug disclosure, a concept that goes by a euphemistic mouthful: “precompetitive information sharing.”

Drug makers may realize that the financial and medical value of sharing such information outweighs the competitive risk, said Dr. Gigi Hirsch, the executive director of the M.I.T. Center for Biomedical Innovation, the locus of the drug project. “There should be more information available about failed compounds in the interest of the greater good,” Dr. Hirsch said.

The traditional response from the pharmaceutical industry is one that is familiar to Open advocates – that intellectual property and proprietary platforms are necessary for the returns which drive investment in these spaces. But, this ignores two things.

First, the act of sharing information on failed assay hits helps to reduce the cost and time of development. The decision to invest in a particular R&D project is driven by returns, and returns are driven by development costs and the time it takes to get “money back”. While being more open about internal failures and successes will do little to change the cost of marketing, clinical trials, and many aspects of development, it will reduce a large portion of the time and cost of initial R&D (because of the wider availability of information) and the cost of failure (as there would be no need to pursue avenues of research on paths that have already been deemed a failure). So even if the prices and number of drugs sold diminish slightly due to the inability of a company to hold on to some early-stage proprietary advantage or the release of some of the details on their compound library, the time to market and cost of development diminish as well, helping to preserve the return on investment necessary to provide for the level of drug innovation and discovery that patients and doctors want.

Secondly, a move to openness does not necessitate unprofitability. It wouldn’t be realistic to ask companies to pursue a path which destroys the shareholder value they’ve been entrusted to protect. But, the fact that technology companies like Google and Nokia have been able to push open standards and open source yet retain profitability and innovation should hopefully signal to bio/pharmaceutical companies that it is possible to have both shareholder value and openness.

The path to profitable openness that technology industry practitioners like Google pursue is no different than the path that any company pursues: specialization. Google, for example, has specialized on high quality search results, effective advertisement targeting, and IT infrastructure management. As a result, there’s no reason for Google to prevent the broader technology industry from having access to the source code for its Chrome web browser, Android mobile operating system, or Google’s rich APIs to access the information you can find on its websites. In fact, Google seems to have understood that keeping its information closed would reduce innovation on the web, which would in the long-run hurt its own growth and profitability prospects.

I’d humbly wager that the value of protecting early stage failure and platform information is relatively minor in the grand scheme of pharmaceutical company value (and in fact some companies do publish failures, albeit only years after the experiment). I’d even humbly bet that major drug companies probably have much more significant expertise and differentiation in the steps after initial R&D, such as in compound refinement, clinical trials operation, process development, and computational analysis, etc. All of this should, at the minimum, shield existing drug companies from the “risks” of opening up on early-stage R&D failures and could even help existing drug companies compete by emphasizing these new capabilities as the determinants of success.

Nobody is saying that this path will magically materialize and produce awe-inspiring levels of profitability and growth overnight. But, when an industry is on the edge of a patent cliff (most blockbuster drugs are expected to become generic in the next couple of years), when its primary source of “value creation” seems to be in buying smaller companies, and when nations around the world are struggling with healthcare costs, I’d assert that the bio/pharmaceutical industry needs to change its practices.

As for how – I would propose the following compromise.

1. First, the NIH, PhRMA, or some other neutral authority should define a set of standards for what information should be contributed (balancing the desire to foster innovation through openness and the desire for companies to maintain the closedness they need to build proprietary advantages along other dimensions), create a standard for secure information sharing (which protects any individuals and patients and proprietary pipeline-related information) and govern compliance.
2. This body should then set up an information exchange/database for participating companies, academic institutions, government research centers, and medical institutions to share information and prevent non-compliant companies from gaining access (it’s not a perfect solution, but it could help assure companies who are worried that they will give up all of their information but not receive any in return).

This road would likely be a long and difficult one, but given the stakes and the potential benefits, I think it is one well worth taking.

(Image credit) (Image credit)

In a world with flashy distractions like YouTube and Modern Warfare 2, how the heck do you get students to be interested in monocyte recruitment?

One idea that the Federation of American Scientists is proof-of-concept-ing is the use of video games as tools for science education. To that end, the FAS developed, in conjunction with game studio Escape Hatch Entertainment, a game called Immune Attack (trailer below):

The premise of the game is pretty creative. A patient who suffers from a non-functioning immune system needs the player’s help to train her immune cells on how to fight off a bacterial infection. More detail can be found in the lesson plan on the Immune Attack website, but the game itself covers multiple phases showing:

• how leukocytes move from bloodstream to infection site
• how leukocytes are recruited by chemical signals
• how the immune system can recognize pathogen-associated molecular patterns
• phagocytosis (how white blood cells devour pathogens that they find)
• how white blood cells can recruit additional immune cells with chemokines
• how natural killers and MHC molecules can identify cells infected by viruses

While the game’s concept is original, the production value of the game is not quite up to a full-fledged professional studio. Although, to be fair, for only a ~500MB download and from an effort that wasn’t backed by a major game company, the quality was fairly impressive. The problem, though, is that the game mechanics are oriented around maneuvering about the 3D world to train the patient’s immune system how to respond to infection. The game is thus very dependent on the quality of the controls and the graphics. As I was playing on a Thinkpad T400 using a Trackpoint, it was actually fairly difficult at times to do the maneuvers necessary to move on to the next level.

The interface was also somewhat klunky – being similar enough to a standard first-person shooter controls but with enough variations to make the controls a little awkward (the need to hold down the right mouse button while steering with the mouse and the inability of the keyboard to change the pitch of motion were annoying). The software also didn’t feel complete bug-free. Just to see what would happen, I deliberately failed a mission requiring me to identify and destroy 5 infected cells before a viral infection destroyed 5 healthy cells. When I re-started the mission, the count of destroyed healthy cells began at 5 – is it any wonder that I failed the mission, again?

With all that said, I do believe that this was a very impressive effort that just needs a little polishing. The music and graphics were a little hokey, and the lesson plan materials need to be fleshed out a bit better, but the game mechanics were designed very well to ingrain visually and physically how monocyte transmigration worked, how white blood cells are recruited, and how basic viral and bacterial pathogens spread infection. While I wouldn’t say I’m yet fully convinced that this approach will work, I am optimistic that this is a good method to help scientists convey very complicated phenomena to students.

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.

(Image Credit)

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)

We’ve previously covered the computer modeling solutions being used to model and track the paths of near-earth asteroids (especially those which might treat Earth like a dartboard), but for those of you not content to just sit at home while NASA scientists do all the tracking, the asteroid trackers at NASA’s Jet Propulsion Laboratory have made it now easier to follow what’s going on in the world of near-earth asteroids from the comfort of your own home.

The first little gadget they’ve developed is a computer widget (pictured on the left) which is compatible with the Mac OS and Yahoo widget engines.

What it will show is a list of the next five near-earth asteroid approaches (within ~20x the distance of the moon) and an estimate of their size (including a pictogram depiction of what that size means) as well as their distance. The widget will also make it easy to find more information about the particular asteroids it is identifying (an example is linked here) which will show off a dynamic Java applet map of the asteroid’s orbit through the inner solar system (which you can manipulate so you can see how the orbit looks in 3D) as well as a wide range of data on the asteroid such as the eccentricity of an asteroid’s orbit (in layman’s terms, how oval-like versus how circular), the orbital period (the time it takes for an asteroid to complete one rotation around the sun).

The second thing the brains at NASA’s JPL have put together for researchers and amateur astronomers is a Twitter account (@AsteroidWatch), which accompanies NASA JPL’s main Asteroid Watch site. The feed went live on July 29, 2009 and, although not written in the cutesy voice of the MarsPhoenix twitter account (which followed the exploits of the Phoenix Mars probe NASA launched a while back), the AsteroidWatch feed so far has reported on near-earth asteroids and new reports and articles issued by NASA’s official asteroid tracking team.

You can follow the BenchPress team on Twitter! You can follow us at Anthony (@AnthonyPhan), Ben (@BenjaminTseng), Eric (@EricSuh), and Kevin (@Kevin_Tseng).

Watch out. That person who just fragged you in Counter-Strike might’ve been using eye-tracking software to do so. COGAIN, an EU-funded network of excellence on Communication by Gaze Interaction. While most eye-tracking software is used simply for typing on an on-screen keyboard, COGAIN enhances eye-tracking capability by providing a real-world gaming experience. Aimed at helping those disabled with motor neuron disease and cerebral palsy, COGAIN’s eye-tracking software allows users to play computer games with just the movement of their eyes. Their innovative technology uses commercially available eye-trackers which use cameras to monitor the gamer’s eyes, and COGAIN’s intuitive interface allows for a user-friendly experience.

Glancing to the left or right will turn the virtual character in that direction, for example, while staring at the centre of the screen will make the avatar run forwards. Because the software is independent of the game itself, it can be used to play virtually any game that requires mouse and keyboard inputs.

Currently, COGAIN has pre-programmed 12 different gesture sequences which will activate different keyboard and mouse events. More commands can be programmed if the user wishes. COGAIN hopes their free software will be fast enough to play real-time 3D games.

COGAIN’s eye-tracking software is particularly refreshing because it demonstrates how technology can impact and aid the disabled. As technology evolves and progresses, it’s important that we not only think up what sort of applications we can adapt technology to we should be mindful of people with disabilities and allow them to have as rich a computer experience as others.

The heartbeat of the news.

Ever since June 25, 2009, Michael Jackson’s death has been the talk of the nation, his face plastered over web articles, newspapers, and television stations. His death broke the record for the number of users on Yahoo news at any one point in time, topping even President Barack Obama’s inauguration, and even Google believed its servers were under attack due to the sudden spike in web searches for the moon-walking legend. However, have you ever wondered why the news of the King of Pop’s untimely death has stayed in the media for so long, while other news topics, such as the death of another cultural icon, Farrah Fawcett, quickly died out?

Jon Kleinberg, Jure Leskovec, and Lars Backstroma, from the computer science department at Cornell, sought to answer these types of questions by tracking the life-cycle of news articles for a three month period during 2008. Their research included 20,000 mainstream media sites and over 90 million articles. Using a complex algorithm which could identify certain phrases in different news articles such that the computer could mark them as being of the same subject (a task that has proven to be very difficult time and time again), the team tracked the movement of news using across blogs and news sites across the Internet. Armed with an extensive pool of data to sift through and analyze, the three researchers discovered an astounding pattern that was shared throughout most news topics.

They found a consistent rhythm as stories rose into prominence and then fell off over just a few days, with a “heartbeat” pattern of handoffs between blogs and mainstream media. In mainstream media, they found, a story rises to prominence slowly then dies quickly; in the blogosphere, stories rise in popularity very quickly but then stay around longer, as discussion goes back and forth. Eventually though, almost every story is pushed aside by something newer.

Before research like this was done, many editors and journalists perceived something they described to be a “news cycle.” However, with no quantifiable data, there was no way to be confident whether this was just their perceptions or an actual phenomenon. With the information collected by these Cornell researchers, they believe the latter to be the case and have started to create mathematical models which would accurately describe the life-cycle of news.

The slow rise of a new story in the mainstream, the researchers suggest, results from imitation – as more sites carried a story, other sites were more likely to pick it up. But the life of a story is limited, as new stories quickly push out the old. A mathematical model based on the interaction of imitation and recency predicted the pattern fairly well, the researchers said, while predictions based on either imitation or recency alone couldn’t come close.

This type of news excites me because it shows how technology and the Internet have produced a tangible result (in this case, a physical model to the life cycle of a news article) to a question that would have been unsolvable 20 years ago. Truly the capabilities of technology to solve even the most abstract problems are limitless.

(Image Credit)

In 2003 an unknown virus suddenly emerged in Guangdong China and proceeded to spread rapidly around the world. The SARS coronavirus disseminated around the world via the global air transportation network with stunning efficiency, highlighting one of the unintended consequences of the globe’s vast airline system. After the SARS outbreak, a group at St. Michael’s Hospital in Toronto, took it upon themselves to study the SARS outbreak in detail. The end goal to develop effective strategies to deal with future epidemics. Their project dubbed Bio.Diaspora took a multidisciplinary approach in analyzing air traffic patterns and the distribution of infectious diseases. Their self proclaimed mission:

Understand global patterns of human travel via commercial airlines as a way to predict how emerging infectious diseases are most likely to spread around the world – and consequently apply this knowledge to help the world’s cities and countries better prepare for and respond to global infectious disease threats of tomorrow.

The Bio.Diaspora team believed that not only more applied research into the impacts of global population mobility on public health and security is necessary, but access to quality data on global air transportation and traffic patterns is needed as well. They sought to fulfill this need by:

[D]eveloping a data warehouse for the sole purpose of conducting methodological and applied research on commercial air travel and emerging infectious disease threats. This report embodies rigorous analysis of these data from multiple scientific perspectives – medicine, infectious diseases, public health, health policy, biostatistics, geographic sciences, network analysis, computer sciences, and mathematical modeling.

Their thorough analysis accounted for numerous factors and yielded a report just prior to the emergence of the H1N1 influenza (Swine Flu) pandemic. One of the really interesting parts of the Bio.Diaspora report was the numerous simulations done on potential H5N1 avian influenza transmission from emergence in numerous potential cities around the world.

Click through for interactive version.

The above graphic illustrates the likelihood of importation of H5N1 avian influenza into various areas of the world with an epidemic beginning in São Paulo, Brazil. This caught my eye as it seemingly foreshadowed the H1N1 epidemic. After the emergence of H1N1, the Bio.Diaspora team went back to study the air traffic patterns of the initial stages of the spread (March and April 2009) from Mexico. Running simulations like those from the Bio.Diaspora project’s report they were able to produce predictions based on the flight itineraries (data shown below) that correlated highly with the observed transmission pattern. Their complete analysis is published in the New England Journal of Medicine.

Destination Cities and Corresponding Volumes of International Passengers Arriving from Mexico between March 1 and April 30, 2008.

The Bio.Diaspora project team’s work on both the SARS epidemic and now the H1N1 pandemic illustrate that there’s still much to learn about managing public health crises on a global scale thanks to the highly interconnected nature of today’s cities. It’s a much smaller world now and new tools and ideas will be necessary to deal with future emerging diseases.

(Bio.Diaspora)(Spread of a Novel Influenza A (H1N1) Virus via Global Airline Transportation)

On Bench Press, we usually discuss technologies to empower scientists to do research or to better communicate with each other and with the public. But, technologies can also help the “casual” fan appreciate science as well. Case in point: Google recently announced a new application available for Android phones called Google Sky Map. The concept is quite ingenious. If ancient navigators used starcharts and compasses to determine their location, why can’t a phone that knows its location (via built-in GPS) and its direction (via magnetometer and accelerometer) be used to figure out what stars are up above?

Or in other words, Google took this physical setup (very cute setup from Google for how Google Sky Map works) of what is basically a sextant, compass, and calendar:

And replaced it with a smartphone:

I haven’t had a chance to play with it (as I don’t own a G1), but the application looks very nicely packaged. You can use it to figure out what stars are right above you. But, the coolest feature is the ability to use the application to point you in the direction of something you’re interested in seeing (e.g. the planet Saturn).

More details are in the video below. You can get Sky Map for Android through the Android Market. For anyone who’s tried it, let us know what you think in the comments!

(Image credit – Google)