Bench Press

Some scary news if you’re an IT guy (although promising if, like us, you believe in the power of alternative processors), but basically it shows that the Playstation 3′s super-powered Cell processor really is useful for more than just Metal Gear Solid. 

Brilliant visual depiction of research described below

By using the computational power of a cluster of 200 PS3s, researchers were able to create a fake certificate allowing them to usurp certification authority from Verisign’s RapidSSL public encryption method. What that means is that the researcher’s were able to create their own certificates, meaning that they could fool any browser into believing whatever identity the researchers threw at them. Translated into real-world terms, it means that the researchers could have, had they wanted to, convinced your browser that they were your bank, your ISP, eBay, or potentially a legitimate Microsoft/Apple software update. 

Image of the "Playstation Lab" cluster which executed the hack.

The source of the hack comes from a weakness in using MD5, a popular hash-generating function which is supposed to turn large files into short 128-bit “passwords”. A 128-bit password may not seem like much (imagine converting a 200 page book into a short 200-letter sentence, you can’t recreate the book from that sentence), but the magic is that, like other cryptography methods, it is supposed to be incredibly difficult to create two files with the same MD5 “password” — a so-called “collision”. 

However, MD5 is not perfect, as a computationally intensive means of finding collisions was demonstrated in 2007, and while many certificate authorities had switched away from MD5, there were few who genuinely believed that the computational power was readily available to break it. And, while 200 Playstation 3′s is not super-easy to come by, given the profitability of such a scam, this recent exploit demonstrates that it no longer requires a massive multi-million dollar supercomputer to do the number-crunching needed (the researchers estimated that only $20,000 worth of computing power on Amazon’s Elastic Compute Cloud was needed to generate the fake certificate).

Thankfully, Verisign has confirmed that they are committed to phasing out MD5, and Microsoft and Mozilla have been fully briefed on the risk. Let us hope that is more than just empty promises.

(Image source: Playstation Lab cluster)

Like many of you reading this blog I’m continually impressed with the Web 2.0 revolution. Wikis, blogging, and social networks are reshaping media and communication by creating new norms about content (creation and consumption) and participation. With the usefulness of these technologies on display everyday adapting them for use in science is a logical step to many scientists. This has set off a rush of experimentation and discussion on the potential of Science 2.0. As is common in the scientific world the acceptance of new methodology for doing pretty much anything can be hotly debated and the adoption of Science 2.0 is no exception.

Being a tech geek and a young scientist I find it easy to see the promise presented in adapting internet technologies to science. The community empowering nature of Web 2.0 technologies seems to me a perfect fit for scientific work and is what drew me to start taking the plunge into Science 2.0. As I started to delve into the tools and communities that are currently present a few things thoroughly impressed me:

• Integration of tools – Citeulike and Friendfeed are an awesome integration of two separate services. Allyson over @ The Mind Wobbles (I hope that title sticks ) has a great post detailing the power and general experience of Citeulike and Friendfeed.
• Availability - Despite the somewhat fledgling status of Science 2.0 it’s easy to google for several different science social networks, find science focused groups on places like Friendfeed, or find various lab notebook replacements (e.g. OpenWetWare).
• Great community – The Web 2.0 movement would be nothing without the people that generate and participate in the various communities. This holds just as true for Science 2.0 and the quality of the science community is put on display each and everyday through amazing blog posts (just pick any of the blogs on the right), online discussions, and development of new tools.

While my dip into science on the web has been very positive, there are a few things that I think could be done to help push Science 2.0 further:

• Consolidation of some communities – I know I talked about the easy availability of a variety of services as something that impressed me, but duplication of sites (wow there are a lot of social network sites for science) also produces an unintended consequence of diluting the community. While I love the fact that you get really used to seeing the same people participating in discussions on say Friendfeed, I’d be more than willing to exchange a bit of familiarity for larger membership in a few central communities.
• Social Networks – I’ve really only had a chance to look at Labroots in any real detail so far but from first impressions and from commentary I’ve seen I think it holds true that the scientist specific social networks still leave a lot to be desired. They are mostly me-too services with few if any compelling/differentiating factors that can draw a critical mass of users. If anyone has found one in particular that stands out above the others feel free to drop me a line I’d definitely be interested in checking it out.
• Spread the word – Ultimately the best thing we can do as a community is continue to talk about science on the web to our colleagues, mentors, and bosses. Helping to grow the community one member at a time is something we can all do.

Overall everything I’ve seen and been able to use so far makes me very optimistic about the direction Science 2.0 is headed. As 2008 ends I look forward to seeing what 2009 will bring (hopefully not lightsaber wielding raptors…).

(Image Credit: Visualization of the relationships of over 700,000 scientific papers published between 2001 and 2005)

As the problems scientists solve become more and more complex, so do their demands for computational power. One approach to addressing this has been to build faster, more powerful computers, potentially with chips better suited to performing advanced calculations (like graphics cards or IBM’s Cell processor). But, this approach has serious limitations — mainly that it’s expensive to build and to maintain these supercomputers.

Some researchers, however, have turned to a radically different approach. Instead of building a bigger, better mousetrap to deal with more mice, the distributed computing approach takes the approach of placing many small, cheap mousetraps. The result is cheap “supercomputers” which are able to “pool” the computing power of many computers connected over a network.

This approach has been used by projects like Folding@Home and SETI@Home which are able to combine computing power from volunteers over the internet to do the number-crunching needed to simulate protein folding or scan deep space for extraterrestrial life. SETI@Home was the first such large-scale distributed computing platform. This platform, now the Berkeley Open Infrastructure for Network Computing (BOINC), is today used for many other distributed computing projects such as attempts to search for gravitational waves, do climate modeling, and simulate particle collisions in the Large Hadron Collider.

Folding@Home, a project started by the Pande group at Stanford to use distributed computing to study protein folding uses a similar approach, albeit with different underlying software (is it any wonder that a Stanford group doesn’t use Berkeley’s distributed computing platform?! ) . It has probably been the most successful distributed computing approach to date, and, as a testament to the power of distributed computing, has become known as the first computing system to break the petaFLOPS barrier – e.g. capable of one quadrillion floating point calculations per second! This has enabled the team to do protein-folding simulations on a scale of ~10 micro-seconds.

But, as impressive as the science achieved by distributed computing projects is, what impresses me the most is that projects like Folding@Home and SETI@Home have defined some brilliant new ways to do science:

• Use the internet – It’s a common theme on Bench Press, but with more and more people having faster and faster access to the internet, the potential for distributed computing becomes greater and greater. As Folding@Home demonstrated, such approaches can produce computing systems as powerful (or potentially more powerful) as leading supercomputer systems at a fraction of the cost.
• Mobilize the public – We’ve discussed ways for the scientific community to reach out to the public like using social media and creating interactive applications/tools for the public to use, but efforts like Folding@Home illustrate a way to not only reach out to the public but to get them vested in science. In a world where high school science teachers find it difficult to get teens interested in science, initiatives like Folding@Home have created a system where teams of individuals compete on who can contribute the most to the effort! Instead of simply hoping that the public will continue to fund and listen, why not borrow a page from the many existing cancer-walk-a-thons and make it easy for the public to get involved?
• Leverage new technology – It may not come as a surprise to our readers that a significant amount of the computational power at Folding@Home comes from graphics cards and Playstation 3’s. But, while many “mainstream” supercomputers ignored the new power afforded by these new chip types, Folding@Home developed software so that volunteers could quickly and easily use these powerful chips to boost their Folding@Home scores. The Folding@Home initiative also developed software to take advantage of innovations AMD and Intel included in their chips (new multi-core architectures and special instructions to speed up calculations). Is it any wonder, then, that Sony, NVIDIA, and AMD have all publically announced support for the initiative with their products?

I don’t pretend that every scientific problem is amenable to a distributed computing initiative, but to some extent, I believe that every scientific endeavor has something valuable to learn from the success of Folding@Home and SETI@Home and their brethren. To that end, I sincerely hope to see an open-source distributed computing architecture like BOINC but with:

• Support for new chip technologies – To provide greater value to the scientific effort, the architecture should support new chip technologies like Intel’s SSE extensions, SMP, or stream processing
• Client contribution tracking – To make it easier for volunteers to know how much they’ve contributed and/or have contests on how much they’ve contributed, a simple system to enable users/administrators to track the effort is needed
• Better security – Medical initiatives and volunteer privacy concerns demand that very fine and specialized security controls are necessary. Support for sophisticated encryption and authentication are a must.
• Linkage to social media – This probably seems extraneous, but since distributed computing efforts depend on motivated volunteers actively seeking out new volunteers, a successful architecture needs to make it easy for volunteers to share their progress with their friends whether it be via blog, or social network, or Twitter, or anything.
• Tie-in with new cloud computing systems – Along the theme of cutting costs, it is reasonable to assume that as offerings like Google’s App Engine and Amazon’s EC2 and technologies like MapReduce become better developed, we will see cash-strapped research groups using the power of “Clouds” to hold their computing power – after all, what is distributed/grid computing other than a specific variant of cloud computing (de-localized, pooled computing)? It’s probably necessary, then, for the new distributed computing architecture to more easily link with EC2 or MapReduce or App Engine.

Anyone else have any thoughts?

(Image Credit – picture of the internet) (Image Credit – Folding@Home computing power)

Obsolete?

You see the car commercials. Short clips of dummies getting whiplash. Air bags expanding in slow motion. The message is always the same. “Our vehicles have been tested and proven to be safe.” But how do you really know that those plastic and steel doppelgangers are accurate representations of their organic counterparts?

Welcome to virtual crash-test dummies. A group of engineers at the University of Virginia’s Center for Biomechanics have joined together to create virtual test dummies modeled inch-for-inch after a human body to help simulate car accidents. While they might not be as flashy as crumpled cars and flying shards of glass, these virtual test dummies may represent a breakthrough in accident simulations. No detail of the human body is left unaccounted as this team of engineers is going to model many of the major organs in the body including the heart, lungs, and liver.

Richard Kent, one of the team leaders at the University of Virginia, had this to say:

“We are creating models, based on the actual anatomic details of the human body, that will respond to stress and strain and impact in the same way the actual human body does, so we can see precisely how injuries occur,” Kent said. “The ultimate result will be cars with far better safety systems, minimizing the severity of injuries and the frequency of fatalities.”

What I find most intriguing about this project is how it has the potential of revolutionizing safety. With this technology, researchers will be able to have a panoramic view of how a neck breaks or a bone is shattered. We can correct possible safety hazards within vehicles and bring safety regulations to an unprecedented high standard. Automotive developers will be able to run millions of simulations without spending millions of dollars in supplies. Accident investigators will be able to recreate an entire accident scene without needing to make too many guesses on how the crash transpired. And these are just a few of the implications on how test dummies will affect the automotive industry. Think of how NASA, Six Flags, or the military could use these virtual dummies in their work. Not to mention how this might pave the way to model all things virtually: bridges, buildings, elevators, etc. And all this with the ability to run millions of simulations with just the click of a button.

Part of why I became so interested in science as a kid (apart from watching Bill Nye) was seeing the application of science in medicine. Seeing the development of new medicinal techniques thanks to innovative research made a lasting impression on me. I guess that’s why a level of childhood excitement tends to pop up when I read about things like new imaging technology and future surgical innovations.

A schematic of Dr. King's cancer filtering concept. E-selectin attracts the cancer cells thereby exposing them to TRAIL as they "roll" along the device wall. This triggers the cancer cell's death. Image: Kuldeep Rana

Once again I felt that childhood excitement popping up as I read about a new device being developed by Dr. Michael King and his group at Cornell designed to someday remove cancerous cells from a patient’s bloodstream. King’s device takes advantage of a well studied mechanism of our immune system which is the recruitment of white blood cells to blood vessel walls with adhesion molecules known as selectins. Since selectins recruit cells based on specific carbohydrates Dr. King realized that this adhesive property could be utilized for slowing down cancer cells in order to target and destroy them.

After slowing down the cancer cells to a “roll” the cells can then be exposed to a protein called TRAIL (Tumor Necrosis Factor Related Apoptosis-Inducing Ligand) resulting in the release and then the apoptotic death of the cancer cells. This makes King’s device more than a simple sieve as he explains, “It’s a little more sophisticated than just filtering the blood, because we’re not just accumulating cancer cells on the surface”.

King’s device is impressive in it’s simplicity and tests of the device’s efficacy appear promising.

King’s research showed that the device can capture and kill about 30 percent of cancer cells flowing past it a single time, with the potential to kill more in the closed-loop system of the body. Used in combination with traditional cancer therapies, King said, the device could remove a significant proportion of metastatic cells, “and give the body a fighting chance to remove the rest of them.”

The team also showed that a system in which the cancer cells “roll” over the target molecules – presenting their entire surface to the molecules – is four times more effective than a static setup in which the cells and proteins make contact at a single point.

Of course as excited as I am to see this type of work being done, as Dr. King points out moving his concept to the clinic may take many years. I’m looking forward to reading the paper in Biotechnology and Bioengineering and seeing what others will come up with from Dr. King’s work.

No they haven’t actually, although Eric’s girlfriend threw me for a loop by sending me an IM with that headline.

However, my disappointment quickly melted by the website she linked me to and the adorable particles therein:

The Higgs Boson - found!

They’re brought to you by “The Particle Zoo”, which was inspired when an aspiring physicist realized that each particle seemed to have its own “personality” — why not make them into little plushies? I happen to think the Gluon and Dark Matter are especially cute:

Particle Zoo promises the release of “anatomically correct” particles (so probably breaking out some of the particles into their quark “components”) and some sort of “quantum duck” in 2009.

The real question now is, who will buy me one for the holidays?

Having spent the past couple weeks helping pack up and move the lab. I noticed my lab had an abundance of ancient data storage devices. Various floppy/zip disks and future museum pieces (Macintosh LC anybody?) were found hiding in all manner of locations. While I’m certain that we have paper copies of any data that could be found in those disks and computers archiving or even simply accessing the data on many of them might be impossible today.

An article from Physorg.com discusses the potential of a “digital dark age” resulting from an unintended consequence of continued technological innovation. Much like the inaccessible data that I found during my lab’s move, society’s rapid digital advancement has rendered it vulnerable to what Jerome P. McDonough, assistant professor in the Graduate School of Library and Information Science at the University of Illinois at Urbana-Champaign terms a “digital dark age”. The whole article is fascinating as it details several potential data black holes. A few interesting examples:

Magnetic tape, which stores most of the world’s computer backups, can degrade within a decade. According to the National Archives Web site by the mid-1970s, only two machines could read the data from the 1960 U.S. Census: One was in Japan, the other in the Smithsonian Institution. Some of the data collected from NASA’s 1976 Viking landing on Mars is unreadable and lost forever.

It’s a shame that valuable data from, not only a historic event, but also one of such exploratory significance is now lost forever. McDonough goes on to talk about the potential loss of political and popular culture due to data obsolescence and closed platforms.

McDonough also cited Obama’s political advertising inside the latest editions of the popular videogames “Burnout Paradise” and “NBA Live” as an example of something that ought to be preserved for future generations but could possibly be lost because of the proprietary nature of videogames and videogame platforms.

“It’s not a matter of just preserving the game itself. There are whole parts of popular and political culture that we won’t be able to preserve if we can’t preserve what’s going on inside the gaming world.”

McDonough’s discussion of videogames is only the tip of the iceberg. The enormous amount of user generated content that currently provides so much amusement (youtube, failblog, etc…) is a large part of modern culture and it’d be a shame if measures aren’t taken to ensure that future generations have access to it. Hopefully we’ll heed the warnings of information scientists like McDonough and begin making progress towards protecting our digital information by attempting to future proof as best as possible.

Personally after sorting through and moving the “digital archives” of my lab I’m ready to start taking some steps to future proof my digital existence.

Steps that I plan on taking:

• Reducing my reliance on proprietary file formats (bye bye Word).
• Duplicating my backups onto various media periodically.
• Migrating to new storage technologies, such as “the cloud” (Google engineers can figure out how to keep my data safe, right?)
• Make sure this blog’s future proof =).

Any suggestions on other steps I could take?

A completed magnetometer.

The age old dilemma of magnetic resonsance imaging: do you sacrifice precision for size, or size for precision?

Generally, behemoth MR machines are required to produce images of great detail. The downside? Price, immobility, and an inability to take the device to the field. The tradeoff of using their smaller, less expensive counterparts, however, is their lackluster resolving power. This could all change with John Kitching’s new developments in MR technology. Kitching, a physicist at the National Institute of Standards and Technology, is working on smaller, less expensive MR machines with resolutions that rival their larger cousins. Taking a new spin on an old idea, Kitching has adapted the procedure of producing atomic magnetometers and taken it to a significantly smaller scale.

The result: highly sensitive magnetic sensors about the size of a grain of rice. Kitching believes that mass production is not too far off in the horizon, and with an army of tiny magnetic sensors, the possibilites are endless. Pocket-sized MRIs, anyone?