Monthly Archives: September 2011

Security

Gamers crack AIDS puzzle

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The news is about some amazing efficiency in solving problems found by using a “protein folding game” called Foldit.

Researchers have for over a decade been unable to solve the structure despite using many different methods. Even recently, the protein-folding distributed computer program Rosetta@home that uses thousands of home computers’ idle time to compute protein structures, was not able to give an answer. The Foldit players using human intuition and three-dimensional pattern-matching skills, however, were able to solve the problem within days.

The scientific article published by Nature Structure & Molecular Biology (“Crystal structure of a monomeric retroviral protease solved by protein folding game players”) concludes with some amusing analysis by the scientists.

The critical role of Foldit players in the solution of the M-PMV PR structure shows the power of online games to channel human intuition and three-dimensional pattern-matching skills to solve challenging scientific problems. Although much attention has recently been given to the potential of crowdsourcing and game playing, this is the first instance that we are aware of in which online gamers solved a longstanding scientific problem. These results indicate the potential for integrating video games into the real-world scientific process: the ingenuity of game players is a formidable force that, if properly directed, can be used to solve a wide range of scientific problems.

This reminds me of both my high school chemistry and physics teachers who would always start lab work by saying something like “now, let’s make this fun”. So the first question I get from this story is why it has taken the scientific community so long to recognize the power of channeling human intuition through an interface that doesn’t suck.

I have my theories, of course. When I worked on systems used for digital imaging and communications in medicine (DICOM), and more specifically on radiology technology, I found an odd dilemma in the medical field — the most advanced interfaces were the least desired by highly-trained practitioners.

Medical researchers had me deploying new Irix workstations with high-end graphic processors to develop 3D fly-through capabilities of the human body. After a CT or an MRI scanner was done taking images in “slices” of the body these Unix systems would put all the images back together again into a virtual human. The researchers expected doctors to jump at the chance to use 3D.

To the untrained eye, let alone a gamer, the ability to fly through a patient’s body looked like a fantastic advance in medicine. However, when surgeons and radiologists sat down to look at the big screens (20 inches was big back then) they were unimpressed.

I’ll never forget one late evening when a surgeon rushed in for a pre-op debriefing. I was called in for support, and I stood behind him as he scrolled around the 3D body. Then he said “I can’t use this nonsense”, stood up, and walked over to a wall of old fluorescent-lit white boxes covered in greyscale film images of the brain. He scanned the wall, made some “mmm hmmm” sounds and left.

I stared at the wall of “slices” of the brain. There were literally hundreds of pictures that the surgeon had to put back together in his mind. It seemed like an impressive skill but it also made me wonder why the ability to put a 2D world into 3D would prevent the ability to see in 3D.

That’s a long way of getting to the point that the history of doing things a particular way in medicine creates ruts of reliability. It takes a long time, perhaps even years, for the industry to assess, approve and then adopt technology that a gamer might take less than 24 hours to try and like.

Anyway, this story reads to me like the scientific community has finally found a way to do what others have been doing for years — leveraging gamers to solve problems. And who better to solve 3D problems than people who are highly trained in 3D visualization? That being said I also noticed a slight dig against gamers in the phrase “ingenuity of game players is a formidable force that, if properly directed”.

Are we to believe that gamers are not a formidable force if undirected, or that their own direction is not as formidable as one led by scientists? Seems to me the scientists are the ones who were in need of direction.

Poetry, Security

Kwame Dawes on Breaking in to the Theater

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The University of Nebraska at Kearney’s new hire in poetry does not hide the fact that he started out as a hacker:

Poet Kwame Dawes shared selections from his collection of 15 published books along with the stories behind the poems Thursday.

“I learned to write for the theater by befriending all the janitors and security guys in the theaters in Kingston,” the former Jamaican resident said. “I couldn’t afford tickets, so the janitors would let me in so I could watch rehearsals.”

Here is his poem “Storm” for the Pulitzer Center on Crisis Reporting

History, Security

Today in History: The Battle of Antietam

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Early in the morning on this day in 1862 soldiers of the Union stopped the Confederate offensive march north at the creek of Antietam in the fields of Maryland.

Soon we began to hear a most ominous sound which we had never before heard, except in the far distance at South Mountain, namely, the rattle of musketry. It had none of the deafening bluster of the cannonading so terrifying to new troops, but to those who had once experienced its effects, it was infinitely more to be dreaded. These volleys of musketry we were approaching sounded in the distance like the rapid pouring of shot upon a tinpan, or the tearing of heavy canvas, with slight pauses interspersed with single shots, or desultory shooting.

Nearly 100,000 men were ready to fight throughout the day. As the sun set only 77,000 were standing and 4,000 lay dead — the most casualties in one day in American history.

The majority of the Union effort was amassed at the center of the battlefield while smaller groups attacked first on the left, then center, and then the right. Their plan was to push in from a flank and only then drive forward with a numerical advantage. The initial attacks were mostly unsuccessful in making ground, however, and so the Union’s largest division never was fully engaged. The Union General was conservative and slow to react, despite having acquired a paper copy of the Confederate battle plans.

The Confederates then abandoned their offensive and retreated at night. This is believed to have been enough of an end to their march north that President Lincoln was able to issue the Emancipation Proclamation a few days later. Two months later, the Union General in charge at the Battle of Antietam was removed for failing to pursue the Confederates and win more decisively.

Update: Some interesting details in this video on how the battle set the stage for the President to renounce slavery

Energy, History, Sailing, Security

Do we know how to make software?

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Jeremiah asked and I did my best to answer without getting wrapped around the axle because he bragged to me about buying a big American car during the fuel price rise.

Here is my response:

Well, maybe you knew I couldn’t resist commenting on your automobile engine analogy. I’m still laughing from the time last year you told me ‘when gas prices went up, prices on Suburbans went way down, so I bought one to drive my five miles to work’. Clearly we still don’t see eye-to-eye on managing risk.

You say “the United States ruled the automotive industry; an industry we created from a machine we invented”. For brevity sake I’ll concede the industry was largely built by the US (not created) but I can’t let you assert that the machine was invented in the US. The engines of steam, electric, internal combustion, diesel; all were invented outside the US in the 1800s. I mean by comparison the US at that time was stuck in a rut over whether slavery was a viable engine to power its industrial production!

Yeah, ok, I know Ford gets lots of credit for ramping up his assembly line and blowing a whistle at his workers, but even that was an application of British automation developed and built 100 years earlier to support the quality and speed necessary for their military during the Napoleonic wars. Imagine watching a steam engine-driven system in 1808 that produced over 100 thousand blocks (pulleys) for the Navy. The Block Mills of Portsmouth proved that with an assembly line and machines just 10 men were made able to work as quickly as 100.

More to the point you say “The trend is that we (in the U.S.) invent something new, create an industry around it.” That seems to skip right past the fact that most industries in the US were started by European immigrants based on European ideas in place for many years before the US copied them. From Budweiser to Champagne, Cheddar Cheese to Chandeliers, what the US has really done well is bring down the price of goods and make them more accessible. In fact, that was an obsessive element to the Nixon administration that success would be determined entirely by the availability of goods. A steak on every table. And it’s true our shelves were stocked our pantries full while others in the world were still paying more for fewer goods, but somewhere in that heady explosion of prosperity out of the 1900s the US lost its sight of quality as a measure of success in “efficiency”.

You bought that Suburban, you said, because you perceived value, right? Did you feel like you were buying innovation? Quality? Maybe a trip to a car show to look at the latest models (all outside the US now) will change your perspective:

http://www.nytimes.com/2011/09/11/automobiles/as-frankfurt-show-opens-industrys-balance-shifts.html

“If it seems as though German manufacturers are on the leading edge of new, gas-free urban transportation solutions, it is due in no small part to the European Union’s strict pollution controls. ‘Today, all the innovation in the auto industry is coming from the German manufacturers…A little from Japan. None from the U.S.’”

NONE from the US. Our amazing ideas of “efficiency” apparently were not so.

I mean a four-door all-wheel-drive station wagon made by Volvo is expected to be available next year that delivers better horsepower than a Ferrari 308 and a Camaro Z28, yet will also provide 100 mpg. That should have been an American made vehicle. No reason that it could not have been built and sold here. We have the weather, the open roads, the crap to haul around. Oh, no reason except people were for some reason still buying Suburbans. You know I could go on about this forever and someday I MAY convert you to a highly resilient low-risk source of energy for transportation, even if I have to do it on the mat…but I’ll try to get back to the point of your post.

I think your definition of software may be too narrow. You say “software must be built by highly skilled people, whose skills are not trained up quickly or easily.” But isn’t that the very opposite of what is causing so many problems in code? Code is being written by many more people less trained and using toolkits. It is based on a massive rise in the amount of shared/borrowed/stolen code available. I see this most in recent cases of malware mutations — so many more people developing (or at least modifying) more code more rapidly than ever. The mobile app stores are another example. Anyone with a cheap personal computer and a few online tutorials now is in place to build and release software to hundreds of millions of users. Compare that to the training, samples and platforms of twenty years ago. Software is just flying off the wires now and it’s going to get even faster as more remote areas are connected.

You say “those who profit by the billions from creating software, like Microsoft, Oracle, and Adobe seem unable to ship multi-million line software projects on a deadline”. You’re looking at the wrong sources of innovation. That’s like criticizing the British Navy for deploying ships late (a critique as old as the British Navy — special note to the Falklands War deployment, which led to the development of ITIL). While the Navy isn’t going away and will continue to find ways to automate production, they are solving massively complex problems. The future of software build efficiency is less about the big guys just like ship building an ocean-going vessel for the masses is at a much smaller scale today. The lessons learned from the big expensive mistakes are applied faster, better and at smaller scales of automation.

So, I’d be one to argue yes, we know how not only to make software but hundreds of millions of people know how to save time by learning from the innovation of others — sharing knowledge and tools to reduce build times. I’d be happy to go more into the myths of commodity and innovation. I also would like to clarify trends and real numbers but I’ll leave those for another day (e.g. Today’s fastest growing telecom company? Skype is barely over 500 mil while India mobile is soon expected to have 1.2 billion subscribers). Alas, it’s time now to go make some more fuel for my engine.

Update: My comment has not yet been approved, so I’m glad I made a copy here just in case. I also have to point out there is some sweet irony; a post about efficiency and automation is taking a long time to approve a comment. Maybe it’s a manual process. :)