The Quantum Tunnel

Science and the World around Us Volume 1, Number 3, May, 8 2011

Volunteer Scientist and Collective Thinking
This article first appeared in the Novenber 2010 issue of The Next Door Magazine

Distributed Computing
While there are several real life citizen science projects, the internet has allowed people to take participate in new and different ways by donating computer resources, either in the form of processing power and storage; this phenomena is known as “volunteer computing”. Some projects require massive amounts of computing power to process equally massive amounts of data or just to perform lots of calculations and while it is possible to use supercomputers for these projects, these machines are expensive and research groups must often compete with each other for processing time. One way to get around this is through the use of distributed computing. A computer can be programmed to perform a specific task, whether it is modeling climate data or cracking encryption codes, and if powerful enough can chug through the calculations all on its own in a reasonable amount of time. But what if we could break the task into smaller bits or work-units, bite sized pieces of data if you may, so that a number of less powerful processors can handle the task (something comparable to your desktop computer) and achieve the same results? In fact, the speed in which the task could be accomplished would depend on number of individual processors you had at your command. All that will be needed is a central computer to coordinate the distribution of tasks and to put everything together. This is the power of distributed computing and it allows research groups to achieve super-computer processing speeds at relatively low costs. But this is still costly as the infras-

David S. Latchman

In Walt Whitman’s, “When I Heard the Learn’d Astronomer” the poem’s protagonist escapes the lecture hall to wander outside and enjoy the majesty of the night-sky above. While many of us feel the same exasperation when confronted by the complex language that pervades any scientific or technical field, this hardly indicates a lack of interest in the sciences. People are naturally curious about the way things work and the world around them and if given a chance to actively participate in a scientific research project, many would jump at the chance to do so. Citizen Science is the term used to describe projects or scientific works in which volunteers, many of whom have no scientific training, perform research related tasks. This allows scientists to accomplish objectives that would otherwise be impossible and can also help promote public engagement with research and science in general. Two of the most popular citizen science projects include the Audobon Society’s Christmas Bird Count which seeks to provide a bird census in the Western Hemisphere through the efforts of volunteer bird counters and the World Water Monitoring Day which builds builds public awareness in protecting water resources by encouraging people to conduct basic water monitoring of local water bodies.

Newsletter Contents:
Volunteer Scientist and Collective Thinking . . 1

The Quantum Tunnel Newsletter

Vol. 1, May, 8 2011

tructure is needed to network all these computers together. What if there was another way? Depending on what you’re doing as you sit by your computer, whether it is typing a letter on a word-processor or just passing the time playing Solitaire, the majority of your computer’s processing power goes unused; this is typically the case for the majority of computer users. But what if we could do the same thing that a distributed computer network seeks to do and use those “wasted” processor cycles all over the world and allow the computers to communicate over the internet, another huge global network? The research group at some university would manage the server that’s in-charge of distributing work-units to interested participants and this would achieve the same results as if they built the network in a room themselves. All users would have to do is download and install an application to communicate with the server and get a work-unit. When the processing is finished the application uploads the finished data to the server. The question that remains is, would people be interested in taking part in such a project? In January 1996, the first such project was started, the Great Internet Mersenne Prime Search (GIMP) to find Mersenne prime numbers. Prime numbers are special, not just because they can only be divided by one and itself but because they elucidate certain properties of numbers which are at the center of the oldest and most profound mathematical problems today. Mersenne primes are extra special in that they fit a certain formula, 2 p − 1, where p is also a prime number. Some questions that abound amongst mathematicians include how many of these exist and what they look like and the only way to solve this is to calculate them, usually through the “brute-force” method of having a powerful computer going through all the possibilities until the next number is found. Within a few months of the project start several dozen people had joined and by the end of the first year, several thousand. This project was so successful that it discovered its first prime before year’s end and over a dozen Mersenne primes have since been discovered, the latest as of April 2009. Several other distributed computing projects would follow but the most popular project to date and the one that received the most media attention was the SETI@Home project.

Computers unite to find ET
SETI, short for the Search for Extra-Terrestrial Intelligence, seeks to discover sentient life in the universe by using scientific methods to search for electromagnetic transmissions on distant planets. For

the past few decades, data has been collected from the Arecibo Observatory in Puerto Rico and this data has been distributed to volunteers around the world to analyze for the presence of intelligent alien life. While nothing has been detected to date, the project has proven one of its other goals, that the concept of ’volunteer computing’ is a viable and practical way to do scietific research. Researchers at SETI would later improve their system to allow other projects from other groups to participate and the Berkeley Open Infrastructure for Network Computing (BOINC) was born in 2002. This is an open platform that allows groups from every field to participate. It is even designed to allow users to participate in more that one project as well as decide how their computing resources can be allocated to each project. Some projects include problems in protein folding, the search for gravitational waves, the search for the best organic compounds for solar cells and energy storage devices as well as testing climate models and the search for drugs to fight cancer. In short, whatever your personal interest there is likely to be a volunteer computing project for you. Distributed Thinking and the Search for Comet Dust While the computational capabilities of computers far exceeds that of human potential, there are limits to what they can do. In 1999, scientists aboard the MIR mounted special glass plates on the outside of the space station to track cosmic rays. As the cosmic rays pelted the glass they left microscopic tracks that were revealed after chemical etching. The best computer image correction and recognition algorithms are inadequate when it comes to identifying these tracks so the lead investigator, Andrew Westphal a UCB physicist, had to manually look at each image for the presence of cosmic ray tracks; a tedious and ofttimes boring process. This experience lead Westphal to the idea of distributed thinking. While this may sound like something the Borg would do, the fictional cybernetic race and antagonists in the Star Trek franchise, it isn’t. Instead of volunteering their computer’s resources, people do something that computers aren’t as capable of, pattern and spatial recognition. At the current rate of progress, it may be several decades before a computer’s image processing abilities will match that of a human. In February 1999, NASA launched a spacecraft that would catch up with a comet and capture its dust in a set of aerogel blocks. Finding these microscopic dust particles embedded in these blocks was similar to the problem that Westphal faced and the Stardust@Home project was started in August 2006; while not a part of the BIONC group at Berkley, the @Home suffix pays homage to the project. This project faced several hurdles in the beginning with 2

The Quantum Tunnel Newsletter

Vol. 1, May, 8 2011

Figure 1: Screen shot of the Seti@Home screensaver program. its users. Just as a scientist must learn to calibrate his instruments to get the best results, project developers needed to find ways to ’calibrate’ participants; users needed to be trained to distinguish between natural artifacts and cracks in the aerogel from the real comet dust they were looking for. The project also had to deal with the issue of cheaters who would flip through as many images as possible to achieve high scores and rise through the rankings. Thus there needed to be a way to assign a skill level that would assess how a participant actually performed as well as determine how many volunteers or ’dusters’ were needed to reach the same conclusion about an image before a result could be believed. opment of many diseases; diseases such as sicklecell, Alzheimer’s, Parkinson’s and mad-cow diseases can all attributed to misfolded proteins. In chemistry, we learned that a molecule’s properties depends on the number of atoms that it is made of but that is only half the story; how twists and turns or if it is laid out straight also affects its properties. This problem is computationally intensive as there are many ways in which a protein molecule can fold. The smallest protein molecule contains several hundred building blocks, or atoms, all of which are free to move. The number of ways each atom can move is known as its Sdegree of free¸ ˇ domT and this results in literally thousands of ways in which a molecule can be folded. A computer must thus go through all these possibilities to arrive at an optimal solution. As users watched their computers chug away and folded molecules on screen, many of them remarked that they could do better on their own and the Foldit game was born. The Foldit program doesnŠt just utilize the image recognition abilities of players but also immerses the player through the use of chat rooms and wikis allowing them to collaborate and solve problems as a group. One of the startling findings of this project is the sense of intuition that humans bring to this project 3

Scientific Discoveries and Games with a Purpose
The Foldit game was born out of the Rosetta@Home project, another BOINC program, that was designed to perform simulations of protein folding. This type of game is known as a “Game with a Purpose” as players solve problems as a side-effect of game play. Accurate simulations of the ways in which protein molecules can fold, or misfold, are important to scientists as it helps them better understand the devel

The Quantum Tunnel Newsletter

Vol. 1, May, 8 2011

Figure 2: Screen shot of the Rosetta@Home screensaver program. that can not, and probably never will, be replicated by a computer. How optimal a fold is defined by something called its “energy state”; the lower the more stable it is and it is these solutions that scientists are most interested in. To arrive at this solution, a computer will manipulate the individual molecules to continuously lower this number until the lowest state is achieved. Humans are able to take a far different approach. Instead of lowering the energy state in the beginning, some players have been known to open up the molecule and raise the energy state, effectively making the problem worse, before folding everything back together and achieving much lower and more desirable energy configuration. In doing so human players have managed to find far better solutions than the best computer algorithm for a given molecule configuration. Whether or not this will happen, the contribution of participants can not be denied. Many of the projects in progress have published papers and named participants, either individually or as a group, in their articles. In an article published in the August 12, 2010 issue of Science, volunteer users have discovered the Einstein@Home project’s first pulsar; a BIONC distributed computing project to detect gravitational waves and search for interesting astronomical phenomena. This discover has been attributed to Chris and Helen Colvin from Ames, Iowa and Daniel Gebhardt from Musikinformatik,Germany; both users have been attributed for the discovery in the recent Science article. In the Foldit game one of the best players, Scott ’Boots’ Zaccanelli, was even given a chance to design a new protein for the Foldit research group. While his protein structure was not as stable or useful as expected, it’s only a matter of time before players are actively designing protein structures that will find its way into new medicines and potentially cure diseases. There are literally dozens of volunteer science projects that anyone can take part in and every field is being represented whether it is biology, chemistry, physics or mathematics. All it takes is a simple download to get started.

The Future of Volunteer Science
The internet has certainly changed the ways in which science is done, especially in the area of human computing. In the end scientists will find new ways to utilize the human volunteers to solve research problems but the question remains as to how long will this happen until people no longer eager to be part of these networks and start feeling exploited by them. One day may come when scientists have to pay their best volunteers to participate these projects.


The Quantum Tunnel Newsletter

Vol. 1, May, 8 2011

Figure 3: Screen shot of the Foldit program.

Web Pages of Citizen Science Projects discussed in this article
• Audubon Society Christmas Bird Count • World Water Monitoring Day • Great Internet Mersenne Prime Search • SETI@Home

• Berkeley Open Infrastructure for Network Computing • Stardust@Home • Rosetta@Home • Einstein@Home • Foldit

A This newsletter was created with the use of a L TEX style template by David S. Latchman. If you are in need AT X class or style files, a Beamer Presentation or any other L T X typsetting task A of your own specialized L E E performed I can be found on Elance. My Elance Page: My Home Page:


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