science - ReadWriteWeb http://www.readwriteweb.com/feeds/tag/science en Copyright 2009 Richard MacManus readwriteweb@gmail.com Sat, 21 Nov 2009 05:00:00 -0800 http://www.sixapart.com/movabletype/?v=4.23-en http://blogs.law.harvard.edu/tech/rss Elsevier's Prototype: Is This The Scientific Article of the Future? ElsevierLogo.jpgGiant science publisher Elsevier announced this week that it is developing what it calls The Article of the Future, a new method of leveraging the web's multi-media capabilities for presenting academic articles online. The company says it seeks to offer readers "individualized entry points and routes through the content, while using the latest advances in visualization techniques." It's got AJAX and it's got real-time web search.

Some parts of the available prototypes are interesting but opinion in the scientific community seems split. Is this ground-breaking stuff or yesterday's news repackaged by another industry threatened by the web? That depends on who you ask.

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The proposed new format incorporates things as simple as bullet point summaries and playable audio interviews with a paper's author and as complex as click-navigable data visualizations and real-time citation analysis. Some of the AJAX implementations are quite smooth and useful looking. The full summary of proposed features is available on Elsevier subsidiary publisher Cell's site and the company is seeking public comment.

Blogs and websites are weighing in with different points of view. James Dacey writes at PhysicsWorld that "I reckon this is another key development in an interesting transitionary period for both the publishing and media sectors." Several commenters on this article on Canadian Law Library blog Slaw were far less generous.

Gary P. Rodrigues, a former LexisNexis publishing exec, had the following to say there:

There doesn't seem to be much in the way of the 'future' in the 'Article of the Future'. Rather, it seems to me to be a collection of everything that it is possible to do now, but for which there is no commercial demand. Reed Elsevier faces a major challenge to its dominant position in the market for scientific journals from the Open Access movement. It needs to do something major to meet that challenge. The prototypes just don't live up to the hype.

Indeed, the article prototypes are reminiscent of what in the tech world was being called the Social Media Press Release, an attempt to make press releases multi-media and filled with social media hooks that could make them more useful to journalists. That effort seems to have petered out as most people in relevant industries found the format more trouble than it was worth.

There is a possibility that The Article of the Future will suffer the same fate. Elsevier says that it hopes the new format will make consumption of scientific research more efficient and interdisciplinary. We suspect, though, that many people who are interested in reading a paper titled "A Dynamic Pathway for Calcium-Independent Activation of CaMKII by Methionine Oxidation," for example, would prefer to keep out the clutter and stick with a familiar, scannable, academic format. Some of the features proposed are undeniably useful, though, and could lead to change that's incremental, if not revolutionary.

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For a more in-depth look at other attempts to disrupt the scientific publishing industry, see Michael Nielsen's article on the topic, this Nature blog post about scientists' use of social networks and this profile of a new social network for scientists called MyExperiment.

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http://www.readwriteweb.com/archives/elseviers_prototype_is_this_the_scientific_article.php http://www.readwriteweb.com/archives/elseviers_prototype_is_this_the_scientific_article.php NYT Fri, 24 Jul 2009 09:38:53 -0800 Marshall Kirkpatrick
A Productive Application of Semantic Search Noesis is a new semantic web search engine that helps scientists studying the environment access and retrieve the research data they need. Developed at the University of Alabama in Huntsville, the new engine has the potential to enable scientists and researchers everywhere to perform more productive and focused searches thanks to the semantic technology Noesis uses.

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The Noesis search engine (PDF) is different than regular search engines because it employs the use of semantics to help its users better shape their search queries. The results of this lead to better, more accurate, and more complete sets of search results. Those results can then be refined even further by Noesis' end users if necessary.

The goal of the Noesis project is to provide scientists working in the field of Atmospheric Science a way to better search through the "hidden web" of scientific catalogs that traditional search engines cannot reach. Because these catalogs are built using a standard vocabulary, the most efficient searches on the catalogs involve using specific terminology.

To create Noesis, researchers simply annotated those specific vocabulary terms with ontologies - the machine-readable definitions for the words that help computers understand the concept of the term and its relationship to other terms. Of course, annotations alone do not make a semantic web search engine. The ontologies must be coupled with a tool that's capable of searching through them. To that end, Noesis employs something they call the Ontology Interface Service (OIS), a SOAP-based web service interface to an inference engine. When a user performs a search, the OIS is also immediately searched for associated concepts. The Specializations and Generalizations discovered are returned in a tree structure which the user can navigate further. Synonyms and related terms are also shown, and, using checkboxes, they can be appended to the original query to refine it further.

Although the project was designed for use in one select area of science, its framework could easily be replicated in other scientific fields of study.

The Semantic Web: Better in Niches?

The main problem with the semantic web today is that the assignment of those above-mentioned ontologies - the pieces of code that allow machines to grasp meanings that humans innately understand - is that there's no solid way to automate their assignment. At the present time, no automatic or semi-automatic processes to do so have been achieved...at least, not to the point that a true vision of a new, intelligent web can be realized.

Most of the time, annotating web resources must be done using manually inserted bits of code placed into various web pages. Obviously, that's a challenge when you consider the size of the internet - it would be impossible to manually annotate this ever-growing resource. Unfortunately, without automated methodologies, a true semantic web will remain an unrealized dream.

However, in smaller communities, the semantic web can easily become a reality. Scientific data catalogs only represent small portions of the web as whole. Because of their limited size, manually annotating the resources they contain is a manageable feat. This is the case with Noesis. It shows there is promise for the semantic web after all - if only in small niches.

Image credit: rule100

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http://www.readwriteweb.com/archives/a_productive_application_of_semantic_search.php http://www.readwriteweb.com/archives/a_productive_application_of_semantic_search.php Semantic Web Wed, 14 Jan 2009 08:01:38 -0800 Sarah Perez
Open Knowledge Sharing for the Dynamic Web The EU-funded OpenKnowledge program is a smart toolkit designed to unlock the hidden resources of the web that can't be accessed by web sites and browsers alone. With a small, downloadable piece of Java code, users can coordinate and share information with each other more directly than through traditional means. To highlight the potential of the OpenKnowledge system, researchers have put it to work in three different areas: healthcare services, emergency management, and proteomics research.

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]]> 1) OpenKnowledge Healthcare

The first demonstration of the OpenKnowlege system is aimed to enhance the abilities of those seeking health-related information on the web. Instead of solely relying on a doctor to prescribe a course of treatment, people today tend to seek out medical information on their own using the web. Unfortunately, that data is often inaccurate and misleading. What OpenKnowledge intends to do is provide patients with structured information that has been checked for accuracy. To test this system, OpenKnowledge is working with Cancer Research UK on a project related to treatment methods.

2) Emergency Response

When there's an emergency situation, there is often a centralized point that disseminates critical information to people in need. But if that system itself breaks down, people are out of luck. OpenKnowledge aims to decentralize those systems so that a "backup" decentralized network of peers could be put into place. There, people could help each other out when the centralized system failed. This is currently being testing with emergency response authorities in Trentino, Italy.

3) Protemoics Research

Protemoics research (the study of the structure and function of proteins) can also benefit from the OpenKnowledge framework. In this area of science, many researchers worldwide rely on a small number of databases, creating a bottleneck of sorts which stresses the infrastructure of the databases themselves as well as those that maintain them. Researchers also find it hard to share data and results directly with other groups. In addition, the quality of the information in those databases is very mixed.

OpenKnowledge aims to solve all three problems by letting the researchers share data with each other directly, peer-to-peer style. This relieves the burden on the databases while the feedback will continually improve the quality of the data shared. This is currently being tested in an existing proteomics network in Spain called ProteoRed.

So...What Is It Exactly?

Understanding how a system like this works is difficult and the Open Knowledge web site doesn't make the process of comprehension any easier. Even despite the cute, Harry Potter-themed slideshow meant to describe the process, the actual details are hard to grasp. Obviously written by brainy researchers, they can't even call the slideshow a "slideshow," instead referring to it as a "simple pictorial introduction."

Ok For Everyone
View SlideShare presentation or Upload your own. (tags: research p2p)

Still, if you can wade through the academic speech on the site, what you may find is a creative idea for sharing information. Basically, through open source downloadable code, OpenKnowledge sets up a peer-to-peer network where users can trade in information and data similar to how BitTorrent users trade mp3s and video files.

In the OpenKnowledge system, anyone can easily become a peer or even create their own peer by sharing existing code or writing their own. In order to become an OpenKnowledge user, you simply need to download the OpenKnowledge kernel from here together with some additional components that you might want to use. In addition to users, services, such as WSDL services, can also be made into peers on the OpenKnowledge network.

OpenKnowledge is more of a framework for decentralizing the systems on the web. It's not so much of a consumer-friendly web app than it is a model for information sharing that can help advance areas of science and research. You may not ever use OpenKnowledge yourself on your home computer, but your life may very well be impacted one day by the innovations it made possible.

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http://www.readwriteweb.com/archives/open_knowledge_sharing_for_the_dynamic_web.php http://www.readwriteweb.com/archives/open_knowledge_sharing_for_the_dynamic_web.php Products Mon, 29 Dec 2008 08:28:49 -0800 Sarah Perez
Smiling in Your Social Network Photos? You Probably Have More Friends Researchers Nicholas Christakis and James Folwer recently published a paper in the British Medical Journal where they examined how a person's happiness is related to the happiness of their friends in their offline social networks. To follow up that study, they examined those same happiness clusters in online networks like MySpace and Facebook. Their conclusion? Happier people tend to have more friends and are more central to the network when compared with their more sullen friends.

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In the original research study that examined offline interactions, the researchers found that social networks have clusters of happy and unhappy people within them that reach out to three degrees of separation. In other words, your happiness is related to that of your friends, your friends' friends, and their friends' friends. They also discovered that happy people tend to be located in the center of their social networks and are found in large clusters of other happy people. For each additional happy friend, a person's probability of being happy increases by about 9%.

Armed with these results, the researchers decided to see if the offline research could translate to the online world as well. Of course, determining happiness in the online world is more difficult - a smiling profile picture does not necessarily equate to you being a happy person.

The Facebook Study

The study began with the researchers examining a group of 1700 college students interconnected on the social networking site Facebook. They took note of the students' profiles and who their friends were. They also noted whether the profile photos contained a smiling face. Next, the researchers looked at the other photos found in the students' Facebook albums, this time paying careful attention to who "tagged" who in the photos. This was important because the people who take the trouble to be in the same place, take a photograph together, upload the photograph, and label ("tag") it, almost always have a closer relationship with each other than they do with the rest of the "friends" found on people's profile pages. These "photo friends" tend to represent a person's real-life friends. In fact, the average student in the study had over 110 friends on Facebook, but they had an average of only six of these "photo friends" (close friends).

To determine happiness, the researchers noted who was smiling in these tagged photos. Although they admitted that smiling is, of course, very different than happiness, it was as close as they could come in the virtual world. Apparently, that may have been close enough.

Happiness Is Contagious

The data from results of the online study ended up correlating to their offline study - the results were essentially the same, they were just translated to the digital world. What the researchers found was that smiling students were surrounded by others who were also smiling in small "happiness clusters." Those who were not smiling seem to be located more peripherally in the network. After performing statistical analysis, they determined that those who smile also tend to have more friends - on average one extra friend, which is good considering that people only tend to have six close friends. Those who smiled were also more likely to be at the center of the network when compared to those who don't.

You can see the results of the study mapped out in the image below. The figure shows just a part of the Facebook network, containing 353 students. The smiling people who are surrounded by other smiling people are in yellow, those frowning or giving any other "serious" look are in blue, and those in green indicate a mix of smiling and non-smiling friends.

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In the end, the main conclusion of the study was that, whether online or offline, "when you smile, the world smiles with you."

Image credits: smile, suchitra prints; network, edge.org; smiling girl, porcelaingirl

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http://www.readwriteweb.com/archives/smiling_in_your_social_network_photos_means_you_have_more_friends.php http://www.readwriteweb.com/archives/smiling_in_your_social_network_photos_means_you_have_more_friends.php Facebook Thu, 11 Dec 2008 08:11:30 -0800 Sarah Perez
"Yes We Can" Director Releases Video About Science Commons Science Commonslogo.jpgFilm director Jesse Dylan, the co-creator of the Emmy award winning Barack Obama support video Yes We Can has released a new work, this time explaining the Creative Commons Foundation's science initiative, Science Commons.

Dylan, who coincidentally is the eldest son of folk legend Bob Dylan, uses his familiar style to aggregate a quick selection of scientists explaining why a web-based revision of copyright policy is so important for the advancement of scientists. "Scientists are the ultimate remixers," one interviewee says, and we agree that Creative Commons in science is a very exciting idea.

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Few media are as compelling as video and we hope that this new short work is helpful in garnering support for Creative Commons in the sciences.

Dylan's work joins a long list of well made Creative Commons videos, which have been helpful in explaining the movement to revise copyright to countless people, no doubt including even President Elect Barack Obama, whose own website was recently put under a Creative Commons license.

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http://www.readwriteweb.com/archives/yes_we_can_director_releases_v.php http://www.readwriteweb.com/archives/yes_we_can_director_releases_v.php Digital Media Mon, 08 Dec 2008 09:16:17 -0800 Marshall Kirkpatrick
Education 2.0: Never Memorize Again? Memorization is a waste of time when Google is only a a few clicks away. That's what Don Tapscott, author of the bestselling books Wikinomics and Growing Up Digital, believes. Tapscott, considered by many to be a leading commentator on our Internet age, believes the age of learning through the memorization of facts and figures is coming to an end. Instead, students should be taught to think creatively and better understand the knowledge that's available online.

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]]> Rote Learning is a Waste of Time

According to Tapscott, the existence of Google, Wikipedia, and other online libraries means that rote memorization is no longer a necessary part of education. "Teachers are no longer the fountain of knowledge; the internet is," Tapscott told the Times. "Kids should learn about history to understand the world and why things are the way they are. But they don't need to know all the dates. It is enough that they know about the Battle of Hastings, without having to memorize that it was in 1066. They can look that up and position it in history with a click on Google," he said.

He doesn't feel that method of learning is anti-education since the information we must all digest is coming in at lightning speed. "Children are going to have to reinvent their knowledge base multiple times," he continues. "So for them memorizing facts and figures is a waste of time."

For the older generations who grew up having to memorize historical dates and mathematical formulas, the idea that memorization shouldn't be a part of the educational experience is somewhat shocking. Of course you need to know the exact year something happened...don't you? Or is it better to just have a general idea so you can focus on better understanding the context and meaning?

Our Wired Brains

Today's students are growing up in a world where multi-tasking has them completely immersed in digital experiences. They text and surf the net while listening to music and updating their Facebook page. This "continuous partial attention" and its impacts on our brains is a much-discussed topic these days in educational circles. Are we driving distracted or have our brains adapted to the incoming stimuli?

A new book on the subject, "iBrain: Surviving the Technological Alteration of the Modern Mind," states that our exposure to the net is impacting the way our brains form neural pathways. Wiring up our brains like this makes us adept at filtering information, making snap decisions, and fielding the incoming digital debris, but sustained concentration, reading body language, and making offline friends are skills that are fading away.

If our brains are, in fact, becoming rewired, wouldn't it make sense that the way we teach students to learn should adapt, too? Actually, there aren't too many people who think so. Most educators, like Richard Cairns, Headmaster of Brighton College, one of the U.K's top-performing independent schools, believe that core level of knowledge was essential. "It's important that children learn facts. If you have no store of knowledge in your head to draw from, you cannot easily engage in discussions or make informed decisions," he says.

Do you agree?

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http://www.readwriteweb.com/archives/education_20_never_memorize_again.php http://www.readwriteweb.com/archives/education_20_never_memorize_again.php Trends Tue, 02 Dec 2008 06:02:56 -0800 Sarah Perez
CERN Officially Unveils Its Grid: 100,000 Processors, 15 Petabytes a Year lhc_grid_logo.pngCERN today officially unveiled the massive computer network that will crunch the enormous amount of data coming from CERN's Large Hadron Collider (LHC). CERN expects that the LHC will produce around 15 petabytes of data every year. While the LHC was in its planning stages, CERN's IT department decided that the only realistic way to handle this amount of data would be by relying on the then still novel idea of grid computing. CERN's grid consists of 100,000 processors at 140 scientific institutions in 33 countries.

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As Science reported last month (subscription required), CERN's IT department quickly realized that no known data center could handle the amount of information the LHC would create. It was not even clear that Geneva's power grid could supply the energy necessary to run this massive data center. In addition, most of the money for the LHC project was going toward the collider itself, so that very little funding was left for the actual computing resources.

cern_data_storage.jpgIn order to distribute this data, CERN relies on dedicated 10Gbit/s fiber-optic lines that connect CERN with the 11 Tier-1 data centers on the grid. The Tier-1 data centers (pdf) will do some processing, but will also function as the main archives for the LHC data. These Tier-1 centers then farm out a large part of the actual data crunching to the Tier-2 data centers spread around the world. The Tier-2 centers are connected to the grid via regular, public Internet connections.

Large Hadron Collider @ Home

While grid computing has been around for quite a while now and has been implemented successfully on the public Internet by projects like SETI@home or Folding@home, CERN's grid is most likely the largest and most powerful grid established for scientific research so far.

CERN has also set up a project similar to Folding@home called (somewhat unimaginatively) LHC@home, which, thanks to the current shut-down of the LHC does not have much to do right now, but will allow individuals to contribute to CERN's efforts by donating computing time on their own computers.

Image of CERN Computer Center used courtesy of CERN.

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http://www.readwriteweb.com/archives/cern_officially_unveils_its_gr.php http://www.readwriteweb.com/archives/cern_officially_unveils_its_gr.php News Fri, 03 Oct 2008 11:28:56 -0800 Frederic Lardinois
5 Great Science Books to Expand Your Mind From the dynamics of social networks to market bubbles, science has a lot to say about the world of technology.

One of the great discoveries of modern science was the realization of how interconnected the world is. The deterministic, Newtonian view of a clockwork Universe was replaced by the much more dynamic, uncertain and entangled world of Quantum Mechanics. The new world is the one where Godel forever cut hopes for completeness in mathematics and Turing showed that computation, like the future, is fundamentally unpredictable. Despite these unexpected setbacks, modern science is wonderful, powerful and thought provoking - and relevant to technologists.

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]]> The recently discovered science of complex systems is about common patterns that span diverse disciplines from physics to biology, from ecology to economics. This recent science of patterns is directly relevant to what we are doing around the Web. In this post we will discuss 5 different books that will get you fired up about modern science.

1. Godel, Escher, Bach, by Douglas Hofstadter

This Pulitzer Prize winning book is a mind-opening journey that spans science, computation, zen, art, music and much much more. The book is most unusual in the way it tells its story. Some chapters are dialogs between Achilles and Tortoise. Other chapters are focused on Bach's fugues and the theorems of great German mathematician Kurt Gordel.

Throughout the book, Hofstadter discusses the work of M.C. Escher, a painter famous for his paradoxical paintings that question how the mind perceives space. In addition, the book features chapters about modern genetics, zen buddhism and neuroscience. All of these seemingly diverse topics come together to discuss recursive structures, the mind, artificial intelligence and computation.

2. Complexity by Mitchell Waldrop

Stephen Hawking once said: "I think the next century will be the century of complexity." Complexity science is one of the most important breakthroughs in recent history. Unlike the traditional specialized approach to science, complexity focuses on patterns and properties that exist across different branches.

Mitchell Waldrop's book introduces readers to complexity by telling a story about the people who brought it into the spotlight. Among the characters we meet are economists, physicists, biologists and computer scientists responsible for establishing the Institute of Complex Systems in Santa Fe New Mexico. Through their stories, Walldrop introduces the reader to the wonderful and profound world of complex systems.

3. At Home in the Universe, by Stuart Kauffman

Dr. Stuart Kauffman is one of the characters in the Walldrop's book. He is one of the most passionate, dedicated and original thinkers about Complex Systems. A few decades ago, while in medical school, he wanted to understand gene networks and came up with a model known as K-N nets. Fascinated with the ideas, he choose science instead of medicine and went on to work on complexity.

In this book he explores a range of fascinating topics - like gene networks, auto-catalytic sets, rugged landscapes. It ultimately leads to the question of the origin of life. In this challenging book, Kauffman postulates that life is not an accident, but an expected and even inevitable consequence of the laws of self-organization.

4. The User Illusion, by Tor Norretranders

During the twentieth century scientists made amazing discoveries about the brain. They also discovered just how little we know about the function of what is likely to be the most interesting and powerful object in the universe. Among the large number of books written on the subject, this book written by Danish journalist Tor Norretranders is a standout.

The books builds on physics, particularly thermodynamics, to explain the fascinating aspects of human consciousness. While the first few chapters are somewhat challenging, the crux of the book will give you a unique, eye-opening perspective on the interplay between the human brain and mind. Among the shocking things in the book is a notion that it takes a half a second for our consciousness to process an event. Knowing that, it is difficult to think about the world in the same way.

5. Programming the Universe, by Seth Lloyd

Quantum Information Theory is one of the hottest topics in science and Seth Lloyd is one of the hottest figures in the field. Famous for his bold predictions about the computational capacity of the universe, Dr. Lloyd belongs to the club that thinks that we live inside of a gigantic quantum computer. Sounds interesting? It is!

The book works the readers through the ideas of quantum information theory, explaining qbits, quantum superpositions and computation based on atoms. He argues that random fluctuations in the quantum foam produced higher-density areas, then matter, stars, galaxies and life. His conclusion is the same as Kauffman's - life is not an accident nor its divine. Rather, life is a consequence of the laws of computation and self-organization.

Conclusion

There are so many great science books on topics ranging from physics and biology to economics and social science. These books discuss patterns in the world around us. And many of the themes are very familiar to us, technologists. This is why it is important for us to keep up and know what is going on in the world of science. Besides being fascinating, it is increasingly applicable and useful.

And now, please share with us your favorite science books - the ones that made a big impact on you and helped expand your mind.

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http://www.readwriteweb.com/archives/5_great_science_books.php http://www.readwriteweb.com/archives/5_great_science_books.php Book Reviews Wed, 01 Oct 2008 20:52:39 -0800 Alex Iskold
Tim Berners Lee Launches World Wide Web Foundation - Will it Be Effective? wwwfoundationlogo.jpgTim Berners Lee, the inventor of the World Wide Web, announced this weekend the formation of a new organization dedicated to studying how the web works and expanding access to the billions of people who can't get online today. The World Wide Web Foundation kicked off with $5 million in support from media funders the Knight Foundation.

Can yet another organization really make a difference? Some observers seem to be suffering from Organization Fatigue, but we're interested to see what Berners Lee can do. A group dedicated to deep study of the web and the obstacles to its growth sounds like a great idea to us. Not everyone agrees.

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The Foundation launched with a three part plan, including:

  • Web Science and Research

  • Studying the web "as an interconnected complex system (that combines disciplines of science, biomedical science, social science, and computer science, for example)" and creating curriculum for other Web Scientists to be trained with around the world.

  • Web Technology and Practice

  • Advancing standards.

  • Web for Society

  • "To learn from people in socially or economically deprived communities how the Web can better serve them." (Nice that it's phrased this way.) Creating programs to extend access around the world.

Concerns

We are a little concerned about a conversation Berners Lee had with the BBC prior to unveiling the Foundation where he argued that there needs to be some way to brand trustworthy websites as trustworthy. That strikes us as either silly or frightening, possibly both.

Web standards guru and blogger Molly Holzschlag sums up what is probably a common feeling of ambivalence about the new Foundation.

I would love to feel optimistic about this, but at this point I've really decided that creating more groups is just adding layers of problems on top of what we're already doing.

On the other hand, if this empowers greater outreach, education and fosters real influence in returning to the core ideals of an interoperable Web for all, then I'm all for it.

Eran Hammer-Lahav, Open Web Evangelist at Yahoo! and party to the founding of another group, the Open Web Foundation, has sharper words for Berners Lee's group.

Seems odd to ask for money, and a lot of
it, with so little detail as to what this organization is about?...We've been asked many times why a new org, and I think it is fair to ask it back. Seems to me that most of this should/could be done within the W3C. If the W3C is no longer able to promote its own mission, it raises the question: should the same leadership be trusted to run a new effort that seems to try and fix what their first effort failed to accomplish?

We are sympathetic to both opinions here. The problems being engaged with are thorny enough that we applaud anyone for trying tackle them - and the inventor of the web certainly brings credentials to the effort. Also, it's not our $5 million so we're not going to lose too much sleep even if the effort goes no where.

What do you think? Does the World Wide Web Foundation website give you hope that the organization will be effective? If these topics are of interest to you, see also the Digital Divide Network.

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http://www.readwriteweb.com/archives/tim_berners_lee_launches_world.php http://www.readwriteweb.com/archives/tim_berners_lee_launches_world.php News Mon, 15 Sep 2008 11:56:33 -0800 Marshall Kirkpatrick
Mememoir: A Better Wiki For Science mememoir.pngThanks to successful projects like Wikipedia or Wikitravel, wikis have quickly become a standard tool on the Internet, but in academia, the anonymity often associated with publishing in wikis is a key factor that works against them. Tracking down the exact history of changes in a wiki entry can be a convoluted process, yet being able to exactly attribute a certain statement to one writer is at the heart of the academic enterprise. Mememoir aims to provide a wiki that is heavily focused on authorship and can help to dispel the prejudices scientists have against publishing in a wiki-like format.

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Mememoir is a completely new development and as of now, its only deployment is in the form of the WikiGenes wiki. Both Mememoir and Wikigenes, a database of literature about genetic information, were created by Robert Hoffmann, a fellow at Society in Science in Switzerland and a visiting scientist at MIT.

For scientists in academia, publications are the lifeblood of their careers. Having published in a wiki is not going to persuade a tenure track committee anytime soon, but the systems that Mememoir puts in place might just make those contributions stand out a bit more. Besides attribution, Mememoir also gives its users the ability to rates authors and their contributions.

The developers are still looking at their options for possibly open-sourcing the code behind Mememoir. As Robert Hoffmann pointed out to us, the project will look at its options at a later time and is mostly focused on running the Wikigenes project for now.

wikigenes.png

WikiGenes

The information in WikiGenes itself was based on iHop, another project by Hoffman (and not the infamous chain of pancake houses). The idea behind iHop is that information about a single gene can often be dispersed over hundreds of different academic papers, which makes finding and synthesizing all this data extremely hard. IHop used algorithms to parse all this information and bring it together in one database, which was then used to seed WikiGenes.

According to Hoffmann, the idea behind WikiGenes is that it will combat this dispersal of information in the first place, as scientists can enter their research results into the database directly.

Trust and Authorship

WikiTrust, which rates authors on Wikipedia according to an algorithm is trying to do something similar for all of the Wikipedia, but Mememoir takes this to a more personal level. Both systems are, of course, potentially fraught with problems, but it will be interesting to see if scientists will warm up to the wiki model.

We would really like to see Hoffmann and his team open up the code to Mememoir, as the wiki itself is a highly capable piece of code that looks flexible enough to power any kind of wiki - academic or not. In testing it, it turned out one of the easiest to use wikis we have seen so far and it could surely benefit a lot of different projects in the long run. If you would like to see it in action, the project has create a short screen-cast that you can see here.

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http://www.readwriteweb.com/archives/mememoir_a_better_wiki_for_sci_1.php http://www.readwriteweb.com/archives/mememoir_a_better_wiki_for_sci_1.php Products Fri, 05 Sep 2008 11:10:45 -0800 Frederic Lardinois
WorldWideScience: Like Google for Deep Web Science Need to get access to real scientific data but having trouble finding any relevant search results in Google? That could be because a lot of the science and technology documents on the web aren't typically indexed by major search engines. They're a part of the "deep web," the repository of web pages usually generated by database-driven sites that search engines' spiders can't access. One resource to help open up the deep web for scientific research is WorldWideScience. This portal allows you to query more than 200 million documents not typically indexed by today's search engines.

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]]> About WorldWideScience

WorldWideScience is a science portal developed and maintained by the Office of Scientific and Technical Information (OSTI), an element of the Office of Science within the U.S. Department of Energy. The WorldWideScience Alliance, a partnership consisting of participating member countries provides the governance structure for the WorldWideScience.org portal.

When it debuted back in June 2007, it linked to 12 databases from 10 countries. Today, the portal links to 32 national, scientific databases and portals from 44 different countries.

WorldWideScience Homepage

How To Use WWS

To use the portal, you just enter a search term, as you would with any search engine and click "search." An advanced search feature lets you specify more details like title, author, or year, and lets you specify which databases to query.

Unlike Google, where results are ranked based on an algorithm that essentially displays items by popularity, WorldWideScience provides only authoritative scientific information by relevance - a ranking that is noted by the number of stars next to the result. The higher the number of stars, the more relevant the result.

Another difference between WWS and other search engines is that WorldWideScience's results are retrieved in real time. So, as you search and results come in, you may see a box appear with a "include these results" button. Clicking this will update the list with the latest information.

On your search results page, there are several features that make finding the answers you need easy to do. On the left, are "clusters," which let you narrow down a broad subject by specifying topics or dates. On the right, a snippet from Wikipedia provides a quick definition and link to an article about the subject you queried. Below that, a "EurekAlert!" section provides links to relevant articles from EurekAlert!, an online, global news service operated by AAAS, the science society. EurekAlert! is like a PR news wire for scientific research, providing a central place through which universities, medical centers, journals, government agencies, corporations and other organizations can bring their news to the media.

WorldWideScience Search Results

The WorldWideScience portal is a great resource for anyone looking for the most current findings from fields such as technology, energy, medicine, agriculture, environment, and more. You don't have to be a student, professor, or researcher to enjoy the richness of the data provided, either, as WWS has been designed to be easy enough for anyone to use. You can try it out for yourself here: worldwidescience.org

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http://www.readwriteweb.com/archives/worldwidescience_like_google_for_deep_web_science_stuff.php http://www.readwriteweb.com/archives/worldwidescience_like_google_for_deep_web_science_stuff.php Products Mon, 16 Jun 2008 07:29:00 -0800 Sarah Perez
Interview with Neil Young on Music Piracy, MP3 Hell and Finding Freaks on the Web Neil YoungHere at the JavaOne conference in San Francisco Neil Young just announced that his whole life's work will be made available on in a dynamically updating collection delivered on Blu-ray disk. After his Keynote announcement I was fortunate enough to participate in a small group interview with a handful of other bloggers. Young offered interesting replies to questions about Trent Reznor and music piracy, about MP3 sound quality and about the way the web enables his extensive work on electric cars.

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]]> The short version is that Young fully expects his collection to be sent all over the web for free, he hates MP3s and he loves finding freaky scientists on the web and offering them profiles in his next movie.

Free Music

I elbowed in between elder bloggers Tim O'Reilly and Dan Farber in the interview to ask what Young thought of Trent Reznor's giving away free music and RadioHead's saying they aren't going to do so anymore. At first I thought he wasn't going to give me anything good, saying: "The recording business is going somewhere but I don't care about that, I try to remove myself from the business part. The artistic part of me tries to. The world will work it out."

He went on though to point out that his project Living With War always was and still is fully listenable for free on his website. It delivered a message he wanted to get out, he said. His thoughts about the content included in his giant life collection? Blu-ray may be riddled with DRM but Young doesn't think that will be an issue.

"Ten Blu-ray disks doesn't lend itself to P2P," he pointed out. "They [the fans] are going to do that anyway - people are going to copy all this music. We don't have to deal with that. All we're doing is supplying the mother-lode, trying to give them quality whether they want it or not. You can degrade it as far as you want, we just don't want our name on it."

More than just indifference, Young was downright enthusiastic. "It's up to the masses to distribute it however they want," he said. "The laws don't matter at that point. People sharing music in their bedrooms is the new radio." Go Neil!

MP3s Sound Like Shit

Wonder how Young feels about the ongoing debate over the impact of the MP3 format on sound quality? He's pretty clear on it.

[When it first came out] "digital music sounded like shit," he said in the interview. "It was no fun to listen to turned up. Instead of water poured on you it was like being attacked with ice picks. [His recordings on Blu-ray] are like snowflakes."

"I don't listen to music, it's in my head. Putting on headphones is like hell for me. I can hear an mp3 from a half mile away because the air has a chance to make it sound natural."

Young said that MP3 was convenient - but that it's like a vision of paradise that's only inches deep and slams you in the face when you try to walk into it. "I'm a music guy, a sound guy - I went through hell in the 80's," he said. "Now we're coming close, climbing up the quality wall. I make all my music analog, when a new format comes along I will dump all my music to it." Would he advise other musicians to do the same? He said that wasn't realistic. "I'm too rich and elitist, most people can't afford the machines [for analog recording] and the people to take care of them." Young says he's been hoarding tape for a long time, sometimes recording over content that didn't work out.

Finding Freaky Scientists on the Internet

Young spent much of the interview talking about his work building an electric car that users don't have to plug-in to a wall. The end of roadside refueling is his ultimate goal. He and Tim O'Reilly discussed the plans in some length and it was fun to listen to. Nothing else Young talked about is nearly as important. It's also not very relevant to RWW, except for his thoughts on how the web has assisted his work on the car.

"The internet is a fantastic place to find science experiments," he said. "That's my favorite thing about the internet. People who are kooks in their garages - the tools are here for us to look to the edge of the scientific world. You can seek them out and tell them if you think their ideas will work. You can tell them you'd like to connect them with other scientists in other parts of the world and if the work succeeds or fails you'll put them in a movie about the project."

That's not a perspective I've heard about the web before, and I like it.

Neil Young was a personable, intelligent and well spoken interview subject. I'll remember getting the chance to interview him fondly for the rest of my life.

If you enjoyed this post, please click here to digg it!

Disclosure: Sun is a client of my personal consultancy and paid my travel expenses to JavaOne.

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http://www.readwriteweb.com/archives/interview_with_neil_young.php http://www.readwriteweb.com/archives/interview_with_neil_young.php Analysis Tue, 06 May 2008 12:33:31 -0800 Marshall Kirkpatrick
NIH: $29b in Health Science Set to Go Online for Free George Bush signed a $555 billion omnibus spending bill yesterday that included a huge victory for advocates of open science on the internet. All research funded by the US National Institutes of Health (NIH), an agency with a $29 billion research budget, will now be required to be published online, free to the public, within 12 months after publication in any scientific journal.

This should open up a whole world of new opportunities for online research. Readers outside of the academic world but aware of the financial future of health information online in the commercial sector can imagine the analogous excitement about this announcement for academic researchers.

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Researchers, academics and others have loudly criticisized the soaring prices of academic journals - which make access to publicly funded research cost-prohibitive to all but the largest institutions and double-charges institutions that paid for researcher salaries already.

The blog Open Access News has a good round up of science blog responses to the news.

Pubmed is the likely home for much of the research, though the law is likely to breathe more life into online sites of scientific activity like the Nature Publishing Group, the science blog search engine PostGenomic and the Public Library of Science.

Data miner Peter Suber from the Unilever Cambridge Centre for Molecular Informatics discusses just one of many reasons this is exciting news.

The hard work continues. But now all fulltext derived from NIH work will be available on PubMed. Other funders will follow suit (if they are not ahead). So our journal-eating-robot OSCAR will have huge amounts of text to mine.

The good news is that we believe that this text-mining will, in itself, uncover new science. How much we don’t know, but we hope it’s significant. And if so, that will be a further argument for freeing the fulltext of every science publication.

In related science news, tech and science lovers (many of whom have libertarian sensibilities) should take note of a new video floating around the interwebs - Ron Paul doesn't believe in evolution.

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http://www.readwriteweb.com/archives/nih_law_29b_in_health_science.php http://www.readwriteweb.com/archives/nih_law_29b_in_health_science.php Trends Thu, 27 Dec 2007 09:51:02 -0800 Marshall Kirkpatrick