November 2003 Archives

From Open source genetics needed to feed the world:

"This week Australian genetics pioneer Richard Jefferson was recognised by Scientific American, the prestigious international science magazine, as one of the 50 global technology leaders of 2003."

"His latest inventions could unleash a new Green Revolution, giving farmers, researchers and agriculture businesses across the world access to the potential of modern genetics."

"And he’s calling on the global biotechnology community to adopt open access genetics – freeing up the tools of modern genetics and biology from the shackles of excessive patenting."

(my emphasis in bold)

Free / Open Source Research Community presents quality open source research resources, and it is one itself as a result of having collected and organized these research articles.

A must read site for those interested in the interplay of open source software as an actor in the complex network of this thing we call society.

From On the Web, Research Work Proves Ephemeral on the fluidity of URLs and their movement, displacement, and disappearance:
(thanks to slashdot for this reference)

"Problem was, it took about two years for the article to wind its way to publication. And by that time, many of the sites they had cited had moved to other locations on the Internet or disappeared altogether, rendering useless all those Web addresses -- also known as uniform resource locators (URLs) -- they had provided in their footnotes."

I think the problem was perhaps with reliance on those URLs knowing that they can not be relied for an extended period of time.

"Dellavalle's concerns reflect those of a growing number of scientists and scholars who are nervous about their increasing reliance on a medium that is proving far more ephemeral than archival."

It isn't the medium; it is the not so rigorous self discipline of individuals who put serious and valuable scholarly material on websites that are not maintained.

This is why 'permalinks' used by bloggers are so great.

Further, I would like to stress that the problem is not with the internet as a publishing medium, rather with the publishing strategies followed by self publishers. Self archiving could effectively resolve this problem. Or, even better, a publishing framework like MIT's and HP's DSpace that cares tremendously about preservation and permanency of locations. Another such digital library system that can be used to preserve publications and URLs is Greenstone.

From Computers 'hamper the workplace':

"Computer systems at work are not working as they should, despite costing millions, a report says.
The problem lies with people rather than the systems themselves, concludes the iSociety think-tank."

Really? The problem lies with people? Who needs research to figure this out! :)

In SCO: GPL threatens $229B software market InfoWorld reports McBride (SCO's CEO) as stating:

"The world, especially here in America, is shifting to one that is an information society," McBride said. "In the future, is that $229 billion in software still going to be there? Or in the case of the Free Software Foundation's goal, is proprietary software going to go away?"

Well, if our society is shifting to an information society, it also means that the software 'industry' could gain even more importance in such society where the flux of information is critical to people's everyday lives.

In such case, isn't it obvious that the software industry (or should I better say the software development activities) should be also shifting? And why is it wrong if this shift is towards open source software?

McBride is actually making a good point in favor of open source software, and he does not realize it. If we have shifted towards an information society, why should an enormous amount of money be spend in developing commercial software? Instead the software could be as 'free' as the air around us (or become a world public good), and various corporations, non-profit organizations, the governments around the world, etc., can concentrate on more important activities.

In such society, software will no longer be able to provide competitive advantage. Instead, the current commercial software companies will have to reinvent themselves, and people will need to become more skilled in the way they use and integrate various open source software.

Shifts in the means of economic production have changed throughout the history. The philosophy and the economics of software development will have to change sooner or later. Maybe we are already in the midst of such shift.

From Self-Archive unto others . . . - reviewed by Stevan Harnad:

Quotes:
"Yet barriers do deny access to research papers. Tolls – in the form of journal subscription and license fees – must be paid by researchers’ universities for access to the journals in which the research is published. Yet the authors would much prefer it if there were no tolls at all, so that all would-be readers could use their research, and thereby maximize its impact."
...
"If and when the subscribing universities are no longer paying to access the research output of other universities, they will easily be able to pay publishers the peer-review costs for their own research output out of only a third of their annual windfall toll-savings. That way, the essential costs get paid and the research is all openly accessible. And all it needs to make it happen is reciprocal self-archiving by universities, according to the Golden Rule: self-archive unto others as ye would have them self-archive unto you. Universities and research-funders should extend the “publish or perish” mandate to “publish with maximal access” (by self-archiving: http://www.ecs.soton.ac.uk/~harnad/Temp/che.htm)."

From Global society and knowledge-driven education:

Quotes:
"There is overall agreement that various historical transformations are taking place and that in their own way these steps are creating their own dynamics in the process of evolution of the social framework. There is consensus that this inter-action is leading to divergence as well as convergence amid all the changes. The principle of obtaining shared knowledge and the learning process itself, while augmenting mutual growth and understanding, are also creating distinctions. This is partially because global society is not always promoting equitable chances and opportunities for human welfare and there is absence of orderly interaction and sustained cooperation to reduce uncertainties and inconveniences at the global level."

"Knowledge based education has now become central to the creation of the intellectual capacity on which knowledge production and utilisation depend. We have to promote lifelong-learning practices and update knowledge and skills if we are to retain competitive advantage. Traditional institutions have an important role to play in this regard. They have to take advantage of the opportunities offered by the new information and communications technologies. Failure to do so will mean the widening of the digital divide that is facing most of the developing countries, particularly the low-income countries."

In the past week or so I've been testing various Linux distributions to see which one fits better for my needs. For a long time I had installed (dual-boot) RedHat Linux 9.0. I have used RedHat since its earliest releases and was pleased with its stability.

However, the recent announcement by RedHat to discontinue support of its RedHad Linux products prompted me to try other distributions. I installed Mandrake 9.1 (and 9.2), Suse 8.2 (still waiting for 9.0) and obviously RedHat 9.0. Of the three, Suse (download version) appeared to be the most stable in my case, it recognized all the hardware (self build machine) with no problems, etc. While Mandrake has a lots of look and feel bells and whistles, few things didn't go well. So far in my case Suse happens to be the winner.

I also tried to install Fedora Core 1 (the 'successor'' of RedHat Linux 9.0), but couldn't get past the installation due to an error that my hard drive was full, despite the fact that Mandrake and Suse installed on the same amount of space (partition). I'll probably still check Fedora when the next release comes out.

In Broadband net user numbers boom BBC reports on the growing number of broadband (i.e. high-speed) Internet connections at home.

What does it mean? Well, according to Pew Internet Project there is an apparent and substantial difference in social behavior that varies depending on whether you are connected from home via broadband or just plain dial-up connection. The summary of their findings as well as the full report can be found at: The Broadband Difference. They have also published a follow-up report.

More Elsevier cancellations

(courtesy of Peter Suber at Open Access News)
The Cornell University Library is cancelling "several hundred" Elsevier journals and has explained the reasons why in a public letter. Excerpt: "We can no longer subscribe to so many Elsevier journals (including duplicates) that we no longer need. We must now free up some of the money spent on Elsevier journals to pay for journals published by other publishers that are more needed by our users. We have explained this to Elsevier in lengthy discussions, both through our research library consortium and then independently. We have tried in these discussions to broker an arrangement that would allow us to cancel some Elsevier titles without such a large price increase to the titles remaining --but Elsevier has been unwilling to accept any of our proposals. We are therefore planning to cancel several hundred Elsevier journals for 2004. The decisions on cancellations will be made on the basis of faculty input, as well as several years of statistical information on individual journal use....Once the cancellations are complete, we will list the titles on this site."

Public schools: Why Johnny can't blog

"SAN JOSE, Calif.--Evergreen Valley High School has been touted as the future of education in the heart of Silicon Valley, its 1,500-odd students outfitted with school-issued laptops that would create a new learning experience bridging life on and off campus.
...
"They treated the laptops more like their own personal computer instead of school property," said Dennis Barbata, the principal at Evergreen Valley's School of Science and Technology, which recently banned students from taking the machines home. "I'm not convinced that the laptop is the interface device at this point for a 24/7 computer access program for students."

In the same article they rightfully ask the question: "Does technology do more to improve learning than traditional teaching methods?"

SPARC and PLoS Partner to Advocate for Open Access Publishing

Quote:
"Washington, DC -- SPARC (the Scholarly Publishing and Academic Resources Coalition), an academic and research libraries initiative, today announced its partnership with the Public Library of Science (PLoS), the groundbreaking organization of scientists and physicians committed to making scientific and medical literature freely available on the public Internet. The alliance aims to broaden support for open-access publishing among researchers, funding agencies, societies, libraries, and academic institutions through cooperative educational and advocacy activities."

Open Archives Initiative Protocol for Metadata Harvesting (OAI-PMH) Turorial

Quote:
"The essence of the open archives approach is to enable access to Web-accessible material through interoperable repositories for metadata sharing, publishing and archiving. It arose out of the e-print community, where a growing need for a low-barrier interoperability solution to access across fairly heterogeneous repositories lead to the establishment of the Open Archives Initiative (OAI). The OAI develops and promotes a low-barrier interoperability framework and associated standards, originally to enhance access to e-print archives, but now taking into account access to other digital materials. As it says in the OAI mission statement "The Open Archives Initiative develops and promotes interoperability standards that aim to facilitate the efficient dissemination of content."

The Register asks rather the obvious question: So WIPO, why did you scrap the Open Source meeting?

"WIPO is an international organisation dedicated to promoting the use and protection of works of the human spirit. These works - intellectual property - are expanding the bounds of science and technology and enriching the world of the arts. Through its work, WIPO plays an important role in enhancing the quality and enjoyment of life and helps create real wealth for nations."

Good so far ... and then ...

"Given its background and mandate it is surprising that it scrapped its first meeting on "open and collaborative" projects such as "open source software." After all open source software does, indeed rely on intellectual property rights. It cannot exist without them. It is, therefore, bemusing that the US Director of International Relations for the US Patent and Trademark Office apparently opposed such a meeting, claiming that such a meeting would run against the mission of WIPO to promote intellectual property rights. At least one of the major US software companies, probably beginning with the letter "M", is reported to have lobbied against the holding of such a meeting."

No comments...

Open Source Software Institute Releases Components to eGovernment Web Services Platform; Initiates Working Group for Open Government Interoperability Standards

Great development in the open source activities for eGovernment and Education. OSSI has released Phase 1 of Leopard:

"Project Leopard is a web services application framework that provides fast, efficient access and implementation of LAMP technology for eGovernment programs. Phase 1 release of Project Leopard is now available for free download and evaluation at http://leopard.sourceforge.net"

Back in July, prompted by the NewScientist.com's article E-voting system flaws 'risk election fraud' reporting that Diebold Election Systems's e-voting system contains certain flaws that 'risk election fraud', I said I would be more comfortable e-voting if such system is open source where the code is open for public scrutiny.

Well, the Wired.com reports (Aussies Do It Right: E-Voting, also commented by slashdot) that an Australian company has done just that for the Australian election:

"While critics in the United States grow more concerned each day about the insecurity of electronic voting machines, Australians designed a system two years ago that addressed and eased most of those concerns: They chose to make the software running their system completely open to public scrutiny."

"Although a private Australian company designed the system, it was based on specifications set by independent election officials, who posted the code on the Internet for all to see and evaluate. What's more, it was accomplished from concept to product in six months. It went through a trial run in a state election in 2001."

Rep. Rush Holt's bill seems a step in the right direction for the US:

"The issues of voter-verifiable receipts and secret voting systems could be resolved in the United States by a bill introduced to the House of Representatives last May by Rep. Rush Holt (D-New Jersey). The bill would force voting-machine makers nationwide to provide receipts and make the source code for voting machines open to the public. The bill has 50 co-sponsors so far, all of them Democrats."

I've been puzzled for some time as to what is meant by the "semantic web" phrase and what does it mean in practice and research. I've come across the following article The Semantic Web, today that appears to be describing the semantic web concept(s) in a clear and presentable way.

The article makes the following distinction:

"The key point of the semantic web is the conversion of the current structure of the web as a data storage (interpretable only by human beings, that are able to put the data into context) into a structure of information storage."

I can understand the above intention and the attempt to make a distinction between data and information. However, the distinction between data and information that we make in our heads and understanding does not mean much to computer software.

Further, the article states:

"The Semantic Web is based on two fundamental concepts: 1) The description of the meaning of the content in the Web, and 2) The automatic manipulation of these meanings."

As far as 1) is concerned, the description itself is just another data (or information), i.e. metadata (or metainformation). In any case, the proper software tools have to be build to 'understand' the metadata/metainformation.

As far as 2) is concerned and the manipulation of meanings, this is a bit skeptical because to the machines, as I've tried to explain elsewhere here and here, those descriptions are just data it can manipulate and not meanings.

No, I don't believe that metadata and metainformation will not be able to provide a level of quality in the process of information seeking and access to information, I'm just a bit skeptical about the hype and high level of optimism that the semantic web will deliver us from the chaos of the web.

An interesting parallel are the natural languages. Each language is composed of words and phrases that have certain meaning(s) and/or concepts attached to them. To be able to navigate within the conceptual space of the language (i.e. understand the language) one needs to learn what each of the words represents: because each word or phrase is a metadata/metainformation for the actual concept in the particular language. So, it is good to be optimistic that eventually we'll come around to be able to represent the vast and chaotic multitude of information on the web with a set of metadata/metainformation and ontologies that all software will 'understand'.

Well... Esperanto hasn't yet become the world language it was meant to be... And it does not seem that it will became anytime soon... And even if it does, there still will be multiple meanings for various phrases...

Trends in Self-Posting of Research Material Online by Academic Staff:

From the introduction:

"With the rapid uptake of digital media changing the way scholarly communication is perceived, we are in a privileged position to be part of a movement whose decisions now will help to decide ultimately future courses of action. A number of strategies have recently emerged to facilitate greatly enhanced access to traditional scholarly content, e.g. open access journals and institutional repositories."

The Open Source Software economics article explores and presents the open source software (OSS) concept from view different perspective. An interesting read for people familiar with OSS as well as those that want to learn about.

Quote:
"Open Source Software" is not a new concept; it's just recently been coined as a catchy phrase. For decades, people have routinely released source code into the wild, and told people to do what they will with it. I was doing it about 15 years ago, and many others were doing it long before me. What's different is that people consider it a movement, and a movement with some momentum -- and they do have a point, but the situation isn't as simple as it might seem."