Technology Blog

Declan Butler, Breaking the silence: “If this was a test to see whether Indonesia could contain a virus, they failed miserably” Declan Butler, Reporter, May 31, 2006. Excerpt:

Plans by the World Health Organization (WHO) to try to slow or contain a pandemic show that to have any hope of success these would require rapid and decisive action within at most a three-week window from the emergence of a pandemic virus. But the handling of the cluster in Indonesia, as described in [a front-page article I’ve published in Nature tonight], is one of delays and confusion….

To understand the genetics, and link this to the epidemiology and pathology of the virus, we need immediate sharing of all virus samples and data. None of this is happening adequately. National governments’ performance is half-hearted, incomplete and far too slow. International organizations are working with their hands tied behind their backs, for bureaucratic and diplomatic reasons. In short, the level of current efforts is not commensurate with the threat we face.”…

So apparently, no one is opposed to depositing the sequences in Genbank immediately, but no one is taking the decision to do so. In the Nature editorial, “Dreams of flu data” [PS: blogged here 3/20/06] we argued: “….When samples are sequenced, the results are usually either restricted by governments or kept private to an old-boy network of researchers linked to the WHO, the US Centers for Disease Control and Prevention, and the FAO. This is a far cry from the Human Genome Project, in which all the data were placed in the public domain 24 hours after sequencing. Many scientists and organizations are also hoarding sequence data, often for years, so they can be the first to publish in academic journals. With the world facing a possible pandemic, such practices are wholly unacceptable. Nature and its associated journals are not alone in supporting the rapid prior exposure of data when there are acute public-health necessities. Three cheers, then, to Ilaria Capua of the Tri-Veneto Region Experimental Animal Health Care Institute in Italy, who last month threw down the gauntlet to her colleagues by refusing to put her latest data on Nigeria and Italy in these private networks. Instead she uploaded them to GenBank and called on her colleagues worldwide to do likewise. Only in this way can researchers establish and track the global pattern of the evolution of the bird-flu virus.”

Is it perhaps time for the Human Genome Project’s “Bermuda Agreement” on sequence deposition to be applied to all H5N1 sequences?

PS: For background see my April article on OA to avian flu data.

source: More on OA to avian flu data

• ongoing: On Grids
  great article on current grid computing, featuring MPI, MapReduce, Hadoop, and promising a new UNIXy thing from tbray called Sigrid (ha!). Mind-boggling quote from Jim Gray: ‘Memory is the new disk. Disk is the new tape.’
  (tags: grid-computing parallel tim-bray mapreduce hadoop mpi sigrid jim-gray server-farms)
• “patent goo” — self-replicating Paxil
  spontaneously converts the off-patent anhydrous form of the drug into the patented hemihydrate form, which then successively converts more and more of the anhydrous form, Ice-9-style. Never mind “viral” licenses, this takes the biscuit! (via substitute)
  (tags: via:substitute viral-licenses gray-goo paxil drugs chemistry bizarre polymorph ice-9 patents)

Tags:

This post was written by dailylinks, source: links for 2006-05-31

source: New IR at Indian research institute

Andrew Rens, Achal Prabhala, and Dick Kawooya, Intellectual Property, Education and Access to Knowledge in Southern Africa, Trade Law Centre for Southern Africa, 2006. Excerpt:

Books are still largely inaccessible in the south – whether on account of high cost, unsuitability of language and format, or, even more simply, plain unavailability. The open access textbook, on the other hand, costs as much as it does to print and can be available wherever necessary. Even a visible scarcity of knowledge goods in the main languages spoken in southern Africa could be alleviated by the permission-free translation choices presented by open access, since access to cultural goods in turn produces producers of cultural goods. The point to bear in mind is that access as a strategy is not predicated on the assumption that students of the south are ‘consumers’ (and that professors of the north are ‘producers’), but rather, that a complex, interdependent relationship exists between consumption and production – and furthermore, that access to cultural goods is a necessary and significant factor to stimulate production….

[T]he challenge is not insurmountable. In this case, the current needs and potential benefits of expanding access, combined, present a credible case for serious and urgent intervention….

Our scan of the learning environment in southern Africa suggests a serious problem in respect of access to knowledge goods. While there are several factors complicit in producing this access gap, several of the identified problems (excessive pricing, unavailability and unsuitability of material, and government/ institutional resource constraints) can be traced, in significant part, to intellectual property law….Ironically, it is precisely in this disabling legal environment that the SACU [Southern African Customs Union] countries are being asked – by domestic and international publishing industry lobbies – to strengthen the enforcement of criminal sanctions for certain copyright violations, even as they constitute an access mechanism in a context that offers few alternatives.

source: Copyright and access barriers in Southern Africa

The Alliance for Taxpayer Access has issued a press release on the poll:

In an online survey of public attitudes conducted recently and released today by Harris Interactive, 8 out of 10 (82%) adults polled said they believe that “if tax dollars pay for scientific research, people should have free access to the results of the research on the Internet.”

In addition, six out of 10 (62%) adults believe that if these research results are easily available (for free and online), it will help speed up finding potential cures for diseases….

“This expression of support from the American public demonstrates that the demand for public access has reached a critical juncture,” said Heather Joseph, Executive Director of SPARC (Scholarly Publishing and Academic Resources Coalition, an ATA founding member). “As scientists work to counter the Avian flu, develop energy alternatives, and grapple with climate change, public access to taxpayer-funded research is more important than ever. The public recognizes its stake in open sharing of research, and the Harris data gives voice to their stand.”

“The poll results show that research must be a collaborative, informed process between investigators and the public to be successful and increase trust,” said Robert Reinhard, community advisor to NIH’s AIDS vaccine trials. “Time and again the lesson is that improved knowledge in the community furthers the public health agenda.”

The ATA also links to the following files of survey results:

Download six pages in PDF.

A. Since this research is paid for by tax dollars, the results should be easily available (free and online) to doctors. [JPG]

B. If tax dollars pay for scientific research, people should have free access to the results of the research on the Internet. [JPG]

C. Having this information easily available (for free and online) will help those living with a chronic illness or disability get the latest information which will assist people coping with that chronic illness or disability. [JPG]

D. If these research results are easily available (for free and online), it will help speed up finding potential cures for diseases. [JPG]

E. Regardless of who pays for the research, it’s better for scientific journals to publish the information and make it available by paid subscription. [JPG]

Methodology [JPG]

source: More on the Harris poll

Harris Poll, Most Americans Back Online Access To Federally Funded Research, Wall Street Journal, May 31, 2006. Excerpt:

A majority of U.S. adults say federally funded research findings on health issues and other topics should be available for free to doctors and the general public, according to a recent Harris Interactive poll.

In an online survey of 2,501 U.S. adults, more than 80% of Americans say they agree strongly or somewhat that research should be available for free via the Internet because the research is paid for with U.S. tax dollars.

In addition, 81% of Americans say they agree strongly or somewhat that access to such research data will help those living with a chronic illness or disability to get the latest information that might assist them.

And 62% of Americans say they agree strongly or somewhat that making the information available online and for free “will help speed up finding potential cures for diseases,” compared to 10% who disagree somewhat or strongly.

A table of the full results is included in the article but I don’t have room to insert it here.

Comment. This is a shot in the arm for the CURES Act and FRPAA, the two bills now before Congress that would mandate OA to publicly-funded research. Scientists and scholars may not carry much weight in Washington these days, but strong poll numbers from a respected pollster are hard to ignore.

I suspect that these poll results could be replicated in most countries around the world. Could a UK version of this poll save the draft RCUK OA policy from being weakened by publisher lobbying?

Update. When I first posted this news, the poll itself was not yet online at the Harris web site. But now it is.

source: 83% of Americans want OA to publicly funded research

From today’s announcement:

Hindawi Publishing Corporation is pleased to announce the addition of the following five journals to its Open Access journal collection:

• EURASIP Journal on Information Security
• International Journal of Plant Genomics
• Laser Chemistry
• Texture, Stress, and Microstructure
• VLSI Design

The first two journals are new launches, while the remaining three journals were previously published as subscription-based journals and are being re-launched using the Open Access model. All articles shall be distributed under the “Creative Commons Attribution License,” which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

All back volumes of the “Laser Chemistry,” “Texture, Stress, and Microstructure,” and “VLSI Design” will be made freely available online. Some back volumes are already available, while the remaining volumes are being retro-digitized and will be made freely available as soon as the retro-digitization is complete.

Hindawi expects its Open Access journal collection to reach 60 titles by the end of 2006 and is planning further expansions in 2007.

PS: Kudos to Hindawi for another giant step forward.

source: Five more OA journals from Hindawi

source: Switch from print to online increases STM publisher revenue

GlaxoSmithKline now provides OA to summaries of more than 2,600 clinical drug trials on 52 drugs. (Thanks to Research Research.) From GSK’s May 24 press release:

GlaxoSmithKline (GSK) reports today that it has now made available to the public detailed summaries of more than 2,600 clinical trials conducted in 50 countries to study 52 GSK prescription medicines and vaccines.  The information is found in the GSK Clinical Trial Register….

In the current issue of The Lancet, [Frank] Rockhold [Senior Vice President, Biomedical Data Sciences] and Ronald Krall, Senior Vice President and Chief Medical Officer, GSK, note the growing potential of databases like the GSK Register and the possible need for medical journals to adjust policies that discourage publication of data initially appearing online.  “We would urge medical journals to ensure that their prior-publication policies do not unduly restrict researchers who wish to put research results online in a timely fashion,” Rockhold said.

Comment. As recently as December 2005, the International Committee of Medical Journal Editors (ICMJE) rated the major drug companies on their compliance with its data sharing standards, and criticized GSK for providing “meaningless entries” on a key data field in an “astonishingly” high number of cases. I have no idea whether the new GSK data summaries are any better and hope the ICMJE will weigh in on that. But I applaud Rockhold and Krall for calling on journals not to let the Ingelfinger rule block early OA to data.

Note the interesting reciprocity here. Editors of prestigious medical journals (ICMJE) demand that drug companies provide OA to their data. In fact they refuse to publish articles on clinical trials whose underlying data are not OA. Good move. A drug company criticizes journal editors (not necessarily the same editors) for deterring OA to data and calls on them to remove the obstacles. Good move. Both moves are very welcome and turn-about is fair play. But at the same time, both houses need to be put in order. Drug companies not yet complying with the call for full and meaningful data sharing need to start. Journal editors still deterring OA to data need to stop. For that matter, ICMJE editors need to see that OA to articles is as important as OA to data.

source: More on OA to clinical trial data

Sudan: Open-access digital library launched, Reuters, May 31, 2006. Excerpt:

The Rift Valley Institute (RVI) and the United Nations Children’s Fund (UNICEF) on Tuesday launched the Sudan Open Archive, an open-access digital library for Sudan, containing documents that until now were largely unavailable in digital form. “It is a dynamic, expanding archive,” said John Ryle, chair of RVI. “Our aim is to put in historical and contemporary materials of all kinds.”

The first phase of the archive involved the digitisation of around 500 documents drawn from the records of Operation Lifeline Sudan (OLS), the international relief effort that started in 1989. “A lot of the documents were just stuffed away in containers in Khartoum, Juba, Lokichokio and Nairobi,” Ryle said. “The digital archive can bring together material from all over the place, which is exactly the problem in Sudan - documents are all over the place.”

source: Sudan launches OA digital library

John Udell, Re-imagining education, John Udell’s Weblog, May 30, 2006. Excerpt:

I’ve been thinking a lot about how ascendant uses of the Internet — including blogging, podcasting, screencasting, and social software — could transform education in the way that television was supposed to but of course never did….[W]e’re approaching a dual inflection point: widespread access to existing knowledge, coupled with a widespread ability to publish new knowledge.  A compelling analysis of how these trends can improve education, and why that improved educational system will be the right one for the 21st century, comes from John Willinsky, whose podcast talk on these subjects I found by way of Brian Lamb.

Among his themes, Willinsky talks about how he, as a reading specialist, would never have predicted what has now become routine. Patients with no ability to read specialized medical literature are, nonetheless, doing so, and then arriving in their doctors’ offices asking well-informed questions. Willinsky (only semi-jokingly) says the Canadian Medical Association decided this shouldn’t be called "patient intimidation" but, rather, "shared decision-making."

How can level 8 readers absorb level 14 material? There are only two factors that govern reading success, Willinsky says: motivation, and context. When you’re sick, or when a loved one is sick, your motivation is a given. As for context:

They don’t have a context? They build a context. The first time they get a medical article, duh, I don’t know what’s going on here, I can’t read the title. But what happened when I did that search? I got 20 other articles on the same topic. And of those 20, one of them, I got a start on. It was from the New York Times, or the Globe and Mail, and when I take that explanation back to the medical research, I’ve got a context. And then when I go into the doctor’s office…and actually, one of the interesting things…is that a study showed that 65% of the doctors who had had this experience of patient intimidation shared decision-making said the research was new to them, and they were kind of grateful, because they don’t have time to check every new development.

…Access to knowledge, access to publishing. Motivation and context. If an educational system embraced these principles, what would it look like? Willinsky challenges us to figure it out, and anyone with a stake in education — which is to say, everyone — should be asking and trying to answer that question.

source: More on OA for lay readers

Richard Seitmann, Ketten der Wissensgesellschaft - Der Kulturkampf über den Zugang zu wissenschaftlichen Veröffentlichungen verschärft sich, c’t, May 29, 2006, pp. 190-99. Not online or OA, at least so far. (Thanks to netbib.)

Update. The article is now OA. Read the original German or Google’s English.

source: The culture war over access to scientific publications

source: OA can help the Swiss social sciences

Stevan Harnad, Plugging the Loopholes in the Proposed FRPAA, RCUK and EU Self-Archiving Mandates, Open Access Archivangelism, May 27, 2006. Excerpt:

The two changes are small but absolutely crucial:

(1) Mandate immediate deposit for all accepted papers (rather than mandating deposit only after an interval determined by the publishers, or after a fixed 6-month embargo).

(2) Only recommend (rather than mandate) immediately setting the access to each deposit as Open Access (OA): allow the option of setting access instead as Closed Access (CA) where deemed necessary (i.e., where it is thought that immediately setting access as OA would contravene the author’s copyright agreement with the publisher)….

The US is probably the only country in the world that has enough collective weight to go even further, because it represents such a large proportion of the authorship of so many journals, and of the funding of so much published research: The US can, I think, with impunity put a cap (of six months, or even less) on the maximal allowable embargo period. The Wellcome Trust has already done this, telling their authors: "If your publisher does not agree to a cap of 6 months on the embargo, choose another publisher!" Wellcome, however, has the advantage, for this admirable and bold move, that they are a private funder. So all an author can do, if he does not like the Wellcome terms, is to choose another funder….

[T]he Dual Deposit/Release (DD/R) policy…does not require either switching publishers or contravening the terms of their copyright agreement. It allows embargoed access-setting but mandates immediate deposit (and then semi-automatic email-eprint requests in the repository software will take care of any gap-period in which the metadata are visible and accessible but the full-text is Closed Access)….

source: More on the dual deposit/release policy

The Canadian Council of Ministers of Education (CMEC) wants to amend Canadian copyright law in order to improve access to online content. From yesterday’s press release:

“Because copyright legislation impacts directly on our policies and
practices in classrooms across Canada, we are most concerned with fair and
reasonable Internet access for students and teachers in their educational
pursuits,” says Minister [Jamie] Muir, whose consortium represents education ministers
in Canada with the exception of the province of Quebec….

Education Minister Muir comments that the Canadian Music Creators
Coalition’s recent meetings with the federal ministers have captured the
public’s interest in the anticipated copyright legislation. He says, “Like
these musicians, the education community is very concerned about the new
legislation. We want the new Copyright Bill to reflect the reality of Internet
usage today and not support outdated and unsustainable business models that
limit access to publicly available Internet materials.”…

“For the education community, we believe a large part of the Internet is
in the public domain, and we don’t want to see Canadian-made fences placed on
the Internet’s public space. We simply don’t want the establishment of
restrictive measures that will negatively affect the quality of education for
today’s Internet-surfing generation and for future Canadian students and
educators.” Minister Muir adds, “We believe that Canadian students and educators have
a right to use publicly available materials on the Internet without a
copyright collective charging a licensing fee for access.”…

“Bill C-60 was wholly inadequate from the perspective of
the education community because it failed to address the educational use of
the Internet….Our proposed education amendment would allow access
to publicly available Internet materials while respecting the rights of those
creators who post on-line for commercial purposes. In our proposal, students
and teachers would be able to access those on-line materials that are ‘free.’
Those materials posted on-line for commercial enterprise would still require
payment should students and teachers wish to access and use them.”….

source: Canadian Education Ministers want fewer access barriers to online educational content

In a rare spin into politics, ebay’s Meg Whitman has written to eBay community members asking them to write members of Congress to get them to support Network Neutrality legislation. (eBay’s policy statement on NetNeutrality is here. )

This is a critical time. Congresswoman Zoe Lofgren is my favorite leader on this issue. After just barely squeezing a victory in the House Judiciary Committee last week, the press is on now for the vote on the floor. The Congress Daily (which can’t be linked to) estimates about a $1 million per week is being spent on ads by telecom and cable companies to fight neutrality legislation.

SaveTheInternet.com has an action site. There’s another (overly fancy) site I hadn’t seen before: It’s Our Net. But whether you like fancy or plain, spread the word.

source: Network Neutrality: Critical push

source: New blog for data sharing in archaeology

David Flaxbart, Public Science, Public Access, Issues in Science and Technology Librarianship, Spring 2006. An editorial. Excerpt:

Advocates for open access to the scientific literature were heartened recently by the surprising introduction of a Senate bill that would require most recipients of federal research funds to make their findings freely available within six months of publication. The “Federal Research Public Access Act of 2006″ would expand and add teeth to the watered-down NIH policy which has been ignored by the vast majority of life scientists since its introduction in 2005. FRPAA is even more remarkable given that its co-sponsor, Sen. John Cornyn (R-TX), is otherwise known for an aggressive pro-business stance.

Naturally, it didn’t take long for the publishing industry’s lobbyists, led by the eminently hissable American Association of Publishers, to shake off their cocktail-circuit stupor and begin frothing at the mouth at this dangerous exercise in socialist engineering. They immediately trotted out their tired and discredited mantras about the loss of subscription revenue, removal of investment incentives, and threats to peer review, in addition to the accusations that the government is trying to fix a system that — for them at least — isn’t broken.

Brian Crawford, a vice president of the American Chemical Society, mouthed this ludicrous statement in an AAP press release: “Americans have easy access to scientific and medical literature through public libraries, state universities, existing private-sector online databases, as well as through their professional, academic, or business affiliations, [and] low-cost online individual article sales.” While this absurd claim won’t fool anybody with real-life experience, these and other inaccurate sound bites could be swallowed whole by politicians and policy makers inclined to oppose government intervention.

It is sad that some of the loudest anti-OA rhetoric is coming from some non-profit publishers and societies who should really know better by now, and whose pretense at protecting the integrity of science has long since been exposed as a ploy to protect their revenue streams…. Journals are actively abdicating any responsibility for investigating fraud, which further erodes their credibility (Altman 2006). Publishers’ persistent defense of this tattered fig leaf of “added value” is starting to sound rather desperate….

The issue of public access to publicly funded science isn’t going away, despite publishers’ hopes to the contrary. Open access may not be the panacea to cure all the ills of a collapsing system, but it is vital that it be allowed to demonstrate its impact, good or bad, in a fair and objective arena. To that end, all stakeholders in the scholarly communication community should unite to support this bill and refute its knee-jerk detractors.

source: Straight talk about OA and its critics

An interesting article on blog-spam countermeasures — Google’s
embarrassing mistake. Quote:

I think it’s time we all agreed that the ‘nofollow’ tag has been a complete
failure.

For those of you new to the concept, nofollow is a tag that blogs can add to
hyperlinks in blog comments. The tag tells Google not to use that link in
calculating the PageRank for the linked site. […]

Since its enthusiastic adoption a year and a half ago, by Google, Six Apart,
Wordpress, and of course the eminent Dave Winer, I think we can all agree
that nofollow has done — nothing. Comment spam? Thicker than ever. It’s had
absolutely no effect on the volume of spam. That’s probably because comment
spammers don’t give a crap, because the marginal cost of spamming is so low.
Also, nofollow-tagged links are still links, which means that humans can
still click on them — and if humans can click, there’s a chance somebody might
visit the linked sites after all.

I agree. At the time, I pointed at
this comment from Mark
Pilgrim:

Spammers have it in their heads now that weblog comments are a vector to
exploit. They don’t look at individual results and tweak their software to
stop bothering individuals. They write generic software that works with
millions of sites and goes after them en masse. So you would end up with
just as much spam, it would just be displayed with unlinked URLs.

Spammers don’t read blogs; they just write to them.

I still think he was spot on.

However, one part of the ‘Google’s embarrassing mistake’ article is a red
herring — I think the chilling effect on “nonspam links” is not to be worried
about; as Jeremy Zawodny
said, life’s too short to
worry about dropping links purely in the hopes of giving yourself Page Rank. I
don’t know if I really want links that people are leaving purely for that
reason.

In fact, I wouldn’t be surprised to hear that Google’s crawler starts treating
“nofollow” links as mildly non-spammy in a future revision, due to their wide
use in wikis, blogs etc.

To be honest, though — I don’t see the problem of blog-spam much anymore.
As I said here:

[Weblog] comment spam should be a lot easier to deal with than SMTP spam. …
With weblog comments, you control the protocol entirely, whereas with SMTP
you’re stuck with an existing protocol and very little “wiggle room”.

On my WordPress weblog [ie. here] — which, admittedly, gets only about 1/4 of the
traffic plasticbag.org does — I’ve instituted
a very simple check stolen from Jeremy
Zawodny. I simply include a form field
which asks the comment poster for my first name, and if they fail to supply
that, the comment is dropped. In addition, I’ve removed the form fields to
post directly, requiring that all comments are previewed; this has the nice
bonus of increasing comment quality, too.

Those are the only antispam measures I’m using there, and as a result of
those two I get about 1 successful spam posted per week, which is a one-click
moderation task in my email. That’s it.

The key is to not use the same measures as everyone else — if every weblog
has a different set of protocols, with different form fields asking different
simple questions, the only spammers that can beat that are the ones that
write custom code for your site — or use human operators sitting down to an
IE window.

Trackbacks, however — turn that off. The protocol was designed poorly, with
insufficient thought given to its abuse potential; there’s no point keeping it
around, now that it’s a spam vector.

Finally, a “perfect” solution to blog spam, while allowing comments, is
unachievable. There will always be one guy who’s going to sit down at a real
web browser to hand-type a comment extolling the virtues of some product or
another. The goal is to get it to a level where you get one of those per
week, and it’s a one-click operation to discard them.

Tags:antispam blog spam nofollow spam weblogs

This post was written by Justin, source: Blog Spam, and a ‘nofollow’ Post-Mortem

• One year without nicotine!
  yay me!
  (tags: non-smoking nicotine addiction cigarettes life progress)

Tags:

This post was written by dailylinks, source: links for 2006-05-30