Category Archives: Open Science

Open Access Day is on October 14th. This day is organized by SPARC, Students for FreeCulture and PLoS.
Why?

Open Access is a growing international movement that uses the Internet to throw open the locked doors that once hid knowledge. It encourages the unrestricted sharing of research results with everyone, everywhere, for the advancement and enjoyment of science and society.

You should participate and register. Already, there are 100 organizations taking part, and the registration closes tomorrow so you have to act fast!
You can help by spreading the word. On October 14th, there will be a lot of stuff to do and some cool videos to watch (and embed into your sites).
And if you are a blogger, get ready for the contest – the details of the blogging competition will be posted next Friday (October 10th) on the Open Access Day blog, on the PLoS blog and right here, on my blog, so come back and check it out next week.

Go to Mimi’s place and state your position:

For a long time, if you wanted to read up on science news or get background information for research, you had to hope that the media got it right, have a subscription to a few journals ( there are thousands though, so you are missing out), or be lucky enough to work at an institute/organization that gives you access to journals online and has a few (hundred) bound copies. Before legislation was passed to make NIH funded research available to the public after a year, no one really knew what was going on in the world of research and development.
This sounds great for some, but for scientists and certain publishing houses, this is a topic of much contention. In fact, OA was in recent legislation again! So I guess the question up for discussion this week is…do you think research should be made available to the public for free or is this going to destroy tiny publishing houses and let the big ones float? How will this affect genetics testing and privacy of subjects? How do you feel about open access?

At Harvard, a week ago:
Recap: Wednesday’s Health and Human Rights Discussion

Yesterday afternoon at the Loeb Theater, Harvard hosted a forum celebrating the tenth edition of their journal Health and Human Rights. This edition is the journal’s first to be presented in open-access format, meaning that anyone can read it without paying the exorbitant fees associated with most journal articles. Bostonist was in the front row as Agnes Binagwaho, Gavin Yamey, Philip Alston, and Paul Farmer (profiled as “a man who would cure the world” by Tracy Kidder) discussed the past, present, and future of global health policy.
The most compelling aspect of the discussion dealt with the dilemmas faced by doctors worldwide, and particularly in areas like sub-Saharan Africa, in instituting the best practices for treating AIDS and other serious outbreaks. Most hospitals have extremely tight budgets, forcing them to rely on free (and sometimes factually incorrect) abstracts of published research, rather than the expensive full papers. This can cause trouble: Yamey noted that one South African hospital worsened its AIDS treatment program because of erroneous information contained in the abstract of a journal article. Yamey went on to say, “removing access barriers will… share the learning of the rich with the poor and the poor with the rich.” This sentiment was echoed by Binagwaho, who heads up the effort to combat AIDS in Rwanda, and noted that increased Internet availability combined with open-access publication will enable rapid implementation of new treatment techniques at the community level.

Making the case for the right to health

Dr. Binagwaho reflected on the irony of research done in developing countries that is never available to the study subjects, and she applauded efforts like PLoS and HHR Journal for working to promote access to a wider audience. In addition, she stressed the need for intellectual exchange. She saw these discussions as “necessary to make the best decisions.” Citing the example of GHDonline.org, she told of the value for herself and others in executive positions to bounce ideas off of each other (for example, should children of HIV-positive parents undergo mandatory testing?) and also the value gained by including field workers in the conversation. “People at the community level may not have the theories, but they have the knowledge,” she said. Finally, she outlined that the sum of these efforts, of fighting for access to health, information, and education, is to eliminate poverty.
Dr. Yamey focused on the need to change the way we look at medical publications. He points out that information is so expensive to access that patients, and many doctors and researchers, can simply not afford to survey the literature and make fully informed decisions. “Only a tiny fraction of the intended audience can read a work. This paradigm is wrong — medical research should be a global public good.” The consequences of the current model are hazardous: often, doctors and patients are forced to rely on abstracts, which convey “dangerous half-truths.” Also, because researchers in the global south often have less access to literature than their counterparts in the north, a dynamic of inequality is introduced in their interactions. The world would benefit from a “knowledge commons,” which would better allow research and practice efforts to “build on the shoulders of giants.” Dr. Yamey was instrumental in getting the journal online in an open access format, and he applauded the journal’s new format.

You probably remember the wonderful new NIH law that passed last year:

On Dec 26th, 2007, President Bush signed the Bill that requires all NIH-funded research to be made available to the public.

The bill mandates all NIH-funded research to be made freely available to public within 12 months of publication.
You probably also remember that the big publishers opposed the law, using some very unsavoury tactics. Well, guess what? They are at it again. They are trying to sneak through Congress a new bill that is, in essence, the repeal of the NIH open access law. The bill, dubbed in a typical double-speak Orwellian fashion “Fair Copyright in Research Works Act (HR6845)” has now been introduced. It may not get out of committee in this Congress, but probably will after the new Congress is seated.
David Dooling writes:

Since Congress voted to encourage NIH to adopt an open access policy for scholarly publications that resulted from research it funded, the journal publishers have lobbied Congress to reverse it. It seems the efforts of publishing companies are beginning to pay off with the introduction of the bill HR 6845. The bill would shift rights away from the article authors, the researchers, and back to large publishing houses. In an age of internet publishing and voluntary peer review, what possible reason could their be for such a shift? How would increasing restrictions on scientific publications increase openness and access to scientific discovery, the very foundation of scientific advancement? These sort of copyright issues cut across the partisan divide, typically aligning members of Congress from both parties from areas of the country with strong content generation industries (TV, movies, music, print). In other words, members of Congress from California, New York, and Florida (Disney) or committee chairs who get a lot of money from these big media companies typically introduce and support these anti-competitive, anti-scientific pieces of legislation. This bill is no exception, being sponsored by John Conyers (D-MI), Darrell Issa (R-CA), Robert Wexler (D-FL), and Tom Feeney (R-FL).

John Timmer says:

In recent years, scientific publishing has changed profoundly as the Internet simplified access to the scientific journals that once required a trip to a university library. That ease of access has caused many to question why commercial publishers are able to dictate the terms by which publicly funded research is made available to the public that paid for it.
Open access proponents won a big victory when Congress voted to compel the National Institutes of Health to set a policy of hosting copies of the text of all publications produced by research it funds, a policy that has taken effect this year. Now, it appears that the publishing industry may be trying to get Congress to introduce legislation that will reverse its earlier decision under the guise of strengthening copyright protections.

And Revere adds:

I am one of those NIH supported researchers whose papers get locked up for decades behind copyright permission firewalls. I want you to have access to my research. I want the journals I publish in to be required to make it available to you after a reasonable time period (the shorter the better) as the NIH policy now does. It helps me professionally by making my work more widely disseminated. It helps me as a professional by making it possible to get access to scientific research, now inaccessible because of the predatory and outrageous charges of the large scientific publishers, the same people behind the Conyers legislation.

You can read more about the intentions of the bill here.
What can you do? Call your congresscritters and ask them to bury this bill. You have only until September 24th to do so!
There is a sample letter under the fold (along with the contact info for Congress), but it is usually much better if you write one of your own. If so, make it short, make it simple (so an average congressman can understand it), make it positive (better than bashing the slimy opposition) and make it personal (why do you personally support Open Access).
Then, use whatever online and offline tools are at your disposal (blogs, twitter, friendfeed, e-mail, newsgroups, personal contact) and spread the word – urge all your friends and colleages to contact their Representatives and Senators and ask them to Just Say No.

Continue reading →

SPARC, Students for FreeCulture and PLoS are organizing the first ever Open Access Day on October 14, 2008. This is also the 5th birthday of PLoS Biology, the oldest of seven PLoS journals.
For this occasion, the organizers have put together a nice website/blog where you can find all the information. You can watch videos (two so far, but there will be more). You can help spread the word:

You can get prizes. Or you can enter the blog contest:

Coming soon…
Prior to Open Access Day, bloggers will be invited to draft a personal post addressing the following key points:
* Why does Open Access matter to you?
* How did you first become aware of it?
* Why should scientific and medical research be an open-access resource for the world?
* What do you do to support Open Access, and what can others do?
We will ask the community to time these posts for release on Open Access Day so that the whole blogosphere gets the message that Open Access matters! A series of videos is also being prepared to address the same questions.
PLoS and (we hope) another prestigious publishing partner will then choose the winner and announce it on their respective sites. A free goodie bag including an iPod Nano, and other items (T-shirts, etc.) will be the prize for the most compelling post.
Watch this space…

But to win the blog contest, you first have to deal with Dorothea… 😉 Steve Lawson seems to have already conceded defeat to her. You should not!

From SciFoo 08:

Victoria Stodden discusses her efforts to create a new license for scientific research which covers both publication and data. She discusses the motivations behind the new license and the issues brought up by releasing scientific research and data under and open source license.
Copyright 2008 O’Reilly News. All Rights Reserved. Filmed at Scifoo 2008 at the Googleplex in Mountain View, CA by Tim O’Brien.

Jean-Claude Bradley reviews Happy Accidents: Serendipity in Modern Medical Breakthroughs by Morton A. Meyers. Morton says:

An applicant for a research grant is expected to have a clearly defined program for a period of three to five years. Implicit is the assumption that nothing unforeseen will be discovered during that time and, even if something were, it would not cause distraction from the approved line of research. Yet the reality is that many medical discoveries were made by researchers working on the basis of a fallacious hypothesis that led them down an unexpected fortuitous path.

Jean-Claude adds:

We can share our failed experiments. We can share our research plans. We can discuss science freely admitting what we don’t know. We can record our talks at closed meetings and make them public. We can initiate and participate in serious scientific conversations going on in the blogosphere without worrying about everyone’s title and rank.
Basically, we can collaborate in ways that are most conducive to serendipitous discoveries. The free social software, databases and other infrastructure now available make this information exchange easier than ever.

For those of you interested in the science publishing business, there is an interesting paper out about Impact Factors, where they do the math to try to explain why the IFs are apparentluy always rising from year to year, and to figure out the differences between disciplines. They remain agnostic pretty much about the whole hot controversy about the validity of IF, but their data explain some facts about IF that can be added, IMHO, into the growing lists of reasons why IF should be abandoned:
Althouse, B.M., West, J.D., Bergstrom, C.T., Bergstrom, T. (in press). Differences in impact factor across fields and over time. Journal of the American Society for Information Science and Technology DOI: 10.1002/asi.20936

The bibliometric measure impact factor is a leading indicator of journal influence, and impact factors are routinely used in making decisions ranging from selecting journal subscriptions to allocating research funding to deciding tenure cases. Yet journal impact factors have increased gradually over time, and moreover impact factors vary widely across academic disciplines. Here we quantify inflation over time and differences across fields in impact factor scores and determine the sources of these differences. We find that the average number of citations in reference lists has increased gradually, and this is the predominant factor responsible for the inflation of impact factor scores over time. Field-specific variation in the fraction of citations to literature indexed by Thomson Scientific’s Journal Citation Reports is the single greatest contributor to differences among the impact factors of journals in different fields. The growth rate of the scientific literature as a whole, and cross-field differences in net size and growth rate of individual fields, have had very little influence on impact factor inflation or on cross-field differences in impact factor.

Christina looks at their math and summarizes the paper as well:

Impact factors of journals are a perennial discussion topic – used by libraries (with other measures) for collection development and by researchers to decide where to publish. They’re also mis-used, abused, and misunderstood. But this article isn’t about all that. This article looks at whether the impact factors are going up, what aspect of the impact factor provides the greatest contribution or explains the increase, and if the increase is different in different disciplinary categories?

Michael Nielsen’s talk at SciFoo’08:

Boston Globe has an interesting article about Open Science, citing the routine list of worries that usually get associated with this idea, e.g., :

But in the world of science – where promotions, tenure, and fortune rest on publishing papers in prestigious journals, securing competitive grants, and patenting discoveries – it’s a brazen, potentially self-destructive move. To many scientists, leaving unfinished work and ideas in the open seems as reckless as leaving your debit card and password at a busy ATM machine.

But, as John Hawks says:

I think that’s a pretty simplistic rendering of how scientific credit is assigned. It ignores all the factors that depend not on your results but on networking. Who you know may be vastly more important than what you do.
I think that if more researchers were independent (not tied to someone else’s lab) and if they spent less time grant-writing, we’d see more open collaborations. Right now the biggest barrier to openness is centralization.

Eva Amsen: How to get scientists to adopt web 2.0 technologies:

Many, if not most, scientists are not in the habit of putting things online. The ones that are might be tempted by the concept of sharing the papers they read, letting everyone look at their lab notebook, joining a forum or writing a blog. If you’re reading this in your RSS feed or clicked through from FriendFeed, you’re probably one of those people. But think about your friends and colleagues who only turn on their computer for work and e-mail. They’re not going to tag their favourite papers or discuss the process of research with total strangers on the internet. It’s an extra thing to do that’s not already part of their lives, and no matter how appealing they might find the concept of open data or sharing information, they won’t join these sites or movements because it’s not something they are already doing.
So what are they already doing?

See also discussions on FriendFeed about this insightful article.
What do you think?

Reed Elsevier caught copying my content without my permission:

I was not asked for, and did not give, permission for my work to appear on that page, much less in that format. Needless to say, I felt a little slighted.
The website in question appears to be a custom version of the LexisNexis search engine. This particular version appears to be Elsevier’s own custom version, intended for internal use. I don’t have conclusive proof of that, but the title bar at the top of the page reads, “Elsevier Corporate”, and the person who accessed my blog from that page had an IP address that’s registered to MD Consult, which is an Elsevier subsidiary. My guess is that Elsevier’s keeping track of news articles and blog posts that mention them, along with the context in which they’re mentioned.

For-Profit Scientific Publishers and the Culture of Entitlement:

The relationship between publishers and the scientific community is not a partnership. It’s parasitic.
And it gets worse, because the parasite doesn’t even have the decency to try and hide what it’s doing. Instead, the major academic publishers seem to feel that they are entitled to continue to make enormous profits selling scientific research to scientists at outrageously inflated prices.
—————
Were it not for their track history, I suspect that neither the Mad Biologist or I would have been quite as irritated when they “borrowed” some of our work for internal use. With the track history, though, seeing our words sitting, without proper credit, permission, or attribution, on a page that bears a prominent notice protecting their copyright becomes something more. It goes from being a minor discourtesy to being another symptom of the company’s lack of respect for the people who do the bulk of the work to produce their profits, and provide the bulk of their customer base.

Reed Elsevier Is Stealing My Words:

I received an email from ScienceBlogling Mike Dunford that Reed Elsevier had excerpted one of my posts. No problem there–I like it when people read my stuff….except for one thing:
The fuckers copyrighted my words.

Copyright violation?:

Apparently, publishing companies don’t always get permission for the materials they use, either. Mike Dunford caught Reed Elsevier copying his content without permission (from Stephen Downes).

Elsevier’s New Open Access Policy…:

Although it is common practice within the blogosphere to quote liberally from other sources, we do this with the understanding that others may quote liberally from us. In fact, we hope that they will–as long as they give proper attribution. While we do this, our own material is made freely available, with running costs being paid for by advertisers (i.e., a pretty standard open access model) or just being footed by the blogger. Elsevier, on the other hand, not only reserves most of its material for paid subscribers, but actively fights the open access movement with insidious initiatives like PRISM.

Reed Elsevier Caught Copying My Content Without My Permission:

I’m including this link mostly because I’m not, you know, surprised. The stuff publishers want to ban us from doing is stuff they routinely do in-house, behind closed doors, where they think nobody will notice.

Elsevier Profits: $1,750 per minute – and growing? :

STM journal prices for the past few decades have risen far beyond inflation, and far beyond the ability of libraries to keep up. For long-term success, a business needs healthy, happy customers. This would also be a good success item to report, for Elsevier’s new Corporate Responsibility Division.

Open Access Wars, part n:

As they say, read the whole thing….

Larry Lessig reports some exciting, huge and important news: free licenses upheld:

So for non-lawgeeks, this won’t seem important. But trust me, this is huge.
I am very proud to report today that the Court of Appeals for the Federal Circuit (THE “IP” court in the US) has upheld a free (ok, they call them “open source”) copyright license, explicitly pointing to the work of Creative Commons and others. (The specific license at issue was the Artistic License.) This is a very important victory, and I am very very happy that the Stanford Center for Internet and Society played a key role in securing it. Congratulations especially to Chris Ridder and Anthony Falzone at the Center.
In non-technical terms, the Court has held that free licenses such as the CC licenses set conditions (rather than covenants) on the use of copyrighted work. When you violate the condition, the license disappears, meaning you’re simply a copyright infringer. This is the theory of the GPL and all CC licenses. Put precisely, whether or not they are also contracts, they are copyright licenses which expire if you fail to abide by the terms of the license.
Important clarity and certainty by a critically important US Court.

(Via, hat-tip)

Pushing Boundaries in Information Visualization: Using Virtual, Immersive and Interactive Technologies in Research & Practice

Saturday, September 13, 2008
9am – 4:30pm
This workshop will showcase some of the innovative uses of technology in terms of virtual and immersive environments for interacting with information. The day’s events will generate attendee discussion around the use, integration and evaluation of such tools (how do we evaluate the use of these technologies? how can research improve practice? how can practice inform research, etc.).
The program will feature a colorful mix of research projects ranging from electrical stimulation of the nervous system with cochlear implant, to scalable visualization of genealogy links, experiential look at the death penalty, visualizing activity on a busy website, and comparing human and yeast cell protein interaction networks. Attendees need not be familiar with the disciplines of these research projects Ð the program will expose you to the use of immersive and interactive technology across a range of disciplines and then encourage discussion about the possibilities.
Event Details:
Saturday, September 13, 2008, 9am – 4:30pm
Renaissance Computing Institute (RENCI), UNC Campus – ITS Manning
211 Manning Drive, Chapel Hill, NC 27599
Free for ASIS&T members, $50 for non-members (ASIS&T student membership is only $40)
Payment must be received by September 8, 2008
Attendance is limited to 45

Discuss on Facebook.

Sometimes people ask me what do I have against Green OA (repositories) as opposed to Gold OA (journals) and I have a couple of stock answers to that, usually including a caveat that I do not really have anything against Green OA per se, but the way it is implemented is not good, yet makes people complacent, which in turn slows the down the progress towards complete OA. Not well implemented? Well, yes, I have seen all of these sins over the past couple of years. Once there is a standard that all builders of repositories adher to, Green OA will be OK (though there are other arguments against its current implementation still standing, i.e., the usual 6-12 month wait which is not inherent to Green OA but just a current bad practice).

Citation Statistics (pdf):

This is a report about the use and misuse of citation data in the assessment of scientific research. The idea that research assessment must be done using “simple and objective” methods is increasingly prevalent today. The “simple and objective” methods are broadly interpreted as bibliometrics, that is, citation data and the statistics derived from them. There is a belief that citation statistics are inherently more accurate because they substitute simple numbers for complex judgments, and hence overcome the possible subjectivity of peer review. But this belief is unfounded.

Information Liberation:

If your child has a life-threatening disease and you’re desperate to read the latest research, you’ll be dismayed to learn that you can’t — at least not without hugely expensive subscriptions to a bevy of specialized journals or access to a major research library.
Your dismay might turn to anger when you realize that you paid for this research. Through the National Institutes of Health alone, American taxpayers funnel more than $28 billion annually into medical research. That’s leaving aside the billions more in public spending on state universities or the tax exemptions granted for gifts to private campuses.

Open Access and the NIH

In 1978, in enacting Section 105 of title 17, Congress faced a choice about what to do with copyrighted works that result from government funding, including basic research funding of scientific, technical, and medical (“STM”) journal articles. One approach was simply to preclude any assertion of copyright, treating such works the same way as works created by government employees within the scope of their employment. That approach would have been simple to apply, but might have inhibited the publication of some STM journals, at a time when hard copy ruled as the method of distribution. Congress chose a middle approach, discussed here in the 1976 House Judiciary Committee report:, which begins by referring to the definition of “work of the United States government”:

An Interview with Heather Joseph:

Heather Joseph talks about her career with SPARC and BioOne. She discusses the NIH mandate that NIH-funded research will be deposited into PubMed Central, and she shares her views on some of the controversial issues the mandate has raised about copyright, peer review, and embargo periods. She also addresses the recent decision by the Harvard faculty to make their scholarly output accessible through the university’s institutional repository, and she suggests ways that librarians can help their faculties prepare for open access.

Heather must be dismayed that her interview is behind the pay-wall.

Watch it here:
The Extraordinary Everyday Lives Show #053 – Open Science:

This show is all about the intersection of Technology and Human desire. This year Dave and I have been focusing on ‘deepening connections’ with those we subscribe to via RSS. Having a chat on a podcast is a remarkable way of doing that we have found. Agenda is loose guide only, we are very stream of consciousness, no edits, no script kinda guys.

The complexity of sharing scientific databases:

Under US law, pretty much anything you write down is copyrighted. Scrawl an original note on a napkin and it’s protected until 70 years after your death. Facts, however, are another matter – they can’t be copyrighted. So while trivial but creative scribblings are copyrighted, unless you choose to release them into the public domain, the information painstakingly discovered about the human genome – DNA sequences, for instance – aren’t. But the containers they’re stored in – the databases they’re held in – can be copyrighted.

Breaking News: Open access to large-scale drug discovery data at EBI:

The Wellcome Trust has awarded £4.7 million to the European Bioinformatics Institute (EBI) to support the transfer of a large collection of information on the properties and activities of drugs and a large set of drug-like small molecules from BioFocus DPI, part of the publicly listed company Galapagos to the public domain.

What scientists are we talking about?:

This discussion seems to have focused on just a small fraction (but an important one) of the number of scientists who would benefit from these tools. These researchers are funded by grants and are in tenure-track positions at 4 year research universities.
More scientists work at non-profits. What sorts of pressures are brought to bear there to prevent open collaboration? How different are these pressures from a research university? Those in business might also benefit from these approaches but have another set of barriers. Can they be surmounted?
This discussion is really important but it also conflates a large number of scientists/engineers who have different needs and pressures. There are 12 million in business who will have different needs than the 1.6 million at research universities.

MedPedia Is Wikifying the Medical Search Space:

The medical industry is one that thrives on innovation and evolution. New procedures, medicines, diseases, and theories are released practically every day. In such an environment, the need for a website to reflect and allow for documentation is apparent.

Open Access to Health and Human Rights:

Here’s another important step forward in the open access movement. Under its new editor Paul Farmer (who is often talked about as a future Nobel laureate), the international journal Health and Human Rights (HHR) has become fully open access.
The entire contents are freely available and are published under a progressive copyright license that allows readers to reuse the materials for any legal non-commercial purpose.

Indexing Institutional Repositories and Authors Self-Archived Collections:

The question then is whether or not ChemSpider can index institutional repositories or authors self-archived collections on their university research group websites. The authors self-archived collections will be very valuable but of course most likely to upset the publishers. We’d like to do both.
I envisage a time when articles are indexed and searchable even before they are published and indexed by others. Why not? If there are changes to the article between pre-and post-publication both can be indexed.

Another Wiki, WikiPathways:

I’ve already made known my “skeptical optimism” for wikis for biological data known in a previous post, reading this later paper, that would still apply here. But right now I’m not going to write beyond that, I’m just going to point you to this paper and wiki. Later (this week, next at the latest) I’ll be critiquing this paper more fully and more generally look at this trend currently to use wikis for community curation and documentation of biological data and databases.

Tracking the openness of databases:

Shirley Fung has launched Molecular Biology Databases, a website to evaluate the openness of databases in molecular biology.
———
Fung evaluates 34 databases to date, under six criteria: Downloadable, Offers Batch Processing, Offers a Query Interface, No Registration Required, Policy is Available, Public Domain. Her website supports the open-data research of Melanie Dulong de Rosnay, described last week by Ethan Zuckerman (and blogged here).
This is a very time-consuming but useful job. Everyone in molecular biology should be grateful, especially if the project leads to more consistent policies on open data across the field.

Fair game: a grad student’s adventures in fair use and copyright:

For scholars who study media, the internet has broadened research horizons and expanded the reach of teaching and publications. But powerful gatekeepers remain. From academic journals seeking to control our intellectual property to lawyers crying foul when we quote from copyrighted material, we are bombarded with a myriad of confusing and dubious restrictions. In short, the implied threat of legal action creates a chilling effect that impacts us all. Some have pushed back, arguing that our educational activities are protected under the “fair use” statute. But this is a risky game to play. The rules aren’t always clear. And when it comes to fair use, we either use it, or lose it.

Where should we spend our money?:

The lesson here seems to be that the digital environment is inevitably going to change the environment for textbooks as it has for most other kinds of intellectual property, for good or for ill. Georgia seems to feel that the publishers will eventually figure the market out and move to new profit models while supporting open access. But I think there is also an opportunity here for institutions to be more proactive and seek ways to invest in open access textbooks on a campus-wide level.

STM publishers imprisoned in their own walled gardens?:

Journals aggregate interesting science – many scientists still very much like a group of qualified editors and peer reviewers providing a filter on the deluge. Secondly, while knowledge discovery requires unfettered access for machines to content, I don’t see why that necessarily implies unfettered access for humans. You can perfectly well have an API that lets machines mine full-text, while still putting up a paywall for humans. As well, I think the versions issue is very challenging, and we are a long way from reliable automatic disambiguation and identification of authoritative copies. Finally, many conference proceedings already are peer-reviewed, and we can certainly imagine peer review extending to other areas, such as data sets.

History of the Journal Nature:

Nature introduced their formal peer review system in… 1967!

Who comments on scientific papers – and why?:

The quality of comments at BMC is high and the vast majority add value to the paper, though the numbers involved are relatively low (would a larger audience reading higher impact papers be different?).
Perhaps unsurprisingly comments on papers are not like comments on blogs; they’re far more formal (only 8% of comments were of the chatty, supportive variety) and it’s not the same people coming back each time (with the exception of the crazy 2%).

A couple of weeks ago, Vedran Vucic gave a talk about Open Access at the law school at the Belgrade University. For those of you who can read Serbian, here is the newspaper report. Glad to see PLoS mentioned…

Bjoern Brembs:

Today’s system of scientific journals started as a way to effectively use a scarce resource, printed paper. Soon thereafter, the publishers realized there were big bucks to be made and increased the number of journals to today’s approx. 24,000. Today, there is no technical reason any more why you couldn’t have all the 2.5 million papers science puts out every year in a single database.
——–snip——–
Precurser to this publishing reform was access reform: scientific papers are the result of publicly funded research and should be publicly accessible. This reform appears now to be well underway and will probably conclude in 2-3 years. Both reform movements have their base in the more general open science movement. The goal of this reform movement is to have full public access not only to the published papers, but also to the raw data, ideas and reagents for sharing among scientists. There are still plenty of problems which have to be worked out before open science can become a reality, if it is even feasible. One of the more easy to solve problems (one that is shared with publishing reform) is that of how to attribute credit. If we all publish in the same database and share ideas online, how can two scientists competing for the same position or grant be assessed objectively?
——–snip——–
Different universities/employers will focus on different aspects of a researcher and value some of his/her contributions more than others. I don’t think there can be too many measures to capture the complexity of scientific output. I’d like to see an aggregating service, maybe based on services like OpenID, where a flexible portfolio can be organized such that employers can easily search for the traits they are looking for and find or compare the people who maximize their efforts on these traits.
——–snip——–
I think most researchers would gladly pay for a service which has a track record of picking the most interesting, groundbreaking and well-done papers from the 2.5 million every year. Today’s professional editors would be a great pool from which such services could recruit employees.

Policy for Open Science – reflections on the workshop:

One thing that was very clear to me was that the attendees of the meeting were largely disconnected from the more technical community that reads this and related blogs. We need to get the communication flowing in both directions – there are things the blogosphere knows, that we are far ahead on, and we need to get the information across. There are things we don’t know much about, like the legal frameworks, the high level policy discussions that are going on. We need to understand that context. It strikes me though that if we can combine the strengths of all of these communities and their differing modes of communication then we will be a powerful force for taking forward the open agenda.

Why are so many scientists reluctant to make full use of Web 2.0 applications, social networking sites, blogs, wikis, and commenting capabilities on some online journals?
Michael Nielsen wrote a very thoughtful essay exploring this question which I hope you read carefully and post comments.
Michael is really talking about two things – one is pre-publication process, i.e., how to get scientists to find each other and collaborate by using the Web, and the other is the post-publication process, i.e., how to get scientists to make their thoughts and discussions about published works more public.
Those of you who have been reading me for a while know that I am thinking along some very similar lines. If you combine, for instance, my review of Rainbows End by Vernor Vinge with
On my last scientific paper, I was both a stunt-man and the make-up artist with Journal Clubs – think of the future! with The Scientific Paper: past, present and probable future, you will see a similar thread of thinking.
But, what do you think?