Category Archives: Open Science

Science in the 21st Century

Bee and Michael and Chad and Eva and Timo and Cameron will be there. And so will I. And many other interesting people. Where? At the Science in the 21st Century conference at the Perimeter Institute (Waterloo, Ontario) on Sep. 8th-12th 2008. And it will be fun. This is the blurb of the meeting:

Times are changing. In the earlier days, we used to go to the library, today we search and archive our papers online. We have collaborations per email, hold telephone seminars, organize virtual networks, write blogs, and make our seminars available on the internet. Without any doubt, these technological developments influence the way science is done, and they also redefine our relation to the society we live in. Information exchange and management, the scientific community, and the society as a whole can be thought of as a triangle of relationships, the mutual interactions in which are becoming increasingly important.

So, register now while there is still space!

I wish more people blogged about their own research the way Karen just did

About a month ago, Karen of The Beagle Project published a nifty paper in PLoS ONE. Now she wrote a blog post with the background story, the ‘tacit knowledge’ that usually does not appear in peer-reviewed literature but is essential for the workings of science – the kind of stuff that is transferred vertically from advisors to students, or horizontally between researchers at conferences.
It is important at this day and age for this tacit knowledge to become public. By hogging it, researchers in big institutions in developed countries hamper the development of scientists in small places and in the developing countries. I wish more scientists wrote blog posts describing the back-story of their research (as I did for my old work before), then posted links to the posts from the papers themselves so people can come, read and learn.

Whassup?

You must have noticed that there wasn’t too much effort on this blog over the past couple of weeks (except for the elaborate and too successful April Fools hoax). I’ve just been so busy lately. So, here is a quick recap, and some pictures.
Back on March 21, I went to Duke University to participate in a panel called Shaping the world, one job at a time: An altruistic/alternative career panel. From education, to public health in the developing world, to science journalism, writing, blogging and publishing. The room was full (80 people? Perhaps 100?!). I am not sure one hour was enough for all five of us to say everything we wanted, but I did manage to explain what PLoS is all about (especially PLoS ONE). Sheril was sitting in the front row and she took these pictures. Abel was sitting right next to her, and wrote more about one of the other panelists. As usually happens at such meetings, the most useful part was the hallway chatter right after. I talked to people who may be interested in publishing with us, or collaborating, or applying for an internship.
On March 22 we met at Miltown in Carrboro to say farewell to our friend Bharat. The weather was nice enough to sit outside. Anton (actually the waitress using Anton’s camera) took this picture. Bharat is going to Vancouver Island, all the way on the West coast of Canada to do some environmental work. There are many science bloggers in that part of the world, so perhaps they can invite Bharat to their blogger meetups (I cannot tell you his blog as I used his real name in this post, but I can facilitate connection).
Then on March 26th, again the weather was good for sitting outside at Milltown for a joint meetup between BlogTogether and the Orange Politics Happy Hour. There were about 20 people there, some old friends (including OP hosts Ruby Sinreich and Brian Russell, the camera master Wayne Sutton and Ginny Skalski from NBC, the Facebook guru Fred Stutzman, the Carrboro mayor Mark Chilton and many others), some new to me and fun was had by all. And we all had Moo.org cards to exchange with each other. They all tried really hard to get me on Twitter, with no success… 😉 Wayne took a bunch of pictures, but here is one of me, so my Mom can see that I look decent when I go out to meet people. Actually, I was dressed up for a funeral I went to earlier that day.
On March 28th, Sheril, Abel and I went to Duke and talked about Science 2.0 and blogging to a class on science/policy communication, which was great fun, and interesting pictures are circulating on the Web (check the links).
In the meantime, I got engrossed in reading the entire Framing Science flare-up, but decided not to write anything myself (except a few comments on a couple of other blogs) as I did not want to draw even more attention to it – that would be bad framing 😉 Greg has collected the links to the first wave of these posts. Now a second wave, quite more sober and mature, is popping up around the blogs so take a look.
Last week I went to the dentist twice. I was always so proud of my perfect teeth…until I lost dental insurance five years ago. Now there is something rotten with pretty much every tooth in my head. Finally employed and insured again, it’s time to aggressively pursue a pearly smile again. They did the two most critical teeth first, those that needed swift rescuing. We’ll do the rest in May and June.
I am also busy organizing my European trip – primarily the first part, in the UK. You can meet me in London or Cambridge. Then I’ll spend a weekend with Henry Gee (and no, I will not divulge all the PLoS secrets to a Nature editor!).
I am preparing myself for two panels (one on Open Access, one on science blogging) for the science FEST in Trieste, Italy, as well as an article in their journal there. I hope Franc will be able to come to Trieste so we can finally meet.
Later, I will be giving a talk about Open Access at the Ministry of Labor in Serbia and, hopefully, also at the Medical school at the University of Belgrade. I will enjoy my Mom’s cooking, meet my highschool and equestrian friends and local bloggers.
Bjoern is organizing a dinner for me and local bloggers in Berlin. On the way back, I will stay one day in London with my cousin and will be back home on May 3rd, just in time for the NC primaries/caucuses – perhaps I will make up my mind by then (and European media may help me clear my mind about US politics). Anyway, if you are in any of those places at any of those dates, please let me know and let’s meet.
I think I’ll take Amanda’s book and Vanessa’s book for airplane reading, then buy some SF once I am finished with these.
This morning I finished my last BIO101 Lab (just the lab – no time for the lecture and lab combined) and turned in the grades, so that is one more thing I don’t have to worry about for a while. And tomorrow I will start working on my poster for the SRBR meeting.
Due to the popular consensus, I have already scheduled all the Clock Quotes for the duration of the trip. I will do the “My picks from ScienceDaily”, and YouTube videos, and “New and Exiciting in PLoS” as regularly as I can while abroad. I will also repost some of the stuff from the Archives, e.g., some Greatest Hits and, as I tend to do every year, my Clock Tutorials for the new readers. And I will post pictures from the trip every day. So, there may not be much of new, long, deeply thoughtful posts next month, but there will be something every day.
Finally last Thursday, I met a bunch of friends at Town Hall Grill. Lenore, Andrea, Catharine, Rosalyn, Sheril, David and Vanessa were there. The food was delicious, and the pictures are under the fold (blurry, as the wine was too good to resist):

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NIH public access mandate

Scared publishers ask for a hearing and get an earful:

Librarians and educators, meanwhile, strongly defended the NIH policy-and spoke of the lengthy process of consideration it has already gone through, urging that implementation now proceed as planned. In its comments, SPARC reiterated that all stakeholders have had ample time to consider the policy dating back to 2004. SPARC said that it has, along with many other stakeholders, created “several programs to help to pave the way for the smooth implementation of the revised policy,” including a range of educational initiatives and practical tools. It also took aim at publishers seeking to block the policy, stating that “a small but vocal number of publishers continue to make the misleading and incorrect assertion that this policy will somehow put authors into conflict with copyright law.”

Read the whole thing and read the comments here.

Triangle Research Libraries Network Launches New Search Function

From the Library Journal:

The Triangle Research Libraries Network (TRLN) pioneered the nation’s first consortial online catalog back in the 1980s, and this week, took that legacy a step further with the launch of “Search TRLN”, which officials say adds “next-generation search capabilities” to the consortium’s combined collection of 16 million volumes. Search TRLN, is a new single-interface discovery tool, enabling users to search across the entire collections of the four member institutions: Duke University, North Carolina Central University, North Carolina State University, and the University of North Carolina at Chapel Hill. It takes advantage of the “faceted searching” and browsing capabilities of Endeca software, and builds on the traditional strengths of TRLN’s cooperative collecting and interlibrary delivery services. In a release, TRLN officials described Search TRLN a “one-stop access to the entire body of TRLN’s collections.”

Author Rights

From here.

SciBarCamp

Toronto SciBarCamp starts tonight and I am so jealous for not being there. Perhaps next time. For now, I’ll just follow it via blogs.

AAAS and NSF Communicating Science Workshop – April 3 – Raleigh, NC

Got an e-mail from AAAS and will try to go if at all possible:

The American Association for the Advancement of Science (AAAS), in partnership with the National Science Foundation (NSF) and North Carolina State University, will be holding a one-day workshop “Communicating Science: Tools for Scientists and Engineers” on Thursday, April 3, 2008. We aim to extend an invitation to the faculty scientists, engineers, and Ph.D. students at your institution who would like to attend this workshop, in order to learn more about communicating science to news media and the general public. Please feel free to forward this invitation to faculty scientists and engineers at your institution.
The AAAS Center for Public Engagement with Science and Technology has partnered with NSF to provide resources for scientists and engineers, both online and through in-person workshops, to help researchers communicate more broadly with the public.
Although traditional scientific training typically does not prepare scientists and engineers to be effective communicators outside of academia, NSF and other funding agencies are increasingly encouraging researchers to extend beyond peer-reviewed publishing and communicate their results directly to the greater public. Further, scientists and engineers who foster information-sharing and respect between science and the public are essential for the public communication of and engagement with science.
There is no registration fee for science and engineering faculty and Ph.D. students to attend this workshop; however, space is limited, and pre-registration is required. Please register by Wednesday, March 26, 2008. A registration form is enclosed. You can register by sending the requested information by email to tlohwate@aaas.org or by faxing or mailing the registration as indicated on the form.
The workshop will be held in the Walnut Room at the Talley Student Center at North Carolina State University in Raleigh. A map and directions can be found at http://www.ncsu.edu/student_center/driving_directions.html. We expect that both those who are interested in science communication and those who are already familiar with ways to communicate science broadly will find “Communicating Science: Tools for Scientists and Engineers” useful and informative.

Here is the program, see you there:
8:30 – 9:00 am Breakfast
9:00 – 9:30 am Welcome and Introduction
9:30 – 9:45 am Who is “General Public?”: Defining Audience
9:45 – 10:30 am Practice Research Messages and Public Talks
10:30 – 10:45 am Break
10:45 – 11:30 am Media Panel
11:30 am – 12:00 pm Enhancing Your Message: Gestures and Language
12:00 – 1:00 pm Lunch – provided
1:00 – 2:30 pm Practice Interviews
2:30 – 2:45 pm Break
2:45 – 3:30 pm Public Outreach Panel
3:30 – 4:00 pm Conclusion and Materials Review

News from JoVE

A new deal: Wiley-Blackwell and JoVE Unveil Groundbreaking Online Video Publications
Moshe on TV:

Science 2.0

On the Wired Science blog – The Internet Is Changing the Scientific Method:

If all other fields can go 2.0, incorporating collaboration and social networking, it’s about time that science does too. In the bellwether journal Science this week, a computer scientist argues that many modern problems are resistant to traditional scientific inquiry.

The title of the post is a big misnomer as the paper does not say anything about the change in the Scientific Method, but about the change scientists go about their work (perhaps “methodology”?). Read the rambunctious comment thread.
The paper is here but you cannot read it because it is in Science so you have to pay, which you are not crazy to do. But I got the paper and read it. I cannot copy and paste the entire text without breaking some maddening copyright law or something, but it is within Fair Use to give you a few key quotes so you can start the discussion (under the fold).

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New in OA

Charles Leadbetter: People power transforms the web in next online revolution
Anna Kushnir: Science Participation and Going Incognito
Wobbler: Digital Scholarly Communication & Bottlenecks
Jonathan A. Eisen: Open Evolution
Peter Suber: Aiming for obscurity (the links within are important)
Stian Haklev: A “Fair Trade” logo for academic research?

Wall Street Journal on Open Access

Information Liberation By DANIEL AKST:

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.

Read the whole thing….

Jane – the Journal/Author Name Estimator

Jane is the cool new tool that everyone is talking about – see the commentary on The Tree of Life, on Nature Network and on Of Two Minds.
In short, the Journal/Author Name Estimator is a website where you can type in some text and see which scientific Journal has the content closest to the text you input, as well as people who published on similar topics. If you click on “Show extra options” you can narrow your search by a few criteria, e.g., you can search only Open Access journals.
The idea is to discover journals to which you can submit your work. Most people know the journals available for their stuff, but this is the way to discover new journals, see which are Green or Gold OA, or find a place for a manuscript that has already been rejected by all of your usual venues 😉
Another use is for editors of broad-topic journals, to find relevant referees for the incoming manuscripts.
So, I did first the obvious test of the site – I copied and pasted the abstract of one of my papers. It gave the correct journal at 100% confidence, and all four co-authors at equal split of 25%. So, it works in that way. The other people mentioned down the list are also relevant researchers who would be appropriate for reviewing such a mansucript.
Then I copied and pasted a small chunk from my unpublished dissertation and got a list of potential reviewers that was pretty much perfect – people I’d suggest if asked.
Then, I typed in a bunch of terms that I know occur frequently in PLoS ONE in different papers, all mixed up – and PLoS ONE came up high on the list (and first among OA journals). So far so good.
Apparently, if you paste non-scientific text, you always get Harvard Business Review – they’ll take anything silly. Figures.
So, what would you use it for? Is it useful?

Biodiversity Heritage Library

Get yourself free PDFs of old biology/taxonomy books and papers courtesy of Biodiversity Heritage Library:

Ten major natural history museum libraries, botanical libraries, and research institutions have joined to form the Biodiversity Heritage Library Project. The group is developing a strategy and operational plan to digitize the published literature of biodiversity held in their respective collections. This literature will be available through a global “biodiversity commons.”
Participating institutions:
* American Museum of Natural History (New York, NY)
* The Field Museum (Chicago, IL)
* Harvard University Botany Libraries (Cambridge, MA)
* Harvard University, Ernst Mayr Library of the Museum of Comparative Zoology (Cambridge, MA)
* Marine Biological Laboratory / Woods Hole Oceanographic Institution (Woods Hole, MA)
* Missouri Botanical Garden (St. Louis, MO)
* Natural History Museum (London, UK)
* The New York Botanical Garden (New York, NY)
* Royal Botanic Gardens, Kew (Richmond, UK)
* Smithsonian Institution Libraries (Washington, DC)
The participating libraries have over two million volumes of biodiversity literature collected over 200 years to support the work of scientists, researchers, and students in their home institutions and throughout the world. The 10 member libraries of the Biodiversity Heritage Library (BHL) members now have over 1.124 million pages of key taxonomic literature available on the web.
The BHL will provide basic, important content for immediate research and for multiple bioinformatics initiatives. For the first time in history, the core of our natural history and herbaria library collections will be available to a truly global audience. Web-based access to these collections will provide a substantial benefit to people living and working in the developing world — whether scientists or policymakers.

Hat-tip: Anne-Marie

SAGE keeps opening up….

I just noticed recently, when looking up a paper in the Journal of Biological Rhythms, that SAGE publishing group is starting to offer the Open Access option to the authors in some of its Journals:

Independent scholarly publisher, SAGE Publications, is now offering authors of papers published on SAGE Journals Online, the option to make their primary research articles freely available on publication. The ‘SAGE Open’ publishing option has been launched primarily to ensure that authors can comply with new stringent funding body requirements, (for example those now in place from the Wellcome Trust), and ensures that relevant journals are compliant with NIH/Wellcome Trust and other grant funder requirements.
The SAGE Open programme will initially operate across a number of biomedical journals in the SAGE portfolio. The fee per article for this service is $3,000USD/£1600GBP and excludes any other potential author fees levied by some journals (such as colour charges, which are additional) as well as taxes where applicable.
Under this scheme, SAGE will allow the deposition of the final paper, (post refereeing, copy-editing and proof-reading), to PubMedCentral and its international equivalents, such as UKPMC, or PMCI on publication. All other SAGE policies regarding open access archiving remain unchanged.
The SAGE Open option will be made available to authors of primary research articles only on acceptance of their paper for publication. This is in order to prevent any potential conflicts of interest, and to ensure that authors’ choice/funder requirements have no influence on the editorial peer review and decision-making.
Payment of the SAGE Open fee will enable articles to be immediately available on SAGE Journals Online to non-subscribers, as well as to subscribers to that journal. It will also permit authors to submit the final manuscript to their funding agency’s preferred archive if applicable.
Initially, this option will be made available for a selection of journals (see below for full list). These journals will publish articles in a hybrid manner. Those authors who do not wish to use this service will be under no pressure to do so, and their article will be published free of charge, in the usual manner. All existing policies on author posting of the final version will then apply.
The following list of journals participate in SAGE Open:
Adaptive Behaviour
Angiology
Chronic Respiratory Disease
Clinical and Applied Thrombosis/Hemostasis
Clinical Pediatrics
Clinical Rehabilitation
Clinical Trials
Human & Experimental Toxicology
Integrative Cancer Therapies
Journal of Biological Rhythms
Journal of Biomaterials Applications
Journal of Biomolecular Screening
Journal of Cardiovascular Pharmacology and Therapeutics
Journal of Oncology Pharmacy Practice
Journal of Pharmacy Practice
Lupus
Multiple Sclerosis
The Neuroscientist
Palliative Medicine
Perfusion
Seminars in Cardiothoracic and Vascular Anesthesia
Surgical Innovation
Toxicologic Pathology
Toxicology & Industrial Health
Trauma
Vascular Medicine
Please send questions or comments not covered by our list of frequently asked questions via e-mail to sageopen@sagepub.com

Very good, SAGE is actively looking for the best ways to adapt to the changing landscape of the science publishing world.

Open Education

There are three interesting, thought-provoking articles on Open Education today:
The Digital Commons – Left Unregulated, Are We Destined for Tragedy?
An Interview with Ahrash Bissell of the Creative Commons
The Open Digital Commons – A Truly Endless Array of Success Stories
Worth your time and effort.

JoVE hits Big Time

Journal of Visualized Experiments signed a deal with Wiley-Blackwell to provide videos for Current Protocols:
Wiley-Blackwell and JoVE Unveil Groundbreaking Online Video Publications
Online methods videos go mainstream
Visual journal partners with Wiley
Related

Discovering scholarly information and data

Next Generation Discovery: New Tools, Aging Standards
March 27-28, 2008
Chapel Hill, NC
Discovering scholarly information and data is essential for research and use of the content that the information community is producing and making available. The development of knowledge bases, web systems, repositories, and other sources for this information brings the need for effective discovery — search-driven discovery and network (or browse) driven discovery — tools to the forefront. With new tools and systems emerging, however, are standards keeping pace with the next generation of tools?

Richard Akerman and my SciBling Dave Munger are among the participants. I’ll try to make it…

How to have your papers deposited into PubMed Central

Are you confused with the new NIH Policy and unsure as to what you need to do? If so, Association of Research Libraries has assembled a very useful website that explains the process step by step. But the easiest thing to do is to publish with a journal that does the depositing for you free of charge and here is the list of such journals. Of course, PLoS automatically does that for you as well.

Anna Kushnir interviews Rose Reis

In my daily interviews I always ask: what new blogs did you discover at the Conference? If anyone asked me that question – and you know it’s hard to surprise me! – one I’d pick would be the INFO Project blog run by Rose Reis, now my daily read.
Now, Anna (where did she get the idea, I wonder?) interviews Rose over on the JoVE Blog and the interview is worth your time. And yes, sooner or later, Rose Reis will be interviewed here as well – stay tuned.

Future Science Cyberstructure

Earlier today I went to UNC to talk about Science On The Web in Javed Mostafa’s graduate course on Enabling Usability of Cyberinfrastructures for Learning, Inquiry, and Discovery. I showed and talked about the following sites:
The rapidly growing List of Open Access journals and how the recent NIH law and Harvard vote are pushing publishing inexorably towards the OA model.
PLoS, Open Access, the TOPAZ platform for a new breed of journals like PLoS ONE (and a couple of examples of user activity on ONE papers), as an example of the leader of OA publishing (and also the story of how I got to work there).
Nature Precedings, and comparison to arXiv, wikis and blogs.
Jean-Claude Bradley’s open notebook chemistry blog and wiki (including a Master’s thesis being written there) and how they used Second Life to do an experiment.
Rosie Redfield’s Vancouver lab with open notebook blogs, and a little about age/generation effect on the adoption of Science 2.0, and about being a “pioneer”.
Science video, in particular SciVee and JoVE as the leaders and how important they are.
Recent advances in science blogging.
My article on the future of the scientific paper – we discussed the SF-like ideas about the future of science communication and the way science will be done, as well as the role of Information Scientists in such an ecosystem.
I did not have time to touch on blog carnivals – a kind of bottom-up, community driven online magazines.
It was fun for me – I hope it was as fun (and useful) to the students as well.

Open Access Beer!

What is the difference between Free Access Beer and Open Access Beer?
You go to a bar to get your Free Access Beer. You sit down. You show your ID. The barista gives you a bottle. You don’t need to pay anything for it – it’s free, after all. You take your own bottle-opener from your pocket and open the bottle. You drink the beer from the bottle. You return the empty bottle to the barista. You go home.
You order you Open Access Beer online or by phone. You pick what kind of beer you want. It gets delivered to your door really fast. The delivery man opens the bottle for you. You are not carded, nor do you have to pay. That beer is now yours to do whatever you want with it – you can drink it out of the bottle, or pour it into a glass. You can use it for cooking or you can use it to water your plants. You can do a chemical analysis of it in your lab and use the knowledge to produce an even better homebrew.
See the difference?
Unfortunately, there is no such thing as Open Access Beer, or even Free Access Beer. Which, it turns out, may be a Good Thing. For science, at least. Especially if you are Bohemian kind of guy. You need to read this very Grim report (from Emmett, via Kevin):
A possible role of social activity to explain differences in publication output among ecologists:

Publication output is the standard by which scientific productivity is evaluated. Despite a plethora of papers on the issue of publication and citation biases, no study has so far considered a possible effect of social activities on publication output. One of the most frequent social activities in the world is drinking alcohol. In Europe, most alcohol is consumed as beer and, based on well known negative effects of alcohol consumption on cognitive performance, I predicted negative correlations between beer consumption and several measures of scientific performance. Using a survey from the Czech Republic, that has the highest per capita beer consumption rate in the world, I show that increasing per capita beer consumption is associated with lower numbers of papers, total citations, and citations per paper (a surrogate measure of paper quality). In addition I found the same predicted trends in comparison of two separate geographic areas within the Czech Republic that are also known to differ in beer consumption rates. These correlations are consistent with the possibility that leisure time social activities might influence the quality and quantity of scientific work and may be potential sources of publication and citation biases.

beer%20and%20science.JPG

Generally, inhabitants of Bohemia (western region of
the Czech Republic) are known to drink more beer than
people from Moravia (eastern region of the country). This
difference was confirmed for my sample of researchers:
researchers from Bohemia drank significantly more beer
per capita per year (median 200.0 litres) than those from
Moravia (median 37.5 litres; Mann-Whitney test: U17,17
2.84, p0.005). Therefore I predicted lower measures of
publication output for the former in comparison to latter
group of researchers (I could not include nominal variable
”region” in regression models because of its significant
interdependence with another effect variable, the beer
consumption). Indeed, researchers from Bohemia published
fewer papers per year (U17,172.32, p0.02), were less
cited per year (U17,172.99, p0.003), and showed lower
citation rate per paper per year (U17,172.30, p0.02).

The question is: do you do less science because you drink too much, or do you drink too much because your science sucks? And, is 200 liters of beer per year too much? Who’s to judge? Moravians? Is there a similar correlation with wine and other drinks? Other non-alcoholic social activities?
Or is beer-drinking one of the possible symptoms of the Impostor Syndrome (see mrswhatsit’s series on it: Part I, Part II, Part III, also Zuska, Sciencewoman, Revere, Laelaps and DrugMonkey to learn more about it).

Open Access at Harvard

When Harvard does something, all the others follow. Perhaps this is the tipping point for Open Access as a whole. Peter Suber and Gavin Baker have the best commentary and all the links to other worthy commentary in a series of posts worth studying:
More on the imminent OA mandate at Harvard
Harvard votes yes
Text of the Harvard policy
Roundup of commentary on Harvard OA policy
More on the Harvard OA mandate
Stevan Harnad’s proposed revisions to the Harvard policy
Three on the Harvard OA mandate
More comments on the Harvard OA mandate
Also read Revere: Unfettered access to scientific work via open access publication
Perhaps the Millennium Conference at Harvard last fall was the straw that broke the camel’s back. A lot of key Harvard people were there, hearing the arguments for and against OA and they, apparently, decided that the arguments For won the day. Also, it is nice to see that this effort was bottom-up, coming from faculty, and not a top-down decree.

Imitation is the sincerest form of flattery

Via Peter Suber, there is now something new – PLoL, or, Public Library of Law:

Searching the Web is easy. Why should searching the law be any different? That’s why Fastcase has created the Public Library of Law — to make it easy to find the law online. PLoL is the largest free law library in the world, because we assemble law available for free scattered across many different sites — all in one place. PLoL is the best starting place to find law on the Web.

It’s just like PLoS, but the material is law, not science (and the two are not affiliated with each other in any way, just thinking in the same 21st century way). And no need to do too much explaining, either – just say “like PLoS, but for legal cases” and everyone will understand.

Obligatory Readings of the Day

The elephants in the room: How the GOP lost its way by Hal Crowther
Kafkaesque Bureaucracies Impede Import of Scientific Goods in Brazil by Mauro Rebelo
Open Science and the developing world: Good intentions, bad implementation? by Cameron Neylon
Alternative Agriculture in Cuba (pdf) by Sara Oppenheim

Harvard considers Free Access

In today’s NYTimes: At Harvard, a Proposal to Publish Free on Web:

Faculty members are scheduled to vote on a measure that would permit Harvard to distribute their scholarship online, instead of signing exclusive agreements with scholarly journals that often have tiny readerships and high subscription costs.
Although the outcome of Tuesday’s vote would apply only to Harvard’s arts and sciences faculty, the impact, given the university’s prestige, could be significant for the open-access movement, which seeks to make scientific and scholarly research available to as many people as possible at no cost.
“In place of a closed, privileged and costly system, it will help open up the world of learning to everyone who wants to learn,” said Robert Darnton, director of the university library. “It will be a first step toward freeing scholarship from the stranglehold of commercial publishers by making it freely available on our own university repository.”
Under the proposal Harvard would deposit finished papers in an open-access repository run by the library that would instantly make them available on the Internet. Authors would still retain their copyright and could publish anywhere they pleased — including at a high-priced journal, if the journal would have them.
What distinguishes this plan from current practice, said Stuart Shieber, a professor of computer science who is sponsoring the faculty motion, is that it would create an “opt-out” system: an article would be included unless the author specifically requested it not be. Mr. Shieber was the chairman of a committee set up by Harvard’s provost to investigate scholarly publishing; this proposal grew out of one of the recommendations, he said.

danah boyd on Open Access publishing

Apophenia, danah boyd’s blog, is one of the first blogs I ever discovered back in the depths of Time, certainly the first non-political blog, even before I found any science blogs. We finally got to meet last year at the ASIS&T meeting in Wisconsin. She just published a paper and, in her last post wows never to publish in Closed Access again. Then she gives a list of bullet points about what to do – see if you recognize yourself in one of them.

Science+Art+Technology+Media – meetings around the World

There were already two Science Foo Camps (in summers of 2006 and 2007) and two Science Blogging Conferences (in winters of 2007 and 2008).
But the hunger for such meetings is far from satiated. So, if you have time and money and can travel, you can choose to attend the SciBarCamp on March 15-16, 2008, where Eva is one of the organizers and Larry will be there.
Or you can go to the International Science Media Fair in Trieste on April 16-20, 2008. I’ll be there, on two panels, one about Open Access, another on Science Blogging.
Or, a little later, you can attend the World Science Festival in NYC on May 28 – June 1, 2008.
Northeast US, Southeast US, California, Canada, Europe – not bad for geographic distribution for now, don’t you think?

Open Students

Open Students is a new blog for students about open access to research. It is run by Gavin Baker (who also recently joined Peter Suber at Open Access News – Congratulations!) and sponsored by SPARC, the Scholarly Publishing and Academic Resources Coalition, as part of its student outreach activities.
The blog will cover the issues of Open Science as it affects the college students and will have frequent guest-bloggers (students, librarians, researchers, publishers…) – of which you can be one if you contact Gavin.

Open Science at PSB 2009

Shirley of One Big Lab blog is trying to submit a proposal for an Open Science session to be held at the next Pacific Symposium on Biocomputing. Although the meeting is a whole year away, the deadline for proposals is only 4 days away. You can read the rules for proposals here and see what Shirley has written so far. With only four days to go, Shirley needs some help in finalizing the proposal and in writing letters to the organizers showing interest in such a session. All the information is here so, if you are interested, please help.

Who’s scooping whom and why this matters?

Aetosaurs. No, I have not heard of them until now. But that does not matter – the big story about them today is the possibility – not 100% demonstrated yet, to be fair – that some unethical things surround their discovery and naming. And not just Aetosaurs. Some other fossils as well.
As I am not on the inside loop of the story, you need to first read the background story on Aetosaurs by Darren Naish – Part 1 and Part 2.
Then, carefully read Darren’s today’s post and responses by Laelaps, Cryptomundo and Paleochick.
For the ethical side of the story, read Janet’s take.
For the gory details of the story, read the timeline, the entire collection of information and the brief summary of it.
Finally, this was all made public today in an article in Nature. In short, it appears that a group of people have made it a habit to scoop their colleagues by publishing other people’s information (shown by colleagues in private) and naming species faster by using their in-house Journal.
Now imagine a world in a not-so-distant future….
You just spent a long, hard, but exciting day in the Gobi desert. You finally get to eat dinner and shower and get back to your tent and turn on your computer. You post on your blog:
“Gobi. Day 23. It was a very exciting day today – we struck gold: an apparently well-preserved fossil of something that is clearly in the X family, and perhaps related to Y species, but astragalus is so weird – look at this picture of it [insert a photo of the bone]. This is most certainly a new species. It will take a year or two to dig this thing out, clean it up, analyze it and publish the full description, but for now, we name it Blogosaurus….”
And there is a time-stamp on the blog post. And a bunch of palaeo-colleagues post congratulations in the comments. And it is aggregated by a bunch of sites (ResearchBlogging.org, Connotea, etc.).
Scoop that if you can!
Everyone knows that you, indeed, are in the Gobi, as they know about your grant proposal for it and they have been following your blog daily, including all the pictures from the trip. They know they did not just see you two hours ago sipping tea in the faculty lounge at your University. They post congratulatory posts on their own blogs. They discuss the pictures and early descriptions that you posted. Over the next months and years, they keep up with the digging, cleaning and analysis by reading your blog. They come to visit and help with analysis. They teach about it in their classes. Finally, when you publish the official description of the Blogosaurus, they add comments on the paper itself.
Of course, as they all also keep blogs, they have changed the official rules of naming, allowing for official publication no matter how many times the name has been mentioned elsewhere, offline or online (as long as the description was not published in another taxonomy journal). And if they discovered that you kept another fossil find a secret, at least for a while, that would raise all sorts of red flags: was there something fishy about the fossil? Why didn’t you immediately tell the world about it if everything was legit? That kind of secretive behavior is automatically suspect, and considered unethical and anti-social.
Sunlight is the best disinfectant…

‘Working with the Facebook generation: Engaging students views on access to scholarship’

Here is a video of SPARC-ACRL Forum ’08 on 12 January, 2008 at the Pennyslvania Convention Center in Philadelphia:

The SPARC-ACRL Forum at ALA ’08 entitled “Working with the Facebook generation: Engaging students views on access to scholarship.” Panelists discuss the merits of student activism, patent reform, blogs as a communication medium for scientists, and students as active members of a discussion about the right to access information for scholarly work. Features Andre Brown, Nelson Pavlosky, Stephanie Wang, and Kimberly Douglas as panelists.

Pay particular attention to Andre Brown and minutes 42-55 as he talks about science blogs and Science 2.0 including mentions of all the usual suspects (Jean-Claude Bradley, Rosie Redfield, Reed Cartwright, Bill Hooker, Peter Suber and me):

SPARC-ACRL Forum ’08 from Matt Agnello on Vimeo.

ResearchBlogging.org

Dave and Co. have been working hard over the past few months and now (actually on Saturday at the Conference) Dave announces that ResearchBlogging.org is live and in action! The BPR3 site, where the entire initiative was hashed out and built will continue to serve as the News Blog.
So, register your blog. Whenever you write a post about a peer-reviewed paper, put in the icon (if you want – you can make it invisible) and go to the RB site to resolve the DOI of the paper so it shows up in your post as a proper reference. Shortly after you publish the post, the link will show up on the aggregator on the main page. And you can browse past entries as well.
Dave provides the details.

The first SPARKY Awards

On the heels of David Warlick’s session on using online tools in the science classroom and the student blogging panel comes the announcement that SPARC has declared the winners of the first SPARKY Awards for student-generated videos on the theme of openess of information. The winner is Habib Yazdi, a senior at the University of North Carolina at Chapel Hill with the video entitled “Share.” The three winning videos are under the fold:

Continue reading

Open Education Declaration

On the heels of David Warlick’s session on using online tools in the science classroom, this initiative is really exciting:

Teachers, Students, Web Gurus, and Foundations Launch Campaign to Transform Education, Call for Free, Adaptable Learning Materials Online
Cape Town, January 22nd, 2008–A coalition of educators, foundations, and internet pioneers today urged governments and publishers to make publicly-funded educational materials available freely over the internet.
The Cape Town Open Education Declaration, launched today, is part of a dynamic effort to make learning and teaching materials available to everyone online, regardless of income or geographic location. It encourages teachers and students around the world to join a growing movement and use the web to share, remix and translate classroom materials to make education more accessible, effective, and flexible.
“Open education allows every person on earth to access and contribute to the vast pool of knowledge on the web,” said Jimmy Wales, founder of Wikipedia and Wikia and one of the authors of the Declaration. “Everyone has something to teach and everyone has something to learn.”
According to the Declaration, teachers, students and communities would benefit if publishers and governments made publicly-funded educational materials freely available online. This will give students unlimited access to high quality, constantly improving course materials, just as Wikipedia has done in the world of reference materials.
Open education makes the link between teaching, learning and the collaborative culture of the Internet. It includes creating and sharing materials used in teaching as well as new approaches to learning where people create and shape knowledge together. These new practices promise to provide students with educational materials that are individually tailored to their learning style. There are already over 100,000 such open educational resources available on the Internet.
The Declaration is the result of a meeting of thirty open education leaders in Cape Town, South Africa, organized late last year by the Open Society Institute and the Shuttleworth Foundation. Participants identified key strategies for developing open education. They encourage others to join and sign the Declaration.
“Open sourcing education doesn’t just make learning more accessible, it makes it more collaborative, flexible and locally relevant,” said Linux Entrepreneur Mark Shuttleworth, who also recorded a video press briefing. “Linux is succeeding exactly because of this sort of adaptability. The same kind of success is possible for open education.”
Open education is of particular relevance in developing and emerging economies, creating the potential for affordable textbooks and learning materials. It opens the door to small scale, local content producers likely to create more diverse offerings than large multinational publishing houses.
“Cultural diversity and local knowledge are a critical part of open education,” said Eve Gray of the Centre for Educational Technology at the University of Cape Town. “Countries like South Africa need to start producing and sharing educational materials built on their own diverse cultural heritage. Open education promises to make this kind of diverse publishing possible.”
The Declaration has already been translated into over 15 languages and the growing list of signatories includes: Jimmy Wales; Mark Shuttleworth; Thomas Alexander, former Director for Education at the Organization for Economic Cooperation and Development; Lawrence Lessig, founder and CEO of Creative Commons; Andrey Kortunov, President of the New Eurasia Foundation; and Yehuda Elkana, Rector of the Central European University. Organizations endorsing the Declaration include: Wikimedia Foundation; Public Library of Science; Scholary Publishing and Academic Resources Coalition; Canonical Ltd.; Centre for Open and Sustainable Learning; Open Society Institute; and Shuttleworth Foundation.
To read or sign the Cape Town Open Education Declaration, please visit: http://www.capetowndeclaration.org.

Go and sign the Declaration!

Update:
David Wiley of the USU Center for Open and Sustainable Learning has more.

Cool new Open Access Journal

From Sage Ross, via John Lynch come exciting news about a new Open Access Journal – Spontaneous Generations: A Journal for the History and Philosophy of Science

Spontaneous Generations is a new online academic journal published by graduate students at the Institute for the History and Philosophy of Science and Technology, University of Toronto. The journal aims to establish a platform for interdisciplinary discussion and debate about issues that concern the community of scholars in HPS and related fields.
Apart from selecting peer reviewed articles, the journal encourages a direct dialogue among academics by means of short editorials and focused discussion papers which highlight central questions, new developments, and controversial matters affecting HPS.

Check out the first issue – there is some very cool stuff in there.

New Media and Science Communication

The Science Communication Consortium presents:

DISCUSSION ON THE ROLES OF EMERGING MEDIA OUTLETS IN COMMUNICATING SCIENCE
Thursday, JAN 31st, 7-8:30pm
Mount Sinai School of Medicine, East Building Seminar Room (1425 Madison Ave at 98th St, NYC)
A discussion of how science is communicated effectively – and ineffectively – through emerging media outlets, such as blogging, podcasts, online multimedia, and more.
Blogs, podcasts, and other new media outlets have changed the way people learn about scientific info, and shortened the shelf life of these stories. This immediacy of information presents new opportunities, as well as certain challenges, for science communication. Join us for a discussion of how scientists and journalists can reach a savvy audience by using new media outlets to communicate effectively about this research, while avoiding pitfalls.
Please join panelists:
CARL ZIMMER, award-winning science writer and author,
CHRISTIE NICHOLSON, science journalist and contributor to Scientific American’s “60-Second Psych” online programming
ELIENE AUGENBRAUN, President/CEO of ScienCentral, Inc.
EITAN GLINERT, project coordinator of science-based video game”Immune Attack”
KAREN FRENKEL, documentarian and science writer
Post-lecture reception will be sponsored by SEED Media Group, publishers of SEED magazine and scienceblogs.com.

UK PubMed Central (UKPMC) Workshop – February 4th 2008

UK PubMed Central (UKPMC) Workshop – February 4th 2008:

Few people would argue that good communication is the lifeblood of good science – and the Web is opening up a whole new world of possibilities.
UK PubMed Central is ideally placed to make the best use of new Web technologies and new ideas in semantics and text mining and so to facilitate sharing of the biomedical and health research literature.
We are entering the next stage of developing UKPMC into an innovative and useful resource for UK researchers. We want to ensure that your needs and ideas are heard and incorporated at the outset and to this end we are holding a free one-day workshop on the 4th February 2008.
If you have an interest in helping us shape this vision, then please register for this free workshop. Places are limited – so respond today to reserve your place.
Location
The workshop will be held at the Wellcome Collection Conference Centre, 183 Euston Road, London. Registration is from 9.30 and the meeting will conclude at 17.00.
Programme
Confirmed speakers include:
Mark Walport – Director of the Wellcome Trust
Matt Cockerill – BioMed Central
Timo Hannay – Nature Publishing Group
Dietrich Rebholz-Schuhmann – European Bioinformatics Institute
Sophia Anandiadou – University of Manchester
Following the speakers, facilitated workshop sessions will enable attendees to discuss their views about different aspects of developing UKPMC – topics such as ‘search’, ‘enhanced content’ and ‘user-specific functions’ will be considered.

Science 2.0 article in Scientific American

M. Mitchell Waldrop (author of the delightful book Complexity: The Emerging Science at the Edge of Order and Chaos) interviewed me and a bunch of others back in August about the changing ways of science communication. I completely forgot about it, but was reminded yesterday when he e-mailed me to say that the draft of the article is now online on the Scientific American site: Science 2.0: Great New Tool, or Great Risk?
The idea is that the draft will be improved by commentary by readers – and sure enough, there are already 19 comments there – before it goes to print in a future issue of the magazine. I urge you strongly to go and add your 2 cents to the discussion – some good people are already there.
As such things go (and I am completely not surprised any more by now), the interview lasted more than an hour during which I talked and talked and talked (those who know me are well aware of this annoying ability of mine) and in the end only one, completely non-profound sentence made it into the article. Ah well, that’s life 😉
Not to mention that my views on the topic have somewhat evolved since August.
But the article is good and you can make it even better if you go and post some comments on it before it goes to print.

The most exciting job in science publishing can be yours!

PLoS ONE is the first and (so far) the most successful scientific journal specifically geared to meet the brave new world of the future. After starting it and bringing it up from birth to where it is now one year later, Chris Surridge has decided to move on.
Do you think you have the skill and experience to pick up where he leaves off? Do you want to be at the cutting edge of scientific publishing? If so, take a look at the new job ad for the Managing Editor of PLoS ONE:

The overall responsibility of this position, which will be located in the San Francisco office, is to lead the editorial staff and editorial board who run PLoS ONE — a ground-breaking online-only publication covering the full breadth of scientific and medical research. PLoS ONE was launched one year ago, and is already publishing over 150 peer-reviewed research articles each month.

While other PLoS journals have a narrower scope (Biology, Medicine, Pathogens, Genetics, Computational Biology, Neglected Tropical Diseases), ONE is supposed to be the ONE place for all areas of science. Thus, your scientific background does not necessarily have to be in biomedical research to be eligible and welcome for this job, if your experience and organizational skills are a perfect match for the job.

New on…..Publishing

In the wake of the signed omnibus bill that funds NIH and ensures open deposition of NIH-funded research, here are some thoughtful questions:
Why the NIH bill does not require copyright violation:

The great advantage of the requirement to deposit in Pubmed (rather than simply to expose on a publisher or other website) is that the act is clear. You can’t “half-deposit” in Pubmed. They have the resources to decide whether any copyright statement allows the appropriate use of the information or is suffiently restrrictive that it does not meet the NIH rules.
At some stage the community will get tired of the continual drain on innovation set by the current approach to publihing. Whether when that happens many publishers will be left is unclear.

What does USD 29 billion buy? and what’s its value?

So, while Cinderella_Open_Access may be going to the ball is Cinderella_Open_Data still sitting by the ashes hoping that she’ll get a few leftovers from the party?

What is peer review, anyway?

A final question is perhaps the most difficult: How do we identify journals offering acceptable levels of peer review? Who’s to say whether a given journal is good enough? After all, even the most rigorous scholarly journals sometimes make errors — indeed, one of the most important parts of the scientific process is identifying and correcting problems in earlier work. Indeed, too rigorous a standard of peer review can stifle research just as much as too lax a standard.

Victory for Open Access!

Yesterday, President Bush signed the Consolidated Appropriations Act of 2007 (H.R. 2764) which, among else, mandates the repository of all NIH-funded research into PubMedCentral within at most 12 months after publication.
Until now, the placement of NIH-funded research papers into publicly accessible repositories was not mandated, but recommended. However, only about 5% of the authors actually did it, as the process was complex and not always clear. This number is growing, but far too slowly. From now on, authors will have clear guidelines and assistance in making sure that all the research becomes public a year after publication in a scholarly journal.
As you may recall, the original version of the bill was vetoed by President Bush. However, the language of the Open Access provision remained intact throughout the process, with no resistance from the Administration. This did not happen easily and the good people of SPARC and the Alliance for Taxpayer Access (as well as NIH itself) are to be commended for their tireless efforts in educating the Congress about the issue and congratulated for the success.
There has been opposition to this provision of the law mounted by some of the giant publishing houses. They hastily put together PRISM, an astroturf organization designed to lobby the Congressmen against this provision. However, they overreached, and the alert blogosphere caught their dishonesty as well as their breach of the copyright law. The information spread virally across the internet and was seen by hundreds of thousands of people. The outcry by the concerned citizens who, by the thousands, contacted their Representatives, effectively neutralized the efforts of the opponents and the Open Access language sailed through the two full rounds of the legislative process unscathed.
There has been quite a lot of celebration on science blogs today so, as I often do, I will post links to some of them here:
Peter Suber was the first to blog the announcement and the press release by The Alliance for Taxpayer Access. He is also tracking the online responses.
Jonathan Eisen is giddy with excitement.
Glyn Moody predicts that this will have a “knock-on effect around the world, as open access to publicly-funded research starts to become the norm.”
Peter Murray-Rust expects that having the papers Open will uncover new science as the data are mined by robots.
John Gordon wonders if Bush is even aware of what he signed and jokes about the Alliance for Taxpayer Access for having a “diabollically clever name” 😉
Leslie Johnston reminds everyone there is no need to wait exactly 12 months to deposit the papers.
Charles Bailey, Klaus Graf, Paula Kaufman, Oliver Obst, Dorothea Salo and David join in the celebratory mood.
There is also a long comment thread on Slashdot, the site that spread the word about the copyright infringment by PRISM.
Brandon Keim on the WIRED Science Blog also mentions the dubious tactics of the opposition.
Rich is a student happy that he will be able to read the articles from now on.
Marshall Kirkpatrick also sees how this will open up a whole new world for scientific research.
Kevin Smith is thinking about the ways librarians can help.
Georgia Harper is a step ahead of everyone else, suggesting the mechanisms for making the transition smooth.
Richard Akerman provides the appropriate movie clip.
Mark Patterson:

One of the most effective ways to comply with this new requirement is for researchers to publish their work in fully open access journals such as those of PLoS. As part of the service we provide to authors, we deposit every article in PubMed Central so that it can be a part of this evolving and important online archive. And this happens as soon as the article is published – so that anyone with an interest in the work can immediately read it and build on it.

Peter Suber collected even more blogospheric responses.

The Impacted Factor in need of Cleansing

I buried this among a bunch of other cool links yesterday, but there was a study the other day, in the Journal of Cell Biology, that seriously calls in question the methodology used by Thompson Scientific to calculate the sacred Impact Factor, the magic number that makes and breaks lives and careers of scientists.
Apparently, it is really a magic number calculated in a mysterious way, not in the way that Thompson Scientific claims they do it. Who knows what subjective factors they include that they do not tell us about?

When we examined the data in the Thomson Scientific database, two things quickly became evident: first, there were numerous incorrect article-type designations. Many articles that we consider “front matter” were included in the denominator. This was true for all the journals we examined. Second, the numbers did not add up. The total number of citations for each journal was substantially fewer than the number published on the Thomson Scientific, Journal Citation Reports (JCR) website (http://portal.isiknowledge.com, subscription required). The difference in citation numbers was as high as 19% for a given journal, and the impact factor rankings of several journals were affected when the calculation was done using the purchased data (data not shown due to restrictions of the license agreement with Thomson Scientific).
Your database or mine?
When queried about the discrepancy, Thomson Scientific explained that they have two separate databases–one for their “Research Group” and one used for the published impact factors (the JCR). We had been sold the database from the “Research Group”, which has fewer citations in it because the data have been vetted for erroneous records. “The JCR staff matches citations to journal titles, whereas the Research Services Group matches citations to individual articles”, explained a Thomson Scientific representative. “Because some cited references are in error in terms of volume or page number, name of first author, and other data, these are missed by the Research Services Group.”
When we requested the database used to calculate the published impact factors (i.e., including the erroneous records), Thomson Scientific sent us a second database. But these data still did not match the published impact factor data. This database appeared to have been assembled in an ad hoc manner to create a facsimile of the published data that might appease us. It did not.
Opaque data
It became clear that Thomson Scientific could not or (for some as yet unexplained reason) would not sell us the data used to calculate their published impact factor. If an author is unable to produce original data to verify a figure in one of our papers, we revoke the acceptance of the paper. We hope this account will convince some scientists and funding organizations to revoke their acceptance of impact factors as an accurate representation of the quality–or impact–of a paper published in a given journal.
Just as scientists would not accept the findings in a scientific paper without seeing the primary data, so should they not rely on Thomson Scientific’s impact factor, which is based on hidden data. As more publication and citation data become available to the public through services like PubMed, PubMed Central, and Google Scholar®, we hope that people will begin to develop their own metrics for assessing scientific quality rather than rely on an ill-defined and manifestly unscientific number.

Of course, this was written in a polite language of science. But on a blog, I can say that this is at least very fishy and suspect. And several other bloggers seem to agree, including Bjoern Brembs, The Krafty Librarian, Eric Schnell, Peter Suber and Stevan Harnad who each dissect the paper in more detail than I do, so go and read their reactions.

New on…. Open Access and Science 2.0

Subscription-supported journals are like the qwerty keyboard:

Are there solutions? One reason for optimism is that changing how we pay the costs of disseminating research is not an all-or-nothing change like switching from qwerty to Dvorak keyboards. Some new open-access journals are very prestigious. Granting agencies are giving strong ‘in-principle’ support to open access publishing, and my last grant proposal’s budget included a hefty amount for open-access publication charges. And libraries are looking for ways to escape the burden of subscription charges.

This is an interesting idea: an Open Access journal for brief notes and updates, i.e., parts of papers.
Is the End of the Print Journal Near?: New ARL Report Examines This Issue
Related to the three posts above: The Scientific Paper: past, present and probable future
Open Access and Accessibility for the Print Disabled. Of course. Open for Everyone!
Sharing, Privacy and Trust in a Networked World “on the potential roles of social networks for libraries”.
At this lab, everyone is required to maintain a science blog, and response: Why take the risk of writing a research blog? Read the comments on both posts as well.
The Ethics of Being an Open Access Publisher
WHO embargoes health information
Listen to Peter Murray-Rast’s talk at Berlin5 on Open Access.
Listen to the recording of Jean-Claude Bradley’s talk on Open Notebook Science.
Sequence the genomes of microbes or yourself, then plug the genomes into the Interactive Tree of Life.
Nurturing your talent in academia – some good ideas to think about.
CC, Open Access, and moral rights and Intellectual Property Rights: Wrong for Developing Countries?.
Re-writing for Proseminar:

It’s time to share another round of student writing! I asked students in the Proseminar course at USU (in which all faculty take three week turns introducing students to their research interests) to put together a paper about issues related to open education. The twist (there always is one) is that they were to write as little of the paper as possible. You see, wholesale plagiarism is discouraged, but weaving together a coherent piece from ten or fifteen different extant sources is tough and an excellent chance to get some first hand experience with reuse. =) Here are links and some summaries to these re-writing exercises, in which students assembled papers from pre-existing pieces:

Behold! The New Anti-Open Access FUD
Both this article and this article completely forget that scientists at universities are also academics and also bloggers (just look around scienceblogs.com for a start)!!! Why such focus on the humanities blogs in the first place? Where did that come from?
Dancing with words:

There is a great attraction to publishers in finding ways to describe Restricted Access as open. Carried to its logical conclusion, all publications thus become Open Access. Some are Delayed-For-A-Bit Open Access, others are Quite-A-Lot-Delayed Open Access, some are Very-Delayed Open Access and the rest – where the publisher never intends to make them freely available at all – are simply Permanently-Delayed Open Access. You see, what is there to complain about?

Open Science project on domain family expansion
Bursty work. Sort of… how science works, too. Not detectable from publications, though.
Corie Lok: Bringing science out of the dark ages
John Wilbanks: No tenure for Technorati: Science and the Social Web and Seeding the Social Web for Science
Is knowledge ‘property’?

Encouraging authors to place their papers into open repositories

How to move an article from TA to OA? It does not even have to be from a peer-reviewed journal. Graham Steel explains: he contacted the author and asked him to deposit the article into an open repository. So, now you can read it either here (and pay) or here (for free).

The benefits of Open Access Publishing for students in higher education

The benefits of Open Access Publishing for students in higher education (video):

Most students in higher education have some experience with Open Access when doing their deskresearch. They appreciate the free access of scholar publications on the World Wide Web.
But students in higher education also develop their competences as junior researchers and publishers. Can Open Access Publishing help them to get some reputation in the international academic society? And how appreciate they the readers’ feedback on papers published on the internet?
The Millennium Generation has grown up with free accessible information. They are supposed to embrace the idea of Open Access Publishing. However, students also may be anxious for publishing (preprints of) their papers, for instance for copyright reasons. It seems that good communication about the possibilities of Open Access Publishing by their educators (tutors, professors and librarians!) is very important. Peter Becker and Jos van Helvoort, professors teaching Library and Information Science in the Netherlands, would appreciate to discuss these topics with an international public.

Hat-tip and commentary: Peter Suber

The Scientific Paper: past, present and probable future

Communication
Communication of any kind, including communication of empirical information about the world (which includes scientific information), is constrained by three factors: technology, social factors, and, as a special case of social factors – official conventions. The term “constrained” I used above has two meanings – one negative, one positive. In a negative meaning, a constraint imposes limits and makes certain directions less likely, more difficult or impossible. In its positive meaning, constraint means that some directions are easy and obvious and thus much more likely for everyone to go to. Different technological and societal constraints shape what and how is communicated at different times in history and in different places on Earth.
Technology – Most communication throughout history, including today, is oral communication, constrained by human language, cognitive capabilities and physical distance. Oral communication today, in contrast to early history, is more likely to include a larger number of people in the audience with whom the speaker is not personally acquanted. It may also include technologies for distance transmission of sound, e.g., telephone or podcasts. This is the most “natural” means of communication.
Smoke signals and tom-toms introduced new constraints to communication – the messages had to be codified, short and simple and much of verbal and non-verbal communication had to be eliminated. Invention of writing, on stone tablets, clay tablets and papyrus, and later on paper and in print, changed the constraints further, making some aspects of communication easier and others more difficult, leading to the development of universal rules and norms of written communication. Unlike oral communication, the written communication is unidirectional, from one to many, making feedback from the audience difficult or impossible. Thus, it is necessarily linear. Its permanence also requires greater care be taken about the form and content. Finally, physical constraints (i.e., the size of a book) impose a structure to written communication, e.g., breaking down the work into chapters, subheadings and paragraphs, placed in a particular order. Also, written communication introduces the concept of authorship (and readership) while oral communication is “owned” by all the participants in the conversation.
Society – What and how is communicated differs dramatically if the audience is small and familiar (e.g., one’s children or neighbors) or large and unfamiliar (speaking at a conference). Written communication is, by definition, aimed at a large and unfamiliar audience, which has an effect on form, style and content of communication. Local habits and traditions further determine the forms and styles of communication.
Conventions – Different types of communication within particular groups of people are often officially codified, often precisely defining the language, style and format. Legal and scientific literature are probably the most extreme examples of a very strict code imposed by official societies. Such strict formalization of communication was initially very useful, imposing order (positive meaning of “constraint”) to an otherwise chaotic and undependable mish-mash of communication forms, allowing all the members of the community to understand and trust each other. However, when such strict forms last for decades and centuries, they are often made out-dated by the passage of time, invention of new technologies and societal changes, thus making the negative meaning of ‘constraint’ more and more obvious.
Scientific Communication
Development of communication of science reflects the development of science itself. Communication of information about the facts about the world did not differ much from other forms of communication for most of history until science itself started distinguishing itself as a special type of human endeavor, different from philosophy and religion. The way science communication evolved parallels the changes in our thinking about the scientific method. At the time when trips to the countryside and armchair thinking were still regarded as science, much of communication was in the form of books. When the hypothetico-deductive aspect of the scientific method “won” as the scientific method, the fledgling scientific societies, led by the Royal Society in the UK and the Academy in France, designed the form and structure of the scientific paper – the form we still use today: title, author, abstract, introduction, materials and methods, results, discussion and references.
Today, we understand that the hypothetico-deductive method is just one of several elements of the scientific method (see this) and that the standard format of the scientific paper is perfectly unsuitable for publication of findings reached through other methods.
Description of new species (extant or extinct) requires a monograph format, for which specialized journals exist that cater to this particular format. Ecological surveys are often straight-jacketed into the standard format, with addition of unwarranted mathematization – not all science requires numbers and statistics. Finally, science is getting more and more collaborative – single-author papers are becoming a rarity, while the papers boasting 10, 20, 50 or even 100 authors are becoming a norm, which challenges the way authorship in science is determined (see this and links within).
But what really made the limitations of the standard format obvious is the genomic revolution. Sequencing a genome is not hypothetico-deductive science – it is akin to an ecological survey: apply a technique and see what you get! Now that the excitement of publication of the first few genomes has receded, the existing journals are inadequate platforms for publication of new genomes. While sequencing is getting easier with time, it is still expensive and time-consuming. Yet, the techniques have been standardized and there is really not much to say in the introduction, materials and methods or discussion sections of a genome paper. All that is needed is a place to deposit the raw data as tools for future research in an easily-minable format that makes such future research easy. The data would be accompanied by the minimal additional information: which species (or individual) was sequenced, which standard method was used (and if it was modified), and who did the work. It is not, any more, an intellectually creative endeavor, as useful as it is for the progress of biology and medicine.
Science On The Web
When e-mail first became popular as a communication method, some people understood it as an extension of the written communication (letters) while others took it to be a new form of oral communication (telephone). Of course, it is both and more. Two people can rapidly exchange a large number of brief personal messages (as in a phone conversation), or one can send a long e-mail message to a large group of people, written with proper grammar, capitalization, punctuation and formatting (as a pamphlet). And yet, it is also neither – unlike oral communication, there is no way to convey non-verbal communication (thus the invention of emoticons 😉 ). Unlike written communication, it is fast, informal, not usually taken very seriously or read carefully, and is easy to delete. E-mail is now a communication form of its own.
The communication on the Web is, likewise, a whole new form. Again, some people see it as written communication (putting an article or book online in order to reach more readers and nothing more), while others see it as a more personal, oral communication that is written down (and such people, unlike the first group, love podcasts and videos which add the non-verbal components of communication to the text). The former prefer static web-pages with their ‘feel’ of permanence. The latter prefer Usenet, livejournals and blogs. The latter perceive the former as stodgy, authoritarian and boring. The former perceive the latter as wild, illiterate and untrustworthy. Again, they are both right and they are both wrong – it is a whole new way of communicating, fusing and meshing the two styles in sometimes unpredictable ways – it is a mix of written and oral communication that combines permanency and authority with immediacy, honesty and the ability for rapid many-to-many communication. The younger generation will use it naturally (though this does not mean that many senior citizens today did not grasp it already as well).
So, how will the constraints (both positive and negative) imposed by the new technology and new social norms alter the formality of the scientific communication, including the format of the scientific paper?
Online, the constraints of the paper and printing press will be gone. No more need for volumes, or issues, or page numbers, or, for that matter, for the formal scientific papers.
The standard format of the scientific paper will become just one of many (and probably not the dominant or most frequent) form of scientific communication. Different people have different talents and inclinations. One is analytic, another synthetic. One is creative, another a hard worker. One has great hands with the equipment or animals, while another is good with computers and statistics. One has a lot of space and money and a network of collaborators at a prestigious institution, another is stuck in a small office somewhere in the developing world with no research funds at all. And each can make a valid and useful contribution to science. How?
One will have a great idea and publish it online. The other will turn the idea into an experimental protocol that tests the idea and will publish it somewhere online. The next will make a video of the experimental method. The next person will go to the lab and actually follow the protocol and post raw data online. The next person will take the data an analyze it and post the results somewhere else online. The next person will graph and visualize the data for easier understanding. The next person will write an essay that interprets the findings and puts them into the broader context (e.g., what does it mean?). The next one will write a summary that combines several of those findings (a review). The next will place that entire research program into the historical or philosophical context. The next will translate it into normal language that lay-people can understand.
They are all co-authors of the work. Each used his/her own strengths, knowledge and talents to contribute to the work. Yet they did not publish together, simultaneously or in the same online space, though all the pieces link to each other and thus can be accessed from a single spot. That single spot is the Scientific Journal, a place that hosts all of the pieces and links them together (also see Vernor Vinge’s vision of the science of the future, combining laboratories at universities with online boards where ideas and results are rapidly exchanged).
In the future, journals will be online hosts for all styles of scientific contribution and ways to link them together (within and betwen journals) – from hypotheses and experimental methods, to data, analyses, graphs to syntheses and philosophical discussions. The peers will review each other in real time and assign each other portions of the available funding according to the community perceptions of the individual’s needs and qualities. Universities will be places for teaching/training the next generations of scientists and for housing the labs. The PhD will be needed for becoming a professor, but not for becoming a worthy and respected contributor to science – that evaluation will be up to peers.
This may sound like science fiction, but we are already living in it. Repositories (like arXiv and Nature Precedings), science blogs, OA journals, Open Notebook Science (what Rosie Redfield and Jean-Claude Bradley do, for instance) are already here. And there is no going back.
So, how do we prepare for this future? Word: slowly but smartly. Science has some very conservative elements (in a non-political sense of the term) that will resist change. They will denigrate online contributions unless they are peer-reviewed in a traditional sense and published in a reputable journal in the traditional format of a scientific paper. Some will retire and die out. Others can be reformed. But such reforming takes patience and careful hand-holding.
The division of scientists into two camps as to understanding of the Web is obvious in the commentary on PLoS ONE articles (which is my job to monitor closely). Some scientists, usually themselves bloggers, treat the commentary space as a virtual conference – a place where real-time oral communication is written down for the sake of historical record. Their comments are short, blunt and to the point. Others write long treatises with lists of references. Even if their conclusions are negative, they are very polite about it (and very sensitive when on the receiving end of criticism). The former regard the latter as dishonest and thin-skinned. The latter see the former as rude and untrustworthy (just like in journalism). In the future, the two styles will fuse – the conversation will speed up and the comments will get shorter, but will still retain the sense of mutual respect (i.e., unlike on political blogs, nobody will be called an ‘idiot’ routinely). It is important to educate the users that the commentary space on TOPAZ-based journals is not a place for op-eds, neither it is a blog, but a record of conversations that are likely to be happening in the hallways at conferences, at lab meetings and journal clubs, preserved for posterity for the edification of students, scientists and historians of the future.
PLoS ONE is a good example of the scientific journal of the future that I have in mind – the ONE place where all the data will be deposited. The commentary space and the Hubs are where all the really interesting stuff will be happening before and after publication of data: hypotheses, methods, videos, podcasts, blogs, debates, discussions, user-user peer-review, etc. The other PLoS Journals will be places, closely connected to ONE and the Hubs, of course, where works of special value will be highlighted – high-quality, media-worthy and large/complete pieces of work, plus editorials, news, etc. – the added value. They are a necessary link between the present (past?) and the future – the showcase of the quality that we can provide and thus hopefully change the minds of the more resistant members of the scientific community.

Cost of publishing in OA journals

Bill Hooker:

But the next time you hear someone talk about the “cost” of publishing in OA journals, please point ’em here.

And the ‘here’ of that sentence is this post which should disabuse you, once for all, of the idea that publishing in OA is more expensive than publishing with the dinosaur publishers. Bookmark that post and have the link ready for whenever you hear that myth pop its head up.

David Cohn on Science Journalism and Web 2.0

David writes:

Community is no longer a dirty or scary word. Sciam, Seed, in the US, Germany and all over the world. Online communities are becoming understood and a valued commodity. When Google bought YouTube I said the price they payed wasn’t for the technology (they already had Google Video) what they bought was the community. News organizations realize that creating niche communities is a way to stay relevant to advertisers and readers.
And science journalism, which de-facto covers a “boring” subject to lots of people, can only benefit by creating a vibrant community of people who have a passion for the subject. What science journalism needs are people who criticize science because they love science (as opposed to people who criticism because they don’t believe in science). That’s what these communities can offer – and how they will improve science journalism.

Welcome to scienceblogs.com

Richard Smith on Open Access

Graham Steel, a vocal Open Access supporter, alerts me that the latest Mansbridge One on One interview on CBC features Richard Smith. You can watch the video here – the talk about Open Access starts about seven minutes into the interview.