CC-BY and – or versus? – open access

Many in the open access movement consider CC-BY, the Creative Commons Attribution license, to be the very embodiment of the spirit of the Budapest Open Access Initiative – giving away all rights to one’s work, including commercial rights, for open access. My own take on this is that while CC-BY can provide a useful tool for those fully engaged in the open access spirit, the license is problematic for open access. This is important now that funding agencies in the U.K. are beginning to require CC-BY licenses when they fund open access article processing fees. That is to say, we are now looking at a situation where organizations that do not have any commitment to (or even liking for) open access, may be required to use this license.

Some questions that I think should be raised at this point:

The CC-BY legal code, as I read it, does not mention open access, nor is there any wording to suggest that the license can only be applied to works that are open access. Here is the URL for the legal code:


1.    Am I missing something in the legal code, i.e. does it say somewhere that this license is only for open access works?

2.    Is there any reason why a publisher could not use a CC-BY license on toll-access works? (Here I am talking about an original publisher, not a licensee).

3.    Is there anything to stop a publisher that uses CC-BY from changing their license at a later point in time? (Assuming the license is the publisher’s, not the author’s).

4.    Is there anything to stop a toll-access publisher from purchasing an open access publisher that uses CC-BY, and subsequently selling all the formerly open access journals under a toll-access model and dropping the open access versions? The license would not permit a third party to do this, but what I am asking about is if the original licensor sells to another publisher.

To sum up, my perspective is that CC-BY, while superficially appearing to be the embodiment of BOAI, is actually a problematic license with significant loopholes and serious thought should be given to this before it is recommended as a standard for open access.

AnimalGarden present “The Chemical Chinese Room” at the American Chemical Society meeting

Henry Rzepa and I have been awarded the Herman Skolnik award of the ACS and will be running a 1-day symposium next week. In my own talk (20 mins) I’ll be looking to the future under the theme “Can we build artificially intelligent chemists?” 3 minutes of this has been hijacked by #animalgarden who have adapted John Searle’s idea of the “Chinese Room” to chemistry.

Here’s Frog and Zog asking Magic Chemical Panda a chemical question and getting an answer.

Who is MCP? What does he look like?

All will be revealed next Tuesday.

Meanwhile here’s a question for anyone:

“What’s the biggest current obstacle to creating artificial intelligent chemistry?”

Please make suggestions. The answer may surprise you.

Fee-free scholarly publishing

A short crowded blog post. I’m off the the ACS shortly and then to VIVO and am concentrating on presentations. Hope to blog those in the normal way.

After kicking off a discussion of publishing models on the [GOAL] mailing list with the traditional Green/Gold/Hybrid approaches I suggested that we should be looking at a “Fee-free” model. This isn’t new and it’s not my idea. Here’s Peter Suber reviewing the situation:

See William Walters and Anne Linvill (August 2010):  ”While just 29 percent of OA journals charge publication fees, those journals represent 50 percent of the articles in our study.”

So there are large numbers of journals that charge nothing to authors and nothing to readers. And they want to remain that way. The problem is that the volume of articles is largely free-supported. We thus have a strange paradox:

  • Lots of small journals prosper without charging excessive fees
  • The large journals charge more, rather than less.

The reason is that there is a vanity market. Fee-supported journals have to argue they produce a better product. And the only product that differentiates them is the market for glory. We hear mantras such as “Researchers must be able to publish where they want.”

Why? If the article is worth reading it will be found. The journal is now primarily a glory label – used not for the excellence of the contents but as an artificial market to determine career progression and funding in universities.

The economic cost of an article is about 250 USD. (Acta Crystallographica do it for 150 USD). Anything higher than that is either inefficiency or sheer profit.

[Stop ranting, PMR and get to the point…]

The point is that lots of people want to create [e-only] publications without these artificial commercial constraints. So we’ve agreed to explore how this can be done, on the OKF’s open Access list (where open Access always means BOAI-compliant). summarises the discussion.

We want to collate information on what works at present. And summarize it so that would be “publishers” can build on the work of others. We are envisaging a “Handbook of fee-free Open Access publishing” which helps people explore sustainable models.

One of the really valuable things about fee-free publishing is that no-one is in it for the money. So the “predatory Open Access” publishers – who publish low quality or even pirated OA material – have no place. There’s no pressure on people to find fees up front. There’s no pressure on libraries – everything is free.

If Steve Coates can get 250,000 people to build a fee-free map of the world, why can’t we do it for scholarly pub. Why do editors have to come from academia? Why do we have to stick with the outmoded “journal” when we have all the tools to manage articles more productively. (If people want journals they can collect together the free material however they want). If the arXiv can manage papers for (I think) 7 USD we don’t need to charge 10000 USD as Nature does. That’s for the glory.

And let’s remember that university libraries take > 10,000,000,000 USD every year from taxpayers and students to pay for journal subscriptions. And only 1 % of the population can read it. If the fee-free community had 1% of this (100 million USD) and distributed it between – say – 1,000 fee-free startups – just to get them going we would see some fantastic developments. So libraries, shouldn’t you be looking to create something new rather than simply fuelling the old, inefficient and avaricious?

Anyway – please join the discussion on open-access. You won’t get shouted down with political Open Access slogans.

PROGRESS (two areas I have been urging on this blog)

  1. Glad to see OCLC releasing a part of Worldcat under a libre licence (ODC-BY)
  2. Wiley have changed their “Fully Open Access” model to one that really is BOAI-compliant (CC-BY). Well done Wiley. Other publishers, be brave – it won’t hurt and may gain you some credit.




CBC Radio Interview August 13, 2012.

This clip of my CBC Radio Early Edition Interview August 13, 2012 with Kathryn Gretsinger (about 10 minutes) is a reflection on the significance of the University of British Columbia Library / Elsevier text-mining arrangement inspired by open data advocate Heather Piwowar. Thoughts on the potential for acceleration of discovery through text-mining from cancer research to humanities, the Elsevier boycott, the added work for libraries with open access.

PLOS ONE Launches Synthetic Biology Collection

Today PLOS ONE is happy to announce the launch of the Synthetic Biology Collection, including over 50 papers published in the last six years that illustrate the many facets of this dynamically evolving research area.

Synthetic biology is an innovative emerging field that exists at the intersection of many traditional disciplines, including biology, chemistry, and engineering, with aims to create biological systems that can be programmed to do useful things like produce drugs or biofuels, among other applications. Despite its potential, the heavily interdisciplinary nature of the research can make it difficult to publish in traditional discipline-specific journals.

However, PLOS ONE’s broad scope allows for the publication of work crossing many traditional research boundaries, making it an ideal venue for many different types of synthetic biology research. For example, the papers in the collection cover topics including DNA synthesis and assembly, standardized biological “parts” akin to interchangeable mechanical parts, protein engineering, and complex network and pathway analysis and modeling, as described in the Collection Overview written by collection editors Jean Peccoud of Virginia Tech and Mark Isalan of the Centre for Genomic Regulation.

The Collection has roots in PLOS ONE’s very first issue, which included two publications from the field. Since then, the number of synthetic biology articles published in the journal has grown steadily. The collection launched today highlights selected synthetic biology articles published in PLOS ONE since 2006, and it is intended to be a growing resource that will be updated regularly with new papers as the field continues to grow and develop.

Collection Citation: Synthetic Biology (2012) PLOS Collections:

Image Credit: Ivan Morozov (Virginia Bioinformatics Institute)

Dear Creative Commons: please drop the gratuitous insult

Creative Commons has a new license chooser with an added feature: it tells us whether or not the license that we have selected is a “Free Culture License”. For the record, I do not agree with whoever has decided what is or is not a free culture license. From my perspective, a truly free culture that uses the nifty Creative Commons tools that I like welcomes and respects people who wish to use licenses that include noncommercial and / or no derivatives terms. Also, a service that wishes to grow does not insult its friends in this manner. CC – please drop the insult.

PLOS ONE Launches Reproducibility Initiative

PLOS ONE is pleased to announce a collaboration with Science Exchange and figshare in a groundbreaking new project: The Reproducibility Initiative. The initiative aims to help scientists validate their research findings by providing a mechanism for blind, independent replication by experts from Science Exchange’s network of more than 1,000 providers at core facilities and contract research organizations.

Reproducibility, or the lack thereof, is a known issue in the scientific community, but few have the time or resources to fully address it. The Reproducibility Initiative is intended to encourage authors to validate their work by facilitating collaboration with an unbiased expert, and offering a Certificate of Reproducibility upon completion. This project will benefit stakeholders from across the research spectrum, including research scientists, drug companies, publishers, funders, and patient groups, all of whom agree that independent confirmation of results improves science and speeds discovery.

When PLOS ONE launched in 2006, a key objective was to publish those findings that historically did not make it into print: the negative results, the replication studies, the reanalyses of existing datasets. Although everyone knew these studies had value, journals would rarely publish them because they were not seen to be sufficiently important. PLOS ONE sought to become a venue for exactly these types of studies. As it happened, however, the submissions were not hugely forthcoming, although we have published a few. (One paper, for example, replicated a previous MRI study but used a higher resolution to confirm the findings, while another failed to replicate a famous psychology study from the nineties.) The Reproducibility Initiative harks back to this original objective, and may even open the doors to more papers whose sole purpose is to correct the literature.

The initiative brings together a number of scientific innovations to create a completely new research space. Science Exchange enables experiments to be performed objectively, free of the pressure to produce positive results that affects most scientists; PLOS ONE provides a formal publication venue that will publish the results of replication studies, even though they are not ‘novel’; and figshare provides a means of sharing raw data quickly and efficiently.

The Reproducibility Initiative is initially accepting 40-50 studies for validation. Scientists can submit their studies here. They will be selected on the basis of potential clinical impact and the scope of the experiments required. The organizers of the project hope that it will be the start of a more overarching system of validation by funders and patient groups, and that’s a sentiment we at PLOS ONE would certainly be happy to see replicated.

Wiley moves toward broader open access

An important announcement from Wiley about their move to broader open access through use of the Creative Commons – Attribution (CC-BY) license for Wiley Open Access Journals. This is a strong indication that Wiley is joining a growing list of traditional commercial scholarly publishers to undertake serious competition for the growing open access environment for scholarly publishing – as is the title of Rachel Burley, Wiley’s VP and Director, Open Access.

While I support the full range of CC licenses for open access, CC-BY is the simplest option for the profit-oriented commercial publisher wishing to be taken seriously about its commitment to open access publishing – important because this perception will help a publisher to be on the list of publishers / journals suitable for those funding open access article processing fees.

Next steps I would recommend to Wiley:

  •  a commitment to publishing journals in a format suitable for data and/or text-mining and that will facilitate re-use of portions of content (for example, a CC-BY license on a locked-down PDF removes legal barriers to re-use, but not technical barriers)
  • a strengthened commitment to support for author self-archiving to allow authors more choice (not all authors have funding support for open access article processing fees)
  • prepare to compete for high quality publishing services at reasonable prices – consider a range of possible future competitors that includes PeerJ with prices starting at $99 for a lifetime of publishing

Kudos and welcome to the open access world to Wiley!

Wiley Moves towards Broader Open Access Licence

John Wiley & Sons, Inc., today announced revised licensing arrangements for proprietary journals published under the Wiley Open Access program. The journals will adopt the Creative Commons Attribution (CC-BY) license which allows commercial use of published articles.

The Wiley Open Access portfolio also includes journals published with society partners, many of which will similarly transfer to the Creative Commons Attribution license.

Wiley is responding to recent developments in funder and government policies and supports the sustainable evolution of scientific publishing. The change will be implemented immediately.

Rachel Burley Vice President and Director, Open Access commented “Wiley is committed to meeting the evolving needs of the authors who wish to provide open access to the published articles that convey the results of their research.”  

Burley continued “Our announcement today concerns Wiley’s fully open access journals. We are also reviewing the licensing arrangements for our hybrid program OnlineOpen, our open access option for individual articles published in subscription journals. In consultation with our publishing partners, we aim to continue to develop and deliver sustainable open access products providing author choice and high levels of service.”

In the first instance, the journals moving to the CC-BY license are Brain and Behavior, Ecology and Evolution, MicrobiologyOpen, Cancer Medicine, Food Science & Nutrition, Evolutionary Applications, Geoscience Data Journal and EMBO Molecular Medicine.

The CC-BY license allows (with the correct attribution of the original creator) for the copying, distribution and transmission of the work. Adaption and commercial use is also permitted.   

More information about Wiley’s open access initiatives is available online.

PLOS ONE News and Media Roundup

Lesions found on coral trout.

Last month, the media covered PLOS ONE papers on germs in airports, skin cancer in fish, a potentially life extending pill, and more!

Research by a team at MIT identified New York City’s JFK, Los Angeles’s LAX and Honolulu’s HNL as the nation’s airports most likely to influence the spread of a major pandemic in the first few days of an emerging disease. The team used geographical information, traffic structure and individual mobility patterns to model contagious disease dynamics through the air transportation network. The study was covered by NPR, CNN, and Wired.

A recent study comparing a hunter-gatherer population with a modern Western population found that daily energy expenditure between the two populations is not all that different; challenging the view that obesity in Western society is largely due to a lack of exercise.  This research may encourage shifting the focus of this debate to the importance of calorie consumption and was covered by The Atlantic, Mother Nature Network and the BBC.

Dark patches found on fish in the Great Barrier Reef have been identified as a deadly form of skin cancer, melanoma. “Evidence of Melanoma in Wild Marine Fish Populations” is the first published study of melanoma in a wild fish population but it is unlikely the problem is new. The Great Barrier Reef sits under the largest hole in the ozone, exposing fish populations there to high levels of UV radiation. The image above is Figure 1 of the manuscript. The study was covered by Science, LA Times and Scientific American.

Autistic children may benefit from getting a pet. According to this study by a French research team, children who received a pet around the age of five showed improved social skills, including increased ability to share with and comfort others, compared to autistic children who either grew up with a pet or never had one. US News, Fox and Time all covered this study.

Findings from the study “Randomized Polypill Crossover Trial in People Aged 50 and Over” suggest that people over fifty may benefit from taking a once daily “polypill” comprised of three blood pressure-lowering drugs and a cholesterol-lowering statin. Read more at CBS, Reuters and ABC.

For more in-depth coverage on news and blog articles about PLOS ONE papers, please visit our Media Tracking Project.