Via Peter Suber and Bora: Obamacto is a new site where you can make recommendations to Obama's Chief Technology Officer and vote on recommendations made by others. Peter's suggestion was this:

Require open access for publicly-funded research

Require open access to the results of non-classified research funded by taxpayers. Extend the exemplary policy now in place at the NIH to all federal agencies.

You can vote anonymously, but registration is a snap -- seriously, the fastest and easiest online signup I've ever seen. Go vote!

It's OA Day, and all the usual suspects are posting entries in the synchroblogging contest. I'm staying off the web except for 30 minutes or so mornings and evenings (because I desire and intend to finish the Project That Would Not Die by the end of the year), and that really only leaves me time to keep up with my feeds and friends.

So, that's my excuse for not having a contest entry (well, that and I dislike contests and prizes... a rant for another time). But I can't let OA Day go unremarked, so check out the official blog and the FriendFeed room. Here is the blog feed (sorry it's Flash, but I don't have time to test other widgets -- and it is pretty):

(Next year, I'm going to treat OA Day as a national holiday and take the day off work in celebration. Maybe one day everyone will do the same...)

With one alteration (viz I have had no differences with Richard Poynder), what Dorothea said goes for me as well. (For more background see Matt at Journalology: 1, 2.)

This is just a for-the-record, public statement that I fully support Richard Poynder's laudable and transparently conducted investigation of SJI and other publishers whose conduct threatens to bring Open Access into disrepute, and that if any such publishers take their legal bullying further than the bluff and bluster we are currently seeing from SJI, I will do what I can to help Richard fight back.

Update 081006: Peter Suber and Stevan Harnad have issued a joint statement in support of the investigative work of Richard Poynder. I was hesitant to do so when it was just me following Dorothea's lead, but now I would like to encourage everyone who is familiar with Richard's work and the SJI story to pick sides and do so publicly. (I have no doubt that every reasonable person will pick Richard's side!)

Check me out:

That means I've got about a week to put together a 30-40 minute talk. I won't have any trouble filling up the time, of course -- the real problem is what NOT to present. I aim to use the web instead of powerpoint, by creating a series of bookmarks that I can open in browser tabs (or from a History sidebar; haven't decided) and move through those like slides. I plan to follow the basic format of my old essays: we're all familiar with Free/Open Source software, the NIH just mandated a kind of Open Access so here's what that means and what that can do, and what else can be Open? leading into Open Data, Open Standards/semantic web, Open Licensing -- in short, Open Science.

The Berglund Center is affiliated with Pacific University, a "a small, private university with a blend of liberal arts, education and health care". I attended the Center's Summer Institute this year at the kind invitation of the director, Jeffrey Barlow, after he read Mitch Waldrop's "Science 2.0" article and noticed that I was local. (Sadly, I could only attend one day, but it was both fun and productive. The whole thing was also filmed, so I'll make a note when the footage and transcripts are available.)

Pacific U's College of Arts and Sciences includes schools of biology, bioinformatics and chemistry, and all three strongly encourage undergraduate research. I hope to tailor the presentation somewhat in the hope of getting faculty in these schools enthused about Open Access and Open Science.

So, my question to you dear LazyWeb, is essentially: what should I present? What are the basic, must-know tools and ideas of Open Science? How can I best introduce the possibilities of Open-ness to faculty and students at a small liberal arts college? Who has given really good presentations from which I can swipe ideas? I have an opportunity here to expand the Open Science community; help me make the most of it.


Update 080909: the slides -- after a suggestion from John Dupuis, I ended up using Google Presentations -- are here, and I'll post when the video becomes available.

There's been a good deal of online chatter about this recent Science article that discusses the effects of online access on scholarship -- see, e.g., discussions here and here and blog entries noted therein.  The report is not available without paying a toll or subscription, but the abstract is freely visible:

Online journals promise to serve more information to more dispersed audiences and are more efficiently searched and recalled. But because they are used differently than print -- scientists and scholars tend to search electronically and follow hyperlinks rather than browse or peruse -- electronically available journals may portend an ironic change for science. Using a database of 34 million articles, their citations (1945 to 2005), and online availability (1998 to 2005), I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles. The forced browsing of print archives may have stretched scientists and scholars to anchor findings deeply into past and present scholarship. Searching online is more efficient and following hyperlinks quickly puts researchers in touch with prevailing opinion, but this may accelerate consensus and narrow the range of findings and ideas built upon.

This seems thoroughly counter-intuitive to me, since I find a good deal more information by direct search now that I can do it online, and browsing has never played a significant role in my literature searching.  (And remember, I'm old -- I started out using Index Medicus!)  Who has time to browse probably-irrelevant journals and tables of contents on the offchance that something might be useful?  I'm far more likely to stumble across things I'd never have otherwise found when I'm relying on a variety of relevance-based search algorithms (PubMed's Related Articles, Google Scholar, NextBio, etc.).

For anyone who thinks that "forced browsing of print archives" makes a lick of sense: we'll pick a topic, then you spend a day or two browsing in meatspace, and I'll spend an hour searching online.  Who do you think is likely to come up with the best (most useful, most comprehensive) set of references?

Moreover, the article's conclusions seem to be based on a couple of unspoken assumptions with which I don't agree.

The first is that citing more and older references is somehow better -- that bit about "anchor[ing] findings deeply intro past and present scholarship".  I don't buy it.  Anyone who wants to read deeply into the past of a field can follow the citation trail back from more recent references, and there's no point cluttering up every paper with every single reference back to Aristotle.  As you go further back there are more errors, mistaken models, lack of information, technical difficulties overcome in later work, and so on -- and that's how it's supposed to work.  I'm not saying that it's not worth reading way back in the archives, or that you don't sometimes find overlooked ideas or observations there, but I am saying that it's not something you want to spend most of your time doing.

Secondly, let's take the author at his word:

I show that as more journal issues came online, the articles referenced tended to be more recent, fewer journals and articles were cited, and more of those citations were to fewer journals and articles.

OK, suppose you do show that -- it's only a bad thing if you assume that the authors who are citing fewer and more recent articles are somehow ignorant of the earlier work.  They're not: as I said, later work builds on earlier.  Evans makes no attempt to demonstrate that there is a break in the citation trail -- that these authors who are citing fewer and more recent articles are in any way missing something relevant.  Rather, I'd say they're simply citing what they need to get their point across, and leaving readers who want to cast a wider net to do that for themselves (which, of course, they can do much more rapidly and thoroughly now that they can do it online).

If that means citing fewer articles now than researchers tended to cite 20 years ago, it probably has more to do with changes in the culture of science than in the electronic availability of research papers.  For instance, I think it far more likely -- to exaggerate, for the purposes of illustration, in the opposite direction to Evans -- that earlier authors, unable to rapidly and comprehensively scan the literature, cited everything they could get their hands on, padding their bibliographies well beyond anything useful in an attempt to lend weight to their arguments.

It's potentially worrisome if more citations are going to fewer journals, but once again I see no more reason to attribute that to increasing online availability than to attribute it to the sharply rising cost of scientific journals in any form.  It's well documented that as journal prices have continued to rise, researchers and institutions have had to cut back on the number of subscriptions they take.  It is not difficult to imagine that "long tail" and "preferential attachment" phenomena (see, for instance, Evans' own references 14 - 18, reproduced below) would drive the concentration of likely subscriptions towards a pool of "must have" journals.  Indeed, publishers actively promote the concept of such a pool and compete strongly to be seen to be part of it.

Finally, and to me most importantly, Evans seems to me to gloss over the question of what proportion of the online archives are freely available, and what effect that has on the phenomenon he is attempting to model.  Here's the crux of what he does say (fair use! fair use!):

I've rearranged the figure so that what were left, middle and right panels are now top, center and bottom panels; in all graphs the abscissae are "Years of journal issues online" and the ordinates are "Herfindahl citation concentration", which is explained as follows:

A concentration of 1 indicates that every citation to [a given] journal [or subfield] in a given year is to a single article; a concentration just less than 1 suggests a high proportion of citations pointing to just a few articles; and a concentration approaching zero implies that citations reach out evenly to a large number of articles.

Here's Evans' interpretation of that data:

Figure 2C illustrates the concurrent influence of commercial and free online provision on the concentration of citations to particular articles and journals. The left panel shows that the number of years of commercial availability appears to significantly increase concentration of citations to fewer articles within a journal. If an additional 10 years of journal issues were to go online via any commercial source, the model predicts that its citation concentration would rise from 0.088 to 0.105, an increase of nearly 20%. Free electronic availability had a slight negative effect on the concentration of articles cited within journals, but it had a marginally positive effect on the concentration of articles cited within subfields (middle panel) and appeared to substantially drive up the concentration of citations to central journals within subfields (right panel). Commercial provision had a consistent positive effect on citation concentration in both articles and journals. The collective similarity between commercial and free access for all models discussed suggests that online access -- whatever its source -- reshapes knowledge discovery and use in the same way.

Wait, what?  Let me unpack that with a rewrite from my point of view:

The number of years of commercial availability appears to significantly increase concentration of citations to fewer articles within a journal, whereas free electronic availability had a negative effect on the concentration of articles cited within journals. If an additional 10 years of journal issues were to go online via any commercial source, the model predicts that its citation concentration would rise from 0.088 to 0.105, an increase of nearly 20%. In contrast, if an additional 10 years of journal issues were to go online via any free source, the model predicts that its citation concentration would drop from 0.088 to just under 0.08 [I had to estimate this by eye, since the data are not available], a decrease of around 10%. Similarly, free electronic availability had only a marginally positive effect on the concentration of articles cited within subfields. Only when considering concentration to journals within a subfield did free availability cause a substantial increase, and even then this effect was considerably less than that driven by commercial availability, which had a consistent positive effect on citation concentration in both articles and journals.

In other words, I take issue with the final sentence of the paragraph I quoted: commercial and free access do not show "collective similarity".  On one of three measures they have the opposite effect, and on the other two measures commercial access has by far the stronger effect.

What this suggests to me is that the driving force in Evans' suggested "narrow[ing of] the range of findings and ideas built upon" is not online access per se but in fact commercial access, with its attendant question of who can afford to read what.  Evans' own data indicate that if the online access in question is free of charge, the apparent narrowing effect is significantly reduced or even reversed.  Moreover, the commercially available corpus is and has always been much larger than the freely available body of knowledge (for instance, DOAJ currently lists around 3500 journals, approximately 10-15% of the total number of scholarly journals).  This indicates that if all of the online access that went into Evans' model had been free all along, the anti-narrowing effect of Open Access would be considerably amplified.

In fact, the comparison between print and online access is barely even possible when considering Open Access information.  The same considerations of cost -- who can afford to read what -- apply to commercial print and online publications, but free online information has essentially no print ancestor or equivalent.  Few if any scholarly journals were ever free in print, so there's a huge difference between conversion from commercial print to commercial online on the one hand, and from commercial print to Open Access on the other.

Indeed, I would suggest that if the entire body of scholarly literature were Openly available, so that every researcher could read everything they could find and programmers were free to build search algorithms over a comprehensive database to help the researchers do that finding, then in fact the opposite effect would obtain.  Perhaps it's true that the more commercial online access you have, the less widely a researcher's literature search net is cast, but as I mentioned above I see no reason to attribute that more to the mode of access than to its cost.

In support of this assertion, consider the expanding body of literature on the Open Access "citation advantage" -- studies which show that the likelihood of a given paper being cited is increased up to several hundred percent if the paper is OA rather than commercially available.  There is some controversy over that literature, but it stands in direct contrast to the idea that online access of any kind tends to narrow citation reach.

There are more data in Evans' paper that speak to the free-vs-commercial issue, and some of those data show free access having a stronger "narrowing" effect than commercial access.  I'd go through it in detail, but I am probably already pushing the limits of fair use so I'll have to refer you to the published article -- in particular, Figure 2 panels A and B.  My response is much the same, that the apparent effect suffers from a loading in "favour" of commercial access, because of the wildly disparate sizes of the two different bodies of online literature. 

-----
refs 14-18 from Evans, JA Science 321:395, 2008:

A. L. Barabási, R. Albert, Science 286, 509 (1999).
R. K. Merton, Science 159, 56 (1968).
D. J. de Solla Price, Science 149, 510 (1965).
H. A. Simon, Biometrika 42, 425 (1955).
M. J. Salganik, P. S. Dodds, D. J. Watts, Science 311, 854 (2006).

Updates 080720:

1. I linked to the FriendFeed discussions but meant to emphasize -- in one of those conversations, Lars Juhl Jensen points out that the single biggest change is information volume:

I cannot help but wonder if this has anything to do with electronic publication, or if it is simply an effect of sheer volume. If researchers have to search through ten times as many articles (because of the exponential growth of the literature), is it really surprising that they don't make it as far back into the past as they used to do?

This is related to, though stronger than, my point about changes in the culture of research.

2. Bora reminded me of another conflicting study by Arthur Eger, this one showing that "a larger [online] content offering coincides with a dramatic increase in Full Text Article requests, and an increase in Full Text Article requests, after about 2 years, coincides with increased article publication". This is not necessarily inconsistent with Evans' claims, especially since the Eger study also showed that the effect of increasing backfile availability is "modest", but I would like to see those increased Full Text requests broken down by date of publication...

3. Tom Wilson doesn't necessarily agree with my (rather blithe?) assertion that researchers are indeed aware of preceding work:

would it were true that authors are not ignorant of earlier work. In my experience as an Editor and a PhD supervisor, I am continually amazed at the extent to which authors and students are unaware of pre-WWW work. It seems that if the work was done before 1995 it is assumed to have no relevance to the present day. In many cases, of course, that will be true and in some cases the research record is a record of building upon earlier work. In the case of many subfields in information science, however, it isn't the case. A great deal of work was done in the 1970s, which is now completely ignored. Researchers rediscover wheels again and again, when a search of the earlier literature would have revealed that what they think of as novel, was novel 50 years ago!

I think this points up my own biases, in that when I think of research I tend only to think of wet lab science, molecular biology in particular since that's what I do for a living. There are many other fields of research! It strikes me that if molecular biologists do in fact reinvent wheels less often than other disciplines, it is perhaps because our online records go back a long way: PubMed reaches back to 1966, and has some coverage all the way back to 1951. Since molecular biology can fairly be said to have come of age as a discipline in 1953, this suggests two things: that Evans may be more right than I think for disciplines outside my own, and that if those disciplines could digitize their archives efficiently it might go a long way towards solving the problem. In other words, the answer to the narrowing effect of online access on scholarship may be to broaden and deepen online access.

This clumsy hatchet job from Nature reporter Declan Butler is beneath him, a poor excuse for journalism and an affront to the respect with which many of his colleagues are regarded by the research community.

Let's start with the title: "PLoS stays afloat with bulk publishing". Loaded rhetoric, anyone? The clear implications are that PLoS is floundering (Butler's own numbers show otherwise!), and that "bulk" is somehow inferior (to, one presumes, "boutique" or some such). PLoS is "following an haute couture model of science publishing" sniffs our correspondant, who goes on to clarify: "relying on bulk, cheap publishing of lower quality papers to subsidize its handful of high-quality flagship journals".

This emphasis on "quality" and the idea that the same somehow equates with scarcity continues throughout: "the company consciously decided to subsidize its top-tier titles by publishing second-tier community journals with high acceptance rates", "the flood of articles appearing in PLoS One (sic)", "difficult to judge the overall quality", "because of this volume, it's going to be considered a dumping ground", "introduces a sub-standard journal to their mix".

The intent is obvious, and the illogic is boggling. Where does Butler think the majority of science is published? Even if you buy into this nebulous idea of "quality" (one knows it when one sees it, does one not old chap? wot wot?) there can be no "great brand" journals without the denim-clad proletarian masses. All the painstaking, unspectacular groundwork for those big flashy headline-grabbing (and, dare I say it, all too often retracted) Nature front-pagers has got to go somewhere.

It gets much worse, though, when we get some measure of what Butler thinks "quality" means:

Papers submitted to PLoS One (sic) are sent to a member of its editorial board of around 500 researchers, who may opt to review it themselves or send it to their choice of referee. But referees only check for serious methodological flaws, and not the importance of the result.

That, along with an earlier remark about "a system of 'light' peer review", is a blatant and serious misrepresentation of PLoS ONE's review process. Here's the actual policy:

The peer review of each article concentrates on objective and technical concerns to determine whether the research has been sufficiently well conceived, well executed, and well described to justify inclusion in the scientific record. [...]

Unlike many journals which attempt to use the peer review process to determine whether or not an article reaches the level of 'importance' required by a given journal, PLoS ONE uses peer review to determine whether a paper is technically sound and worthy of inclusion in the published scientific record. [...]

To be considered for publication in PLoS ONE, any given manuscript must satisfy the following criteria:

• Content must report on original research (in any scientific discipline).
• Results reported have not been published elsewhere.
• Experiments, statistics, and other analyses are performed to a high technical standard.
• Conclusions are presented in an appropriate fashionand supported by the text.
• Techniques used have been documented in sufficient detail to allow replication.
• Reports are presented in an intelligible fashion and written in standard English.
• Research meets all applicable standards, including the Helsinki Declaration, with regard to the ethics of human and animal experimentation, consent, and research integrity.
• Report adheres to the relevant community standards for research, reporting, and deposition of data. (Standards PLoS promotes across its journals).

Which is to say that PLoS ONE^* holds authors to exactly the same scientific standards that every journal should follow. Which is to say that any methodological flaws, not "only... serious" ones, will see a paper revised, or rejected if the flaws can't be overcome. Which is to say that PLoS ONE uses peer review to do what it was designed to do, not to create an artificial scarcity from which to milk profit with scant regard for the integrity of the scientific record. That's not "light" peer review, it's real peer review.

With this scurrilous parroting of anti-OA FUD, Nature makes pretty clear where its interests and its allies are.  Well, you know what happens when you lie down with pit bulls...

There's a lot more, but that was the issue that pushed my buttons the hardest. See Bora for a roundup of responses; here's a quick outline of some of the key issues:

Jan Velterop, responding to Butler's last "investigation" of PLoS finances two years ago, pointed out that it's ridiculous to expect a new journal with a new business model to break even in a few years, when new journals from established publishers take up to a decade to achieve the same goal; DrugMonkey also mentions the "so what" nature of this complaint. Jonathan Eisen remarks that somehow Butler gets from "PLoS ONE is doing well and making money" to "PLoS is a failure"; go read Jonathan to see how twisted your logic has to be to make that particular trip. (Jonathan also provides an important reminder, that we should not confuse Nature Publishing Group as a whole with their many talented and well intentioned employees!) Grrlscientist observes that, while Butler's piece makes it sound as though PLoS' reliance on donations were a bad thing, all journals rely on the donation of time and expertise by unpaid reviewers. Drugmonkey, Jonathan and Grrlscientist all make the point that Nature has its own stable of "second tier" journals with "lower barriers to entry" -- the same mechanism for which Butler criticizes PLoS. Stevan Harnad is famous for making the point (here, for example) that if the funds currently draining into subscriptions were used to pay OA costs, there would be an immense improvement in the utility of the scientific record even if there were no financial saving.

Finally, pretty much every commenter has pointed out the glaring lack of any "conflict of interest" statement on the Nature piece -- having said which, I'd better make one of my own. It's well known and obvious at a glance at this blog that my favorite drink is the Open Access Kool-Aid. I have personal friends who work for PLoS, and I've previously applied to work there myself.


^* originally in lowercase -- so much for my snotty (sic)s!

This is an unpublished post that's so old (Aug '07) that I don't know why I didn't just post the damn thing; I've forgotten what I was intending to do with it. I'm posting it now because it contains pointers to useful thinking by David Wiley and others that is germane to the ongoing discussion of data licensing (see post below). I was reminded of this old draft of mine by Deepak's comment that copyleft may be harmful in the case of scientific data, a point David also makes in respect of his particular Open area, education. Much of what David says maps readily from his field to research, so without further ado:

David Wiley of Iterating Toward Openness has been blogging up a storm about open content licensing:

• Noncommercial Isn't the Problem, ShareAlike Is
• ShareAlike, the Public Domain, and Privileging
• Copyleft and Fish in Water
• Open Education License Draft
• Assymetry, Hypocrisy, and Public Domain
• Why Not CC By?

That's a lot to read, but it's all good stuff. David makes one very strong argument that I want to emphasize here, because it points up the difficult distinction between data and (creative) work.

In the post introducing his draft Open Education Licence, he provides a very useful outline of the aims of open content:

• Reuse - Use the work verbatim, just exactly as you found it
• Rework - Alter or transform the work so that it better meets your needs
• Remix - Combine the (verbatim or altered) work with other works to better meet your needs
• Redistribute - Share the verbatim work, the reworked work, or the remixed work with others

I really, really like that. David's "four R's" resemble the four fundamental freedoms of the Free Software Foundation but do a better job of discriminating between Rework and Remix. The Four R's make immediate sense to me and I will certainly be Reusing and Redistributing that idea.

David goes on to quote some believable numbers and points out that:

Since half of all CC licensed materials are licensed using a copyleft clause and all GFDL licensed materials are licensed using a copyleft clause, this means that over half of the world's open content is copylefted. And while the CC and GFDL copyleft clauses guarantee that all derivative works will be "open," they also guarantee that they can never be used in remixes with the majority of other copylefted works. You can't remix a GFDL work with a By-NC-SA work when the licenses require that the child be licensed exactly as the parent. Each parent had one and only one license - which license would the derivative use? It's just not possible to legally remix these materials; copyleft prevents this remixing. [see David's earlier explanation for details of the incompatibilities among various copyleft licenses]

While promoting rework at the expense of remix - in other words, taking the copyleft approach - is fine for software, it is problematic for content and extremely problematic for education. As educators, we are always remixing materials for use in our classrooms both in the "real" world and online. Your mileage may vary, but over my last 15 years of teaching I would estimate that my remixing activities outnumber my reworking activities 10:1 or more. If other teachers are like me in this regard, then, copyleft is a huge problem for open education.

It's potentially a huge problem for scientists, too, because much of the potential of Open Science and Open Data (see here for an attempt at defining those terms) is in Remix. There are answers in existing datasets to questions their creators never thought to ask; as Alma Swan put it,

...exciting new developments in text-mining and data-mining are beginning to show what can be done to create new, meaningful scientific information from existing, dispersed information using computer technologies. Research articles and accompanying data files can be searched, indexed and mined using semantic technologies to put together pieces of hitherto unrelated information that will further science and scholarship in ways that we have yet to begin imagining.

This is why I join Peter Murray-Rust in being against copyleft for data:

I am not in favour of copyleft for data. I have no fundamental objection to creating a copyrighted work from data as long as there is significant added value. And copyleft is viral - deliberately. If any item in a system/collection/program etc. is copyleft, then the whole is (at least by the algorithm). [...]
I would argue that if I get factual information from WP [wikipedia] then it cannot carry a copyleft. I need the fundamental physical constants and get them from WP. I don't think that my data and programs are thereby copyleft. All algorithms are now slightly fuzzy.

So what do we mean by "data"? What I mean is "facts about the world of sense-perception", as distinct from the presentation and interpretation of those facts. So I might not be free to reproduce, say, a scan of a Western blot from a published paper -- but having looked at that image, I had better be completely free to do whatever I like with the information it gives me about the way the world works, or else science will grind to a halt. Similarly, if a review article (which contains no new facts, and is all reuse and remix) brings together the results of a number of studies to create new information, or a new hypothesis, about the way the world works, I am not free to copy the wording but I must be free to go into my lab and test the hypothesis.

See also (this was a note to myself in the draft, so caveat lector!):

CC-NC considered harmful (Kuroshin)
When is OA not OA? (Catriona MacCallum in PLoS Biology)
CC, OA and moral rights (Thinh Nguyen, Science Commons blog)
Open Data and Moral Rights (Peter Murray-Rust)

-----
In the interests of full disclosure, I have a personal statement for this blog which I hope places the content squarely in the public domain, and for my columns on 3QuarksDaily I use CC-BY so that, if those pieces generate any interest, 3QD might at least get some traffic out of having generously offered me a spot on their roster.

Scientific data are not only hard to come by, they're almost as hard to share, mainly because the scientific infrastructure is armpit-deep and sinking fast in the quicksand of patents, copyrights and ever-multiplying licenses. See Peter Murray-Rust, Antony Williams and Egon Willighagen for the latest dust-up over data licensing; I just want to point out this clear-eyed commentary by John Wilbanks:

The public domain is not an "unlicensed commons". The public domain does not equal the BSD. It is not a licensing option.

It is the natural legal state of data.

It is a damn shame that we no longer think of the public domain as an option that is attractive. It's a sign of the victory of the content holders that the free licensing movements work against that something without a license -- something that is truly free, not just just free "as in" -- is somehow thought to be worse. We've bought into their games if we allow the public domain to be defined as the BSD. The idea of the public domain has been subjected to continuous erosion thanks to both the big content companies and our own movements, to the point where we think freedom only comes in a contract.

The public domain is not contractually constructed. It just is. It cannot be made more free, only less free. And if we start a culture of licensing and enclosing the public domain (stuff that is actually already free, like the human genome) in the name of "freedom" we're playing a dangerous game.

There's a lot more to get at here.

Yes, there is, and you should read the rest of that entry (and keep up with John's blog) if you're at all interested. I'll add just one brief comment: back when John's current job was first advertised, I considered applying for it -- not that I thought I was qualified, but perhaps the SC would want to hire the new director an offsider of some sort. Having had a couple of years to start learning a bit about Open Access and Open Science, I would venture to say that we are all better off with me in the cheerleading section instead of on the field.

As the terminology wars between "Free Software" and "Open Source Software" afficionados demonstrate, as soon as you stick a label on what you are doing, someone will come along and co-opt it. Sometimes, as with F/OSS, there are real disagreements to be had by reasonable people; at other times, well, not so much. This:

"Open science" is liberated from methodological naturalism (MN), even though it begins with an MN position. That is, all scientists start their work in pursuit of natural explanations for events or natural solutions for problems. If evidence and logic point to an end of the road for natural explanations, on rare occasions a scientist using open science would be willing to consider an explanation which does not force him to a naturalistic conclusion. For instance, the genetic code stored in the DNA molecule has no precedent in naturalism, since all codes are the product of a mind. Open science would allow possible supernatural causation as a topic for further research. The scientist would not be restricted to naturalism as the only explanatory option. But alas! Professional scientists do not practice open science. They practice "closed science."

has most emphatically nothing whatsoever to do with Open Science in the sense in which I -- and my friends, colleagues and allies in the nascent movement, see e.g. blogroll to right -- use the term.

Over at Free Genes, Jason Kelly has a nice reminder for those of us who tend to be disheartened by slow rates of progress in our chosen field, be it Open Science or, in Jason's case, synthetic biology. I liked it so much I'm stealing it. This:

is a transistor, circa 1948. Now you can buy the equivalent of many millions of these for pocket change, in a device that will fit on your keychain.

Egon has an interesting angle on Peter Murray-Rust's observation that you can't mine PubMed Central:

I was wondering about this section in the CC license of much of the PMC content, such as our paper on userscripts (section 4a of the CC-BY 2.0):

You may not distribute, publicly display, publicly perform, or publicly digitally perform the Work with any technological measures that control access or use of the Work in a manner inconsistent with the terms of this License Agreement.

CC-BY 3.0 reads differently, but has similar aims. [...] Peter indicates that the NIH has put in place 'technological measures to control access' to the distribution of our work on userscripts (the PMC entry). That is in clear violation of the CC license. [...] What the PMC website should indicate, instead, is that text mining is allowed for the PMC OAI subset, but that they would highly prefer to use the PMC OAI or PMC FTP routes. This is the least they have to do.

No matter what, I still have the feeling that any technical obstacles are disallowed by the CC-license. Any legal expert here, that can explain me if the CC license allows controlling how people have access to my material?

In other words, can they do that? Like Egon, I await legal advice... how 'bout it, Creative Commons?

Heather Morrison points to this excellent post by Glen Newton, wherein Glen proposes that Open Access should explicitly include machine readability:

Open Access must include access by machines:

* At minimum one must allow crawls of the site/content or (to reduce the impact of badly configured crawlers) create a compressed XML file containing all metadata and either content, or direct links to content and make it available for download (and if bandwidth is still an issue put it on a P2P network like BitTorrent).
* Preferable is to offer some kind of API (OTMI) or protocol (OAI-PMH) to get at content and metadata and citations.
* Better is to offer access to the XML of the articles in addition to the PDF and/or HTML; if the XML actually has some semantic content, then we are approaching the optimum.

The end goal is to support and encourage text mining and analysis of the full-text (preferably semantically rich XML), metadata and citations to allow literature-based exploration and discovery in support of the scientific research process.

Most importantly: hear, hear!

I do, however, have a nitpick to make. Heather makes no comment on Glenn's idea that this is an addition to the definition of OA, but in fact I think it's already built in to the accepted BBB definition. Peter Suber refers to the removal of price and permission barriers, to distinguish Open from "merely" free access, which removes only price barriers; I've quoted him on this before, so here he is again:

The best-known part of the BBB definition is that OA content must be free of charge for all users with an internet connection. However, the BBB definition doesn't stop at free online access. It adds an extra dimension that isn't as easy to describe, and consequently is often dropped or obscured. This extra dimension gives users permission for all legitimate scholarly uses. It removes what I've called permission barriers, as opposed to price barriers. The Budapest statement puts the extra dimension this way:

By "open access" to this literature, we mean its free availability on the public internet, permitting any users to read, download, copy, distribute, print, search, or link to the full texts of these articles, crawl them for indexing, pass them as data to software, or use them for any other lawful purpose, without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself. The only constraint on reproduction and distribution, and the only role for copyright in this domain, should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

The Bethesda and Berlin statements put it this way: For a work to be OA, the copyright holder must consent in advance to let users "copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship".

All three tributaries of the mainstream BBB definition agree that OA removes both price and permission barriers. Free online access isn't enough. "Fair use" ("fair dealing" in the UK) isn't enough.

Having said all that, though, I'll add that an explicit description of machine readability requirements would be an addition to the accepted definition of OA -- and one that I would welcome. Peter Murray-Rust recently noted that, according to the "price and permission barriers" view of Open Access, PubMed isn't OA -- even PubMed Central isn't OA.

I'll go even further: can anyone point me to a single Open Access repository? I don't know of even one such site that removes both price and permission barriers. Surely there must be some, but the Big Names (PubMed Central, arXiv, Cogprints, CiteSeer, RePEc, etc -- see ROAR) don't seem to qualify, because digital objects in these repositories carry their own copyrights, rather than being covered by a blanket license provided by the repository.

Can this be true? Five years after the BBB definition came together, more than ten years since Stevan Harnad's subversive proposal and on the first day of the NIH mandate -- widely referred to as an OA mandate! -- can it be that we really don't have a single truly OA repository in all the world? And if it is true, would it help to make the official definition more explicitly machine-friendly?

I'm probably too late with this to do any good, but Shirley Wu is putting together a proposal for an Open Science session at the Pacific Symposium on Biocomputing. You can read a draft of the proposal which already reads pretty well to me, and Shirley could do with letters of support:

One thing that would really help outside of the proposal itself is to have actual letters of support. That way the organizers will know there is serious interest and commitment for a session on Open Science - it's a gamble for them, frankly, but much less of one if there is a good crowd on board.

So if you would like to support this proposal and are willing to commit to participating should it get accepted, please send me an email to that effect (with as many details of your anticipated participation as you can provide at this time), and I will include all the emails as "supplementary material" next Friday.

Er, yes, that's this coming Friday... I did mention I was late with this, no?

So anyway, if you can come up with an idea for a presentation or can simply commit to attending, please drop Shirley a line. She's another graduate student who's caught the Open Science bug, and the more of them we have -- and the more we can do to help and encourage them -- the better.

I'm way behind on this, but anyway: a while back, writer Mitch Waldrop interviewed me and a whole bunch of other people interested in (what I usually call) Open Science, for an upcoming article in Scientific American.  A draft of the article is now available for reading, but even better -- in a wholly subject matter appropriate twist, it's also available for input from readers.  Quoth Mitch:

Welcome to a Scientific American experiment in "networked journalism," in which readers -- you --get to collaborate with the author to give a story its final form.

The article, below, is a particularly apt candidate for such an experiment: it's my feature story on "Science 2.0," which describes how researchers are beginning to harness wikis, blogs and other Web 2.0 technologies as a potentially transformative way of doing science. The draft article appears here, several months in advance of its print publication, and we are inviting you to comment on it. Your inputs will influence the article's content, reporting, perhaps even its point of view.

So consider yourself invited. Please share your thoughts about the promise and peril of Science 2.0. -- just post your inputs in the Comment section below.

It's good to see Science 2.0 getting not just mainstream attention, but well-crafted and balanced mainstream attention.  It's also good to see a "Journalism 2.0" approach being tested, so if you have ideas or opinions, go participate.

On a personal note, I'm pleased but a little embarrassed to have been quoted by name in an article for which I know Mitch interviewed a lot of people who are actually *doing* Science 2.0, not just cheering from the sidelines like me.  It's hard to be critical of choices made in the face of space constraints (the article is destined for print), but there's no such limit online.  I wonder whether Mitch and his SciAm editors would consider putting a longer version online? 

In a similar vein, in comments here Bora asks whether we (John's "usual suspects") couldn't put together a longer article for publication somewhere.  I think I might have a better idea (though it's hardly original with me).  From my point of view, the best thing about my 3Quarks Open Science articles from about a year ago is that they are already wildly out of date.  The -- to me -- obvious way to update them and keep them up-to-date is to turn them into a wiki (probably starting from the Nodalpoint wiki's Open Science page).  I think the articles cover most of the main bases, and each section could relatively easily be turned into a wiki page; with a little attention to style, it should then be fairly easy to re-write the articles from the updated information.  I am, as usual, swamped with work, so I won't be able to wiki-ize anything any time soon -- I do intend to get to it eventually, but in the meantime the articles themselves are all CC-BY and my Simpy bookmarks, which should help with updating, are pub dom and I'd be happy to help if anyone else wanted to take a stab at it. 

Finally, if you enjoyed the SciAm article, you might also enjoy more of Mitch's writing: he has a blog, a new gig at Nature and has written three books to date: The Dream Machine (2001), Complexity (1992) and Man-Made Minds (1987). (I swiped his affiliate links, I hope they still work.)

Being careful with the language of the letter below made me see that, in earlier entries, I've fallen into one of the easy traps in which OA opponents would like to catch everyone:

...of these, 16 are listed as "grey" (won't allow archiving), 23 are "green" (allow refereed postprint archiving -- NIH mandate compliant) and 7 "pale green" (allow preprint archiving; many "pale green" publishers actually allow postprint archiving and are NIH compliant...

...at least 50% of PSP members are already complying with the NIH mandate, and a further 15% at least allow preprint archiving and may even be NIH-compliant.

The majority of journals for which information is readily available are already compliant with the new NIH mandate...

This phrasing is deeply misleading: it's not the journals or the publishers who must comply with the new NIH (or any other) Open Access mandate!

Publishers can choose to allow their authors to self-archive, or not. They are under no compulsion whatsoever. It's the authors -- who have taken public funding, and so are working for the public -- who must comply with the mandate to give the public full value for its money.

There is no such thing as an NIH-compliant, or non-compliant, journal or publisher. That's a phrase that comes readily to hand, a convenient shorthand perhaps, but we should not use it. The mandate simply does not concern itself with the actions of publishers. Beware the rhetorical frame in which the new law is cast as "the government telling publishers how to run their business"!

The obvious replacement phrase, when talking about journals or publishers and their policies, is "mandate-compatible", so I'll be careful to use that from now on.

Peter Suber points out that no members of the AAP/PSP's ill-conceived PRISM "coalition" were ever identified, and that at least nine publishers publicly disavowed or distanced themselves from it; he then asks:

Has AAP/PSP ever consulted its members about its position on the NIH policy? Are AAP/PSP members willing to see their dues spent on a lawsuit to delay it?

I think it's worth finding that out.

Listed at the bottom of this entry are the "green" and "pale green" EPrints/RoMEO publishers listed as members by the PSP (links and names taken directly from the PSP website). On closer inspection, it seems that RoMEO proper lists all of the "pale green" publishers as yellow, and (with one or two caveats concerning journals with long embargo periods) gives them all a "compliant" rating in respect of NIH policy.

Here is a draft of the letter I have in mind to send to each of these publishers:

Dear [Publisher],

the Association of American Publishers' Professional and Scholarly Publishing division (AAP/PSP), which lists [your company] as a member [1], recently issued a press release [2] in response to the new NIH mandate [3] for Open Access to publicly funded research. The press release was highly critical and contained a number of mistaken and misleading assertions; for details, you can read a public, point-by-point rebuttal [4] by Prof Peter Suber, open access project director at Public Knowledge [5] and a senior researcher with the Scholarly Publishing and Academic Resources Coalition [6]. I'm sure you remember PRISM, the AAP/PSP's ill-considered campaign against Open Access [since your company publicy distanced itself from same]; this latest press release is similar in tone and apparent intent.

In stark contrast to the AAP/PSP's public stance, [your company] is listed by Project RoMEO [7] as a [yellow/green] publisher. This means that [your company] policy regarding self-archiving of journal articles was fully in line with the new law even before it became law, and there is absolutely no conflict between your business model and the NIH mandate. In fact, of the 46 PSP member companies indexed by Project RoMEO, 30 have no policy that conflicts with the new law; and of the approximately 6000 journals published by those 46 companies, around 5700 already allow their authors to comply with the NIH mandate.

I write, therefore, to ask: does the AAP/PSP accurately represent its members in its opposition to the NIH mandate? Was [your company], as a member of the Association, consulted before the AAP/PSP respnse was made public? Finally, if [your company] is not in agreement with the AAP/PSP on this matter, would you consider making a public statement to that effect [in the same way you did regarding PRISM]?

sincerely,

Me.

[1] http://www.pspcentral.org/index.cfm?left=member_companies&page=/home/member_companies.cfm
[2] http://www.pspcentral.org/publications/AAP_press_release_NIH_mandatory_policy.pdf
[3] http://thomas.loc.gov/cgi-bin/query/z?c110:H.R.2764:
[4] http://www.earlham.edu/~peters/fos/2008/01/aappsp-response-to-oa-mandate-at-nih.html
[5] http://www.publicknowledge.org/
[6] http://www.arl.org/sparc/
[7] http://www.sherpa.ac.uk/romeo.php

The most obvious thing missing from the draft is "who the hell am I, to be asking you this?" Now, I can send the letter as myself -- concerned citizen, professional research scientist, potential client of publishers -- but I am only an egg, and it would have a good deal more impact as an open letter from a variety of interested and concerned parties, and still more if it came from somewhere official (ARL, SPARC, I don't really know who would be appropriate here).

So -- anyone up for a multi-author open letter? Any other ideas?

Update 080310: decided not to send letters after all; see here, scroll to bottom of post.

The publishers in question:

Pale green:

• Blackwell Publishing
  
• The MIT Press
  
• Nature America
  
• Oxford University Press
  
• SAGE Publications
  
• University of Chicago Press
  
• University of Illinois Press

Green:

• American Anthropological Association
• American Association for the Advancement of Science
• American Geophysical Union
• American Institute of Physics
• American Mathematical Society
• American Psychological Association
• Association for Computing Machinery (ACM, Inc.)
• Cambridge University Press
• Elsevier Science Inc.
• INFORMS
• The Institute of Electrical and Electronics Engineers, Inc. (IEEE)
• Institute of Physics Publishing
• The Johns Hopkins University Press
• Wolters Kluwer Health
• Massachusetts Medical Society
• National Academy Press
• RAND
• Rockefeller University Press
• Springer Publishing Co.
• Springer Science + Business Media
• University of California Press
• The University of Hawaii Press
• John Wiley & Sons, Inc.

The publisher list I've been using in the last few posts actually comes from EPrints.org, using information from SHERPA/RoMEO. I'll refer to the EPrints interface as EPrints/RoMEO from now on.

This wouldn't cause any confusion and I wouldn't bother to point it out, except that RoMEO actually uses a four-colour scheme (green, blue, yellow, white) which EPrints has squished into three (green, pale green, grey).

Update: see Stevan Harnad's comment on the next entry.

Via Peter Suber, Dorothea Salo and Heather Morrison, I see that the AAP/PSP has responded to the new NIH mandate in typical, PRISM-esque fashion. For anything I might have said in response, and much more, read the linked entries -- especially Peter Suber's. I have something else in mind.

The PSP lists its members here ; it didn't take long to compare that list with the list of publishers indexed by SHERPA/RoMEO. Of the 355 publishers in the RoMEO database, 46 are members of PSP; of these, 16 are listed as "grey" (won't allow archiving), 23 are "green" (allow refereed postprint archiving -- NIH mandate compliant) and 7 "pale green" (allow preprint archiving; many "pale green" publishers actually allow postprint archiving and are NIH compliant, but are not listed as green because of various restrictions).

It's not possible to do what I wanted here -- which was to answer the title question. The problem is that the PSP lists 102 about 100 members that aren't indexed by RoMEO. I found that somewhat surprising, particularly since the list includes names I'd have expected to find in RoMEO: FASEB, Stanford U Press, Yale U Press, Cold Spring Harbor Lab Press, NEJM, Highwire Press and others.

Nonetheless, we can say that if the RoMEO-indexed sample (46 of 148, 31%) is representative, then at least 50% of PSP members are already complying with the NIH mandate, and a further 15% at least allow preprint archiving and may even be NIH-compliant.

It's even more unbalanced if we compare the numbers of journals published by each company. Those 46 publishers account for 5901 journals; the grey publishers put out 222 (4%), the green publishers 4243 (72%) and the pale green publishers 1436 (24%).

If the PSP were honest and interested in fairly representing its members, I'd think they would find out (and make public) whether the remaining, non-RoMEO indexed members follow the same pattern. I won't hold my breath.

____
Full disclosure: the numbers above are not 100% accurate, since the comparison between the two lists was not always straightforward. For instance, RoMEO indexes "Yale Law School" and the PSP lists "Yale University Press" as a member. I tried to err on the side of the PSP -- for instance, Yale Law is grey, so I included them. There were a few such problematic instances; I very much doubt that they made any difference to the data expressed as percentages, I'd welcome correction and a better dataset, and if anybody wants the Excel files I used I'll be happy to provide them.
Update: see strikethroughs above; some of the overlap issues can be resolved by searching more carefully -- for instance, NEJM is published by Massachusetts Medical Society, which is in RoMEO, and I have no idea how I missed FASEB the first time around. But again, little or no change to the percentages.

Via Dorothea Salo and Peter Suber, John Mark Ockerbloom reminds me that New Year's Day is also Public Domain Day -- the day on which, each year, a new batch of works enters the public domain:

In countries that use the "life plus 50 years" minimum standard of the Berne Convention, works by authors who died in 1957 enter the public domain today. That includes writers, artists, and composers like Nikos Kazantzakis, Diego Rivera, Dorothy L. Sayers, Jean Sibelius, and Laura Ingalls Wilder.

In countries that use the "life plus 70 years" term, works by authors who died in 1937 enter the public domain, including works by J. M. Barrie, Jean de Brunhoff, H. P. Lovecraft, Maurice Ravel, and Edith Wharton. [...]

In countries like the US and Australia, which are under 20-year freezes of all or most of the public domain, it's not quite as momentous a day. Here in the US, like Bill Murray in Groundhog Day, we're once again waking up to a public domain 1922, as we have since 1998. Our next mass expiration of copyrighted published material is scheduled for New Year's Day 2019, 11 years from now. [...]

Let's not just ask what the public domain can do for us; let's ask what we can do for the public domain. In particular, as of this year more than 14 years have passed since the Web started to explode into public consciousness, with NCSA's release of the Mosaic web browser in 1993. Many of us older Net users started creating web sites that year. And 14 years was the original term of copyright specified in the UK's Statute of Anne, and the US's first copyright law (with an optional renewal term).

As an advocate of more reasonable copyright terms, like those envisioned by our country's founders, I am therefore today dedicating the copyrights of all 1993 versions of my web sites into the public domain. These sites include The Online Books Page, which is still in operation, and Catholic Resources on the Net, which I stopped maintaining in 1999.

Many thanks to John Mark for the informative post, and also for his gift to the public domain. Like Dorothea, I have long since tried to make it clear that I consider my weblog to belong to the public domain. (Do read Dorothea's explanation.) As you can see from comments on my entry, though, an informal statement is suboptimal because people still have questions, and are not confident simply taking whatever they want from the site (as I intend that they should be). It turns out that it's not easy to put something into the public domain without waiting out the requisite copyright term -- it means giving something away for free, and the law is leery of that. So you need meatspace signatures and whatnot, and the Creative Commons Public Domain Dedication is not really much use, even within the USA. I've thought about ditching my homebrew dedication for a CC-BY license, but I don't actually want to place that restriction on the use of anything I post here. Fortunately, CC is on the ball and will soon offer CCZero, which I hope will turn out to be an effective way to dedicate something to the public domain, formally and officially and in a widely recognized and accepted manner. Once I have an option that puts the weight of Creative Commons behind the dedication I want, I'll switch to that. For now, just trust me -- take whatever you want from this site (so long as I made it, of course) and do with it as you please. I'd love to hear back about anything you do with something you found here, but you're under no obligation to inform me.

Rich Apodaca asks whether the new NIH OA mandate marks a new beginning, or more of the same. His argument hinges on the (admittedly unfortunate) phrase "in a manner consistent with copyright law", and he concludes that

Neither HR 2764 nor any form of government intervention will bring widespread Open Access into being.

Here's why I think Rich is wrong.

Point the first: Rich claims that

Most of the journals in question will be hostile to the idea of having their copyrighted material deposited into PubMed Central and so understandably won't allow it to be done by the authors of papers or anyone else.

The available data do not support this. Of the 355 publishers indexed by SHERPA/RoMEO, 66% formally allow self-archiving; more importantly, 56% formally allow archiving after refereeing. (There's a big gap between "formally allow" and "formally forbid", too.) The numbers are even more OA-positive at the journal level. Those publishers between them account for 10199 journals, of which 91% are at least "pale green" -- that is, allow at least preprint archiving. Well over 6000 journals, 62% of the total, are "green" -- that is, allow self-archiving of refereed postprints. You can use the web interface to find out whether your favorite journal or publisher will allow you to self-archive; here's a quick look at the big names (> 50 journals) and a few usual suspects (sorry about the jpg, I can't make html tables to save myself):





Point the second: Rich goes on to give the following hypothetical:

Professor Gross at California University gets his manuscript approved for publication in the Journal of Nanoscale Devices (JND). Professor Gross is fully aware both of HR 2764 and JND's refusal to deposit manuscripts into PubMed Central - the reasons why Professor Gross would choose JND anyway are interesting, but not relevant here. Along with the acceptance letter, JND requests prompt return of a signed copyright transfer agreement. Professor Gross sends in the signed form and from that point on, all rights to his article belong to JND. As is their policy, JND refuses Professor Gross permission to deposit a copy of his paper into PubMed Central within 12 months after publication.

Unless I'm missing something, neither Professor Gross nor JND have violated any laws.

Does Professor Gross have to publish in JND? Pace Rich, the good Professor's reasons are relevant. Let's take a look at those publication-related sins through an OA lens:

• Greed -- the OA advantage should drive the greedy to reject journals like JND which deny them the opportunity fully to profit from their own work
• Envy -- if you want your publication record to be all it can be, publish OA (either by choosing OA journals, or by self archiving)
• Pride -- if you want your science to have maximal impact, ditto
• Wrath -- STM publishing is big business with big fat profit margins; as consumers and producers, let's at least get value for money (i.e., OA) and put the hurt on greedy publishers who won't at least allow us to make our own work OA
• Gluttony, Lust -- see Greed, Envy, Pride
• Sloth -- for just a few keystrokes, you can increase your research impact and professional standing; why would you not?

Given all that, will the good Professor continue to kowtow before the little godlings who publish JND? Or will he simply find himself a journal that will play ball?

Point the third: Rich continues:

The assumption made by proponents of the new law seems to be that to implement the new policy, the Director of NIH will forbid publication by grant recipients in journals that don't allow deposition of articles into PubMed Central.

How many influential scientist do you know of who would tolerate the government telling them which journals they can and can't publish in? The minute such a misguided policy is put in place, the national scientific outcry would more than overwhelm anything Open Access proponents could muster.

How many? All of them. When a funder says "jump", even "influential" scientists say "Was that high enough? Shall I try again?". (Besides which, this is not "the government telling them" anything, this is a funding body making a reasonable demand.) Where scientists do have some weight to throw around is with publishers: the NIH can always get another benchmonkey, but publishers need a steady supply of authors. So if I want to publish in the Journal of Dodgy Results, which won't allow repository archiving, and the NIH says "not if you take our money -- not until they comply with the mandate", I can: look for other funding (believe me, there ain't a lot); fight authority (see Mellencamp, J.C., 1983); or I can try to get the editors of JDR to let me put a copy in PubMed Central after 12 months. Identifying the path of least resistance is left as an exercise for the reader.

Here again, the data (though scanty) are on my side. A 2005 survey of nearly 1300 authors found 81% of respondants reporting that they would willingly comply with a green OA mandate; a further 13% replied that they would comply unwillingly,and 5% claimed they would not comply. Not only is 94% a great deal better than the roughly 4% compliance observed while the NIH policy was voluntary, but I've got five bucks right here that says those 5% are full of it. If push comes to shove, they won't be handing back any grants or handing in any letters of resignation. Most of them, confronted with the evidence, will do what scientists are supposed to do in such cases: say "oh, I was wrong", and change their views and behaviour. The few who don't do that will still comply, they'll just yell at a couple of editors to make themselves feel all tough again.

(Stevan Harnad and Alma Swan have both reported that Arthur Sale's ongoing study of institutional repositories in Australia corroborates these figures, showing that authors comply in much the same way that they claimed they would in the survey. What I've seen of Sale's data is certainly consistent with that notion... but more on that later perhaps.)

So, to recap:

1. The majority of journals for which information is readily available are already compliant with the new NIH mandate; I see no reason to assume that any significant proportion of the remainder will be hostile to the policy.

2. I disagree that the NIH will not be able to enforce the policy; faced with the evidence that OA is a good idea and the fait accompli of an NIH mandate, researchers will comply and journals will have to follow suit. To believe otherwise is, I think, to give the publishing industry too much credit for being able to cow their authors.

3. Voluntary reposit policies simply don't work; we have evidence to suggest that mandates will, and already do. (An aside: the new NIH policy joins 20 funder mandates, 11 institutional mandates, 3 departmental mandates, 5 proposed funder mandates, 1 proposed institutional mandate and 2 proposed multi-institutional mandates. Most of those include growth data in their ROARMAP entries. Why don't we have more data on the effects of mandates?)

Happily, I can finish up on a note of agreement with Rich, who says:

The only things that will change the status quo are: (1) the availability of tools for making it happen; and (2) the realization by individual investigators that continuing to give away their hard-earned copyright makes them far less competitive than their peers who don't.

Open Access proponents should forget about getting the Federal Government to fix the mess that modern scientific publication has become. Instead, they should focus on making Open Access-like options more attractive to scientists.

I've outlined my disagreements above, now let me agree with the more important points here:

1. It is vitally important that tools for OA (and Open Science) be built -- tools that researchers will want to use; to see a graphic illustration of this, listen to the forlorn cry of the repository-rat

2. OA provides a host of benefits, not least the boost to individual impact and standing; the clearer this becomes, the closer we get to 100% OA

3. Modern scientific publishing is a mess, and needs fixing. Making OA more attractive to the benchmonkeys is going to be an indispensible part of that fix (see also #1).

P.S. still on hiatus... sorta. Still haven't put that ms together so posting will remain infrequent at best.

P.P.S. see also Peter Murray-Rust's response to Rich's entry.

Another brief un-hiatus, this one sparked by a question asked by Dave Munger at BPR3:

If you know of a peer-reviewed, open-access journal that does not charge a publication fee, let us know about it in the comments.

Practically every time I talk about OA, online or in meatspace, I hear "I'd like to support OA but I can't afford it, don't all those journals charge, like, $2500 per article?"

No. They don't.

Everyone seems to be thinking of PLoS, never mind that they waive their fees at the drop of a hat; the assumption that most OA journals charge (high) author-side fees is both widespread and completely wrong.

In fact, more than 2/3 of the journals listed in the Directory of Open Access Journals (DOAJ) and more than 80% of OA journals published by scholarly societies charge no author-side fees at all; in contrast, more than 75% of the 247 non-DOAJ journals in a 2005 survey do charge author-side fees (page charges, colour charges, reprint charges, etc) in addition to subscription charges.

Let's unpack those numbers a little (especially since I generated the first one myself, and so you should take a look at how I did that).

In October 2005, the Kaufman-Wills group published a commissioned survey of journal publishing practices, The Facts about Open Access. The study was initially designed to include only full OA journals (listed in the DOAJ, OA immediately upon publication) and delayed-OA ("embargo") journals from the HighWire Press stable, but was expanded to include the full range of financial models by inclusion of journals published by the Association of Learned Professional and Scholarly Publishers (ALPSP) and the Association of American Medical Colleges (AAMC). The final report included responses from 248 DOAJ, 85 HighWire, 34 AAMC and 128 ALPSP journals and showed that:

52.8% of DOAJ journals charge no author-side fees at all. The percentage for subscription journals was much lower: ALPSP journals overall (23.4), ALPSP for-profit journals (44.9), ALPSP non-profit journals (10.1), AAMC journals (14.7), Highwire subset (17.6)

These are the figures that Kaufman and Wills summarize as "...more than half of DOAJ journals did not charge author-side fees of any type, whereas more than 75% of ALPSP, AAMC, and HW subset journals did charge author-side fees."

So -- not only do the majority of OA journals charge nothing on the author side, an even larger majority of non-OA journals do charge author-side fees. If the sample is representative, you're less likely to have to pay to publish if you choose an OA journal than if you don't.

When I first heard these numbers I thought, as Peter Suber did, that they should "recast the debate" around OA. In January 2006 Peter's regular yearly predictions included this forecast:

It will start to sink in that fewer than half of OA journals charge author-side fees and that many more subscription-based journals do so than OA journals.... People will stop talking about "the OA business model" for journals as if there were just one. People will talk less about how OA journals might exclude indigent authors and compromise on peer review and talk more about how toll-access journals do so. We'll start to document the range of models actually in use for OA journals... We'll get more creative in finding models that suit the range of niches...

He has since called this "the worst prediction I've ever made". I confess myself at something of a loss as to why the Kaufman-Wills study has not come to dominate and reconfigure the OA debate; I can only guess that profit-hungry lowlifes have successfully sidestepped it. In this year's predictions, Peter expects more of the same:

Because both Hindawi and Medknow have both been profitable for more than year, you'd think that the fact of their success would start to sink in, with corresponding effects on attitudes toward the sustainability of OA journals and interest in their business models. But well-documented truths about OA tend to sink in very, very slowly, because they have to compete with myths, misinformation, and misunderstanding. With regret, I predict more of the same.

In 2005 the Kaufman-Wills Group discovered that the majority of OA journals charged no publication fees at all. In 2006 I predicted that that fact would start to sink in. I was dead wrong. The fact still hasn't sunk in, and I've learned my lesson.

Caroline Sutton and I discovered last month that the OA journals published by learned societies follow same pattern as OA journals overall: most of them charge no publication fees. But while 52.8% of OA journals overall use no-fee business models (from Kaufman-Wills, 2005), we found that 83% of society OA journals use no-fee business models, a significantly greater fraction. However, I'm not predicting that this fact will sink in any time soon. Likewise, we found 425 societies publishing 450 OA journals, a much larger number than the societies known to oppose OA policies. But neither am I predicting that this fact will sink in any time soon. We'll continue to hear the unargued claim that society publishers are intrinsically vulnerable to OA and predominantly opposed to it.

The Kaufman-Wills study is not the only one of its kind, either. As discussed in the quote above, just last month Peter Suber and Caroline Sutton of Co-Action Publishing released preliminary findings from their ongoing study of OA journals published by scholarly societies. They identified 468 societies which publish, between them, 450 full OA journals and 73 hybrid ("pay-for-OA") journals. Of the full OA journals, only 75 charge author-side fees -- meaning that more than 80% of society journals do not charge such fees.

Finally, there's me. All of the above got me to wondering what proportion of journals in the entire DOAJ database charge author-side fees (since Suber and Sutton showed that when the dataset was expanded, at least among society publishers, the no-fee percentage went up considerably).

Fortunately, the DOAJ now includes a metadata field indicating whether or not a particular journal charges author-side publication fees. Unfortunately, that field is not included in the downloadable comma-delimited metadata file they make available. Fortunately, it's not a whole lot of work to make a replacement file by copy-and-pasting from the "browse by title" page. Unfortunately, you have to do this from the new "for authors" section, because the front-page browsing interface doesn't include the "fee/no fee" field. What's unfortunate about that, for my purposes (though it's a wonderful thing overall), is that the "for authors" browse does include hybrid journals, in which regular articles are subscription-only but authors can pay extra to have their work made OA. (In fact, even the logo at the top is different; on the front page you are seeing the Directory of Open Access Journals, but in the "for authors" section it becomes the Directory of Open Access and Hybrid Journals.) The front page says 2971 journals are indexed, but if you browse by title from the "for authors" page, the totals add up to 4638, the database having apparently added 1667 hybrid journals.

There's probably a smarter way to do this using the OAI-PMH, but that syntax is as impenetrable to me as Ancient High Martian, so I simply pasted the browse-by-title pages into a text document and imported that (colon-delimited) into Excel. Then I filtered on "publication fees", sorted by yes/no/missing and read off the totals from the row numbers. Horrible hack, but it worked.

Including hybrid journals, we get:

charge publication fees: 2185 (47%)
don't charge pub fees: 1998 (43%)
fee information missing: 455 (10%)
total no. of journals: 4638

Given the DOAJ definition of hybrid journal, those should obviously be excluded and the data reworked. This is where a smart person would have stopped and waited for the DOAJ to autogenerate the numbers, but I went ahead and deleted the hybrid entries by hand. (Shut up. I wanted to know, OK?) That yields:

charge publication fees: 534 (18%)
don't charge pub fees: 1980 (67%)
fee information missing: 453 (15%)
total no. of journals: 2967

The second total should presumably be 2971 and it would make sense for the "missing" totals to be the same in both sets, so either there are some errors in the database or I made a couple myself. In either case the errors appear small and make no difference to the percentages, and anyway did I mention this kept me up to 4 am? Actually I suspect some inconsistencies in the database, because the front-page total does not update as quickly as the actual entries, and because there are in fact hybrid journals which don't charge fees (e.g. Emerald Engineering's model).

So now we have three studies (OK, two studies and one ungainly hack) showing that a (strong) majority of OA journals do not charge author-side fees, and one of those studies further showing that a strong majority of non-full-OA journals do in fact charge author-side in addition to subscription fees.

Now, can we please put to rest the myth/FUD/whatever that there is only one OA model, the author-side fees/PLoS model? While we're at it, let's have a few more closely related ideas go the way of the dodo: that OA journals discriminate against indigent authors (because they charge publication fees -- except that most of them don't); that OA journals will compromise on quality (in order to collect payment for manuscripts -- except that most of them don't); that if most journals went OA, universities would have to pay more in author-side fees (which, remember, most OA journals don't, but most non-OA journals do, charge) than they do now in subscription fees.

I swiped that list of candidates for memetic extinction from Peter Suber, and you should go read his full discussion, which offers a lot more detail, especially on that last point. Me, I'm going to take a nap and go back to my blog hiatus. But the next time you hear someone talk about the "cost" of publishing in OA journals, please point 'em here.

I'm not ending my blogging break, but I simply couldn't let this from Cameron Neylon pass by without comment:

The UK Engineering and Physical Sciences Research Council currently has a call out for proposals to fund 'Network Activities' in e-science. This seems like an opportunity to both publicise and support the 'Open Science' agenda so I am proposing to write a proposal to ask for ~£150-200k to fund workshops, meetings, and visits between different people and groups. The money could fund people to come to meetings (including from outside the UK and Europe) but could not be used to directly support research activities. The rationale for the proposal would be as follows.

• 'Open Science' has the potential to radically increase the efficiency and effectiveness of research world wide.
• The community is disparate and dispersed with many groups working on different approaches that do not currently interoperate - agreeing some interchange or tagging standards may enable significant progress
• Many of those driving the agenda are early career scientists including graduate students and postdocs who do not have independent travel funds and whose PI may not have resources to support attending meetings where this agenda is being developed
• There is significant interest from academics, some publishers, software and tool developers, and research funders in making more data freely available but limited concensus on how to take this forward and thus far an insufficient committment of resources to make this possible in practice

This is a terrific opportunity to move Open Science forward; as Cameron points out, existing efforts are scattered and perhaps the most important thing right now is to make connections among the community. The whole idea is that a community approach will be vastly more efficient than the existing hypercompetitive model! This funding could move Open Science into the big time by driving the creation and adoption of working standards, possibly even a BBB-style declaration, and by creating a seed network of cooperative scientists out of which mainstream Open Science could emerge.

Cameron writes, in a followup:

I've made a start with an outline on a GoogleDoc which can be viewed here. I have tried to set out some general headings and areas to be fleshed out and added a little text. This is early days but if anyone wishes to add anything then please feel free. I have given editing rights to all those people who have comments on the original post (as of around 9:30 pm GMT on Thursday 22 November) so they should now have editing rights. I have set the document so that those people with invitations can cascade them to others (I hope). I will continue to issue invitations to anyone who comments on the original post. No need to feel obliged to add anything  - I'm not asking you to write the grant for me - but if you feel so inclined then the assistance will be very welcome.

What I will request is from those who are interested is a short letter stating your current post/position/ambitions, your interest in 'Open Science' and why you would like to be involved in this network. Either email to me at C [dot] Neylon [at] rl.ac.uk or simply drop it in as a comment.

Please, if you have anything to offer, step up. And I cannot emphasize this too strongly: if you're at all interested, you do have something very valuable to offer: a letter of support, as described. It is vital that the powers-that-be (that is, the powers-that-fund) see real commitment to these ideas, from real people. The deadline loometh (next Tuesday), so don't put this off. Your letter doesn't have to be a literary masterpiece -- just stand up and be counted.

The bill to make the NIH OA policy mandatory instead of voluntary is in trouble: from the ATA via Peter Suber (with some editing by yours truly):

The Senate is currently considering the FY08 Labor-HHS Bill, which includes a provision (already approved by the House of Representatives and the full Senate Appropriations Committee), that directs the NIH to change its Public Access Policy so that participation is required (rather than requested) for researchers, and ensures free, timely public access to articles resulting from NIH-funded research. On Friday, Senator Inhofe (R-OK), filed two amendments (#3416 and #3417), which call for the language to either be stricken from the bill, or modified in a way that would gravely limit the policy's effectiveness.

Amendment #3416 would eliminate the provision altogether. Amendment #3417 is likely to be presented to your Senator as a compromise that "balances" the needs of the public and of publishers. In reality, the current language in the NIH public access provision accomplishes that goal. Passage of either amendment would seriously undermine access to this important public resource, and damage the community's ability to advance scientific research and discovery.

Please contact your Senators TODAY and urge them to vote NO on amendments #3416 and #3417. (Contact must be made before close of business on Monday, October 22).

Contact information and a tool to email your Senator are online [here]. No time to write? Call the U.S. Capitol switchboard at (202) 224-3121 to be patched through to your Senate office.

If you have written in support before, or when you do so today, please inform the Alliance for Taxpayer Access. Contact Jennifer McLennan through jennifer@arl.org or by fax at (202) 872-0884.

The ATA has provided a sample email, but I think they miss one important point: Inhofe's amendments are likely to be presented as compromises aimed at avoiding a presidential veto, and that is purely bullshit. (Note to self: find out how much money Inhofe gets from publishers.) Here's Peter Suber's extract from the White House Statement of Administration Policy:

The Administration strongly opposes S. 1710 because, in combination with the other FY 2008 appropriations bills, it includes an irresponsible and excessive level of spending and includes other objectionable provisions....

S. 1710 exceeds the President's request for programs funded in this bill by nearly $9 billion, part of the $22 billion increase above the President's request for FY 2008 appropriations. The Administration has asked that Congress demonstrate a path to live within the President's topline and cover the excess spending in this bill through reductions elsewhere, while ensuring the Department of Defense has the resources necessary to accomplish its mission. Because Congress has failed to demonstrate such a path, if S. 1710 were presented to the President, he would veto the bill.

The Administration strongly opposes provisions in this bill that overturn the President's policy regarding human embryonic stem cell research....

Public Access to Research Information. Provisions in the bill would require that manuscripts based on NIH-funded research be made available to the public within 12 months of publication. The Administration notes that NIH's current policy requesting the voluntary submission of manuscripts has only been in effect for 2 years, and the Administration believes there is opportunity to work with Congress to study the current policy and consider ways to encourage better participation. The Administration believes that any policy should balance the benefit of public access to taxpayer supported research against the possible impact that grant conditions could have on scientific research publishing, scientific peer review and on the United States' longstanding leadership in upholding strong standards of protection for intellectual property....

The Administration strongly opposes...the elimination of the longstanding definition of abstinence education that keeps these programs focused solely on abstinence....

Note that the real reason for the President's objection is the money he'd rather spend on his own priorities. The paragraph that deals directly with the NIH provision shows unsettling echoes of the PRISM propaganda but is really just waffle -- padding to make the list of objections look longer. In fact, as I noted earlier, the NIH estimates that it will cost about $3 million to implement the mandate -- not much of a dent in that $9 billion the President is complaining about. So, here's an alternative sample email, the one I just sent:

Dear Congresscritter,

I am a research scientist and about to become a US citizen. I have worked in the US for four years, having held an NIH T32 postdoctoral fellowship for two of those years. As a scientist and as a concerned member of the US public, I recently wrote to you in support of that portion of the Senate Appropriations Committee's FY 2008 Labor-HHS-Education appropriations bill (S.1710) which directs the NIH to change its policies from a request to a mandatory requirement for free, timely public access to NIH funded research. I have just learned of two last-minute amendments to this bill (#3416 and #3417) proposed by Sen Inhofe (R-OK). The first of these amendments would eliminate the relevant portion of the bill altogethe