Open Reading Frame

An Open Access partisan's view of "Electronic Publication and the Narrowing of Science and Scholarship"

Sat, 19 Jul 2008 16:34:22 -0800

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.

Lie down with pit bulls, wake up with a blogospheric flea in your ear.

Thu, 03 Jul 2008 01:40:46 -0800

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!

Calling all bioinformaticians...

Tue, 01 Jul 2008 17:08:05 -0800

Mike of Bioinformatics Zen is looking for information; please help him out if you can, by taking the survey either here or at BZ. Take particular note of the following:

The raw data entered into this questionnaire, along with any interpretation will be released into the public domain under a creative commons attribution license. If you are unhappy with answering any of the questions please leave them blank. By completing this questionnaire you consent to your answers being released.

(Yes, I know it's repeated at the top of the survey: it's important.)

OA and licensing: why not Public Domain?

Sun, 11 May 2008 20:51:41 -0800

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:

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.

Data are difficult.

Sat, 10 May 2008 13:35:06 -0800

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.

Everyone needs a hobby.

Sat, 19 Apr 2008 22:34:58 -0800

Mine, when I have time for it, is photography. I'll still post some photos, like the mouse below, to this blog; but now I have a separate blog for those images I would (if I weren't worried about sounding like a complete wanker) call "my art". The link is at the top of the new column at left, where I'll manually add thumbnails from that blog. It's at Expressions.com, because I haven't the time to make exactly what I want and of all the photoblogging services I tried, only Expressions gave me enough control over the format to make it (nearly) as simple as I wanted.

So. Fwiw, there it is. Hat tip, again, to Andrew and Ralf.

In which Gavin Baker finds one of my pet peeves

Mon, 14 Apr 2008 15:33:08 -0800

It really chafes my scrote when someone says something like this:

A comment to bloggers. I do my best to credit blog posts by the author's real name. However, if you blog under a psuedonym [sic] and don't make it easy to find your actual name, I may not. Unless you want me to attribute your writings to your silly Internet handle, you should include your name somewhere prominent (if not on every page, on the "About" or "Contact" page).

With all due respect, Mr Baker, it's not up to you where I should or shouldn't put my "real" name; plenty of people have damn good reasons for remaining anonymous online. Nor is it up to you to sneer at someone's "silly internet handle". Put the nick in quotes if you must, and move on. It's a name, it attaches to a person, and it matters -- at least it should matter -- a good deal less than the substance of whatever you're quoting.

I realise that netonyms have been passé among the hipsterati for some time now, and my impression is that it's a good thing, due mainly to being more comfortable online than crusty old luddites like me. Nonetheless, that you haven't been online long enough to have a nick that half your friends use instead of your "real" name is no reason the rest of us should subscribe to your particular view of how the internets should work. You can quote me on that -- you can even use my "real" name if you want.

Damn kids, get off my lawn, mutter grumble mutter mutter...

Term dilution; or, that phrase, you keep using it...

Sun, 13 Apr 2008 15:33:52 -0800

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.

reminder

Sun, 13 Apr 2008 12:58:53 -0800

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.

Good question.

Sat, 12 Apr 2008 23:08:27 -0800

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?

Removal of permission barriers is already part of the definition of OA

Mon, 07 Apr 2008 22:40:54 -0800

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 B B B 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?

Rob's right; or, you say "deserter" like it's a bad thing.

Sun, 06 Apr 2008 11:25:35 -0800

Rob is absolutely correct: anyone who lays down arms and refuses to kill on command is a hero. I don't give a rat's arse which "side" they're on.

Rob's also right in that you won't hear much about this in the "mainstream" media, and whatever you do hear will be propaganda -- which is why I'm pointing to his entry.

I know, I know -- politics is bad for me, not least because if I blog this there are quite literally a thousand other stories I should blog. But I'm not going to fall into that trap; I just wanted to say "Rob's right", because this particular story resonated with me. We now return to our usual semi-silence.

athymic mouse

Thu, 27 Mar 2008 20:20:56 -0800

Andy Michaels is a filthy spammer and I hope he spends eternity as the dingleberry closest to Satan's festering freckle.

Fri, 21 Mar 2008 16:08:01 -0800

Just got this bullshit trackback (on this totally unrelated entry):

I\'m pleased to announce the introduction of two products, the latest is the Ice Cold New Marketer Seminar Series for internet marketers who are just starting out and looking for solid counseling on tools, resources, and services without all the techni...

from this bullshit blog: http://andymichaelsblog.com/ (no Googlejuice for you, asshole).

Andy, you're a disease with opposable thumbs. You're a plague, a pox, a parasite on all that is good and useful. Other people are making the internet into the greatest library that ever was, a scholarly resource, a tool for science, a home for the arts, a conversation, a force for social change -- but you, you're out there shilling. And you're not even selling anything real, you're selling the idea of selling. You mammon-worshipping maggot. You're sucking down bandwidth and making all sorts of worthwhile endeavours more difficult by the day, just to push yourself into people's faces and scream "give me money". You are greed made flesh. You're the reason we have to have CAPTCHA and Bayesian spam filters and blacklists. Blind unmitigated selfishness like yours is why we can't have nice things: it's people like you who piss in fountains and spraypaint inanities on grand buildings and carve their initials into ancient trees.

Andy, you're a soulless meat puppet with the red right hand of a sick, materialistic culture jammed forearm-deep in your pliant rectum. There just aren't enough curses in the world for you -- there aren't enough bad things I can hope will happen to you.

Andy, Bill Hicks has some advice for you.

aw, NUTs

Sun, 09 Mar 2008 18:40:06 -0800

I'm still spending pretty much every waking moment in the lab -- it's OK Mum, I'm having fun and taking care of myself! -- because I have some really neat results and want to send them out into the world asap. (I will do my best to persuade the boss to submit to an OA journal and to put a preprint in Nature Precedings, but no guarantees there.)

So, this entry is just to round up a couple of NUTs -- Nagging Unfinished Tasks.

NUT the first: 2008 Science Blogging Conference -- I never did get around to posting about it, but I have left comments on other people's entries saying most of what I had to say. Mostly, it was a blast and I wish I could have that kind of experience more often, as it really recharges my enthusiasm.

The one thing I meant to do, and didn't get around to, was pointing to the sponsors. I hate advertising, and was even a little put off by the "swag bags" given out at the conference (very much a minority opinion there) -- but sponsorship seems different to me. Provided the recipients do their bit, the sponsors can make a real contribution and raise their profile in a "target market" without having to spam anyone. So, I wanted to do my bit to promote those individuals, businesses and organizations who helped Anton, Bora & Co. to make the conference such a success: if you have a moment, click through to that link and check a few of 'em out.

I also want to highlight the contribution made by the Radisson Research Triangle Park, who weren't exactly sponsors but made a big difference to my stay. It's a very nice hotel, much swankier than my usual budget-driven choices, and they provided a special attendee rate for the conference weekend which made them the cheapest alternative within any reasonable distance of the conference. This was great, because they are in fact walking distance from the Sigma Xi Center where the conference was held, and quite a lot of the attendees took them up on their offer. This made transport easy to figure out, and the after-conference bar sessions lively and fun. I really like not worrying about transport to and from conference venues, and I really like being able to walk from the bar to my room after staying up way too late talking to interesting people, so thanks to the Radisson RTP for making my stay so enjoyable. If you're going to stay in NC, keep them in mind. On the right is a picture of my room there -- yup, two double beds all to myself, same cheap rate. (On the left is a DNA-inspired sculpture that hangs in the central stairwell of the Sigma Xi Center.)

NUT the second: Whatever happened to those letters I was thinking about sending? Well, in the end, I decided not to send them. The bottom line is that, as Peter Suber pointed out to me in email, it's a given that almost none of the recipients of such a letter would respond. I finally decided that such a predictably low response rate would reduce the exercise to little more than muck-raking, since no useful data would come of it. It would take a lot of work to find the appropriate contact person at each company and tailor the letters to their public position on OA, and in the end nobody would gain from it. I hope this is not a great disappointment to the few people who came forward to say they'd sign such letters -- if it is, let me know, and we can discuss possible ways to resurrect the idea or alternative ways to find out the same target information. It's not so much dead as buried under the weight of other, more pressing (and, I hope, more productive) commitments.