I’m off to the 2008 North Carolina Science Blogging Conference! I have to travel all day Friday and Sunday for a one-day conference on Saturday — and it’s well worth every dull airport-infested minute!
Last year’s was tremendous fun; I’m looking forward to an unbroken attendance record down the years. You can still add ideas to the conference wiki, join in virtually via chat room, and watch at least one of the sessions online.
Update: Bora has further details on how you can participate even if you’re not there in meatspace.

Mitch Waldrop on Science 2.0

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.)

Another clarification — actually a correction.

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.

They get letters. Maybe.

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]?
[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:


Quick clarification

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.

Does the AAP/PSP really represent its members?

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.

Changing views of science

I’m always a bit leery of edge.org, seeing as how it’s first and foremost a promotional vehicle for John Brockman’s stable of authors, but I do enjoy the Annual Question. This year’s is no exception:

When thinking changes your mind, that’s philosophy.
When God changes your mind, that’s faith.
When facts change your mind, that’s science.
Science is based on evidence. What happens when the data change? How have scientific findings or arguments changed your mind?”

What struck me about the answers was that a number of them point out, if indirectly, that the wording of the question is utter bollocks. Whoever wrote the question has drunk deep of the “impartial search for Truth” Kool-Aid and needs an infusion of Kuhn1 (or a week in an actual lab), stat.
Roger Highfield comes right out and says it:

I am a heretic. I have come to question the key assumption behind this survey: “When facts change your mind, that’s science.” This idea that science is an objective fact-driven pursuit is laudable, seductive and – alas – a mirage.
Science is a never-ending dialogue between theorists and experimenters. But people are central to that dialogue. And people ignore facts. They distort them or select the ones that suit their cause, depending on how they interpret their meaning. Or they don’t ask the right questions to obtain the relevant facts.

That science is nothing like the simplistic picture we were all fed in school seems to be something of a theme in the answers to this year’s Edge question:
Colin Tudge:

I have changed my mind about the omniscience and omnipotence of science. I now realize that science is strictly limited, and that it is extremely dangerous not to appreciate this.

Francesco de Pretis:

In two weeks I finished the book [that changed my mind] and then my way of thinking changed. I understood that science was not only a pursuit of knowledge but a social process too, with its rules and tricks: a never-ending tale such as human life.

Irene Pepperberg:

I’ve begun to rethink the way we teach students to engage in scientific research. I was trained, as a chemist, to use the classic scientific method: Devise a testable hypothesis, and then design an experiment to see if the hypothesis is correct or not. And I was told that this method is equally valid for the social sciences. I’ve changed my mind that this is the best way to do science. I have three reasons for this change of mind.
First, and probably most importantly, I’ve learned that one often needs simply to sit and observe and learn about one’s subject before even attempting to devise a testable hypothesis. […]
Second, I’ve learned that truly interesting questions really often can’t be reduced to a simple testable hypothesis, at least not without being somewhat absurd. […]
Third, I’ve learned that the scientific community’s emphasis on hypothesis-based research leads too many scientists to devise experiments to prove, rather than test, their hypotheses.

Robert Provine:

Mentors, paper referees and grant reviewers have warned me on occasion about scientific “fishing expeditions,” the conduct of empirical research that does not test a specific hypothesis or is not guided by theory. Such “blind empiricism” was said to be unscientific, to waste time and produce useless data. Although I have never been completely convinced of the hazards of fishing, I now reject them outright, with a few reservations.
I’m not advocating the collection of random facts, but the use of broad-based descriptive studies to learn what to study and how to study it. Those who fish learn where the fish are, their species, number and habits. Without the guidance of preliminary descriptive studies, hypothesis testing can be inefficient and misguided. Hypothesis testing is a powerful means of rejecting error — of trimming the dead limbs from the scientific tree — but it does not generate hypotheses or signify which are worthy of test.

Robert Shapiro:

I used to view the scientific literature as a collective human effort to build an enduring and expanding structure of knowledge. Each new publication in a respected, refereed journal would be digested and debated… [b]ut once it has passed scrutiny, a new contribution would be absorbed into the edifice of science, expanding and enhancing it, while providing a fragment of immortality to the authors.
My perception was wrong. New scientific ideas can be smothered with silence.

Steve Nadis:

At its heart, science is a human endeavor, carried out by people. When the questions are truly ambitious, it takes a great personal commitment to make any headway — a big investment in energy and in emotion as well. I know from having met with many of the lead researchers that the debates can get heated, sometimes uncomfortably so. More importantly, when you’re engaged in an epic struggle like this — trying, for instance, to put together a theory of broad sweep — it may be difficult, if not impossible, to keep an “open mind” because you may be well beyond that stage, having long since cast your lot with a particular line of reasoning. And after making an investment over the course of many years, it’s natural to want to protect it.

A. Garrett Lisi:

…the ambivalence associated with an even probability distribution makes it terribly difficult for an ideal scientist to decide where to go for dinner. […]

Ken Ford:

I used to believe that the ethos of science, the very nature of science, guaranteed the ethical behavior of its practitioners. As a student and a young researcher, I could not conceive of cheating, claiming credit for the work of others, or fabricating data. Among my mentors and my colleagues, I saw no evidence that anyone else believed otherwise. And I didn’t know enough of the history of my own subject to be aware of ethical lapses by earlier scientists. There was, I sensed, a wonderful purity to science. Looking back, I have to count naiveté as among my virtues as a scientist.
Now I have changed my mind, and I have changed it because of evidence, which is what we scientists are supposed to do. Various examples of cheating, some of them quite serious, have come to light in the last few decades, and misbehaviors in earlier times have been reported as well. Scientists are, as the saying goes, “only human,” which, in my opinion, is neither an excuse nor an adequate explanation.

Rebecca Goldstein:

Popper’s characterization of how science is practiced –as a cycle of conjecture and refutation — bears little relation to what goes on in the labs and journals.

1 Yes, I read SSR fairly recently, and it gave me a clear structure for a lot of vague suspicions I’d been entertaining since grad school. I suspect I’m doing that “ooh, philosophy of science, yeah, I read Kuhn” thing that probably drives real philosophers of science bugfuck. By way of mitigation, the latter are invited to recommend further reading.

Public Domain Day

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.