a bit more on PRISM

If you haven’t already, go read Peter Suber’s initial response — it is, as always, clear, calm, comprehensive and compelling. (I hope to meet Peter one day; I imagine him as a kind of unflappable, scholarly James Bond…) This is your one-stop anti-PRISM shop for the time being: if you read nothing else, read this; and whenever PRISM rears its ugly head, make sure Peter’s response gets an airing too.
Peter has also responded to a Publisher’s Weekly article that simply repeats the PRISM propaganda. The by-line is Rachel Deahl, a senior news editor at PW. I wrote to her, as follows:

Dear Ms Deahl,
I write in response to your recent brief article in Publishers Weekly (“AAP Tries to Keep Government Out of Science Publishing”, August 23, 2007), in which you quote or repeat several egregious errors of fact which are being propagated by the newly formed anti-Open Access disinformation factory, PRISM.
Briefly, there is no aspect of the Open Access publishing model which would force anyone to “turn over” anything to the government, nor will OA publishing damage peer review in any way. For a detailed and authoritative response to the PRISM campaign, I refer you to Peter Suber, Professor of Philosophy at Earlham College, on his weblog Open Access News:
In your article, you quoted PRISM and AAP members, but gave no space to the opposing point of view, which is simply that taxpayers should get what they have paid for: the results of the research they fund, and maximally efficient use of those results by the researchers whose salaries they also pay. I hope you will follow your initial report with a more balanced article that includes interviews with Open Access experts and advocates. In case it is of use in your research, I include here, in no particular order, a brief list of potential interviewees:
Peter Suber, as above (contact)
Paul Ginsparg, founder of arXiv (contact)
Barbara Cohen, Executive Editor, Public Library of Science (contact)
Mark Patterson, Director of Publishing, Public Library of Science (contact)
Matthew Cockerill, Publisher, BioMed Central (contact)
Finally, I should point out that I have also published this letter on my own weblog, and you are of course welcome to respond there (www.sennoma.net) at any time.
Best wishes,

I’m not sure whether this will do any good — William Walsh has pointed out that Publisher’s Weekly is owned, once removed, by Reed Elsevier, noted price-gougers and employers of the notorious Publisher’s Pitbull, so Ms Deahl’s options may be limited by her bosses. This is also a good place to point out that if you write to her, being a jerk about it will not only be pointless and stupid but will in fact damage the OA cause. (That should go without saying but these things do tend to get out of hand when emotions run high and email allows one to send in haste and repent at leisure…)

PRISM = Publishers Relying on Insidious Subversion Methods

From Peter Suber:

The AAP/PSP has launched PRISM (Partnership for Research Integrity in Science & Medicine).  I’m quoting today’s press release in its entirety so that I can respond to it at length:

A new initiative was announced today to bring together like minded scholarly societies, publishers, researchers and other professionals in an effort to safeguard the scientific and medical peer-review process and educate the public about the risks of proposed government interference with the scholarly communication process.
[much egregious lying]
Anyone who wishes to sign on to the PRISM Principles may do so on the site.

Fortunately for us all, Peter has already responded; I won’t excerpt his point-by-point rebuttal here, you should go read it all.
This is disgusting. This runs counter to everything that science, academia, scholarship (and scholarly publishing!) stand for.
There are no names on the PRISM site yet — but I’m going to find as many as I can and publish them here. Sunlight is the best disinfectant, and I want to know just who is taking part in this revolting effort to steal from the commons and turn public goods into private profit.
(We can start with the AAP: their members page is essentially one long list of companies and organizations with whom I will assiduously avoid doing business until and unless they dissociate themselves from PRISM, and preferably from the AAP altogether.)
More later. Oh yes indeedy.

Another note on terminology.

In a comment on one of my 3QuarksDaily columns about Open Access/Open Science, Matthias Röder points out that there are more kinds of research than scientific:

One thing that might be worth thinking about is the fact that Open Science is a term that excludes many projects in the humanities and social sciences. I think Open Research might be a good alternative.

By way of illustration he points to a wikipedia entry on Open Research, which in turn points to a number of Open projects, including SCRIBE, with which Matthias is involved:

  1. SCRIBE is an open and peer-reviewed database with information on music copyists and samples of their handwriting.
  2. SCRIBE is a software tool for searching music manuscripts by handwriting characteristics.

He’s got a point. I don’t mean to be exclusionary, and am happy to accept Open Research as an umbrella term, a higher level taxon of which Open Science and Open Anything Else are subgroups.
That said, there’s also no reason not to use the phylum name when you don’t mean to speak for the entire kingdom. I don’t know much about research outside of science; I’ve posted a little about it, but haven’t looked into it with nearly the obsessive care with which I follow developments in Open Science. I’m a scientist; my focus is on science.
I’m happy to learn about efforts towards openness in other fields, of course, but I hope no one is surprised or offended to hear that I’ll be thinking “how can we use this for science?” the whole time. So for now, I will continue to talk about “Open Science”, and I hope that researchers from other fields will not feel excluded but will instead simply look to see whether anything I’m saying is of use in Open Whatever-It-Is-That-They-Do.

sic transit gloria mission statements…

nature.jpgNature recently published an editorial in which they discussed an update to their 1869 (!) mission statement. The editorial is subscription-only, but Maxine published an excerpt on Nautilus, which I further excerpt here:

The original mission statement of this journal, first printed in Nature’s second issue on 11 November 1869, was… running behind the times when it referred to “Scientific men” … In other respects it is well worded — which is why we print it every week in the Table of Contents.
In printing the statement verbatim every week as we have done, making it clear when it originated, we have hitherto assumed that readers will excuse the wording in the interests of historical integrity. But feedback from readers of both sexes indicates that the phrase, even when cited as a product of its time, causes displeasure. Such signals have been occasional but persistent, and a response is required.
There is a convention within the English language by which writers quoting text can indicate their view that a particular phrase is inappropriate. That is to insert sic, a Latin word meaning ‘thus’, after the phrase — in effect expressing the sentiment ‘alas, dear reader, this is what was said’.
This is what we will do in the mission statement from now on. The small, belated change takes place against the vast backdrop of a scientific world where the upper echelons of academia, academies and prestigious awards are still numerically greatly dominated by men, and where outright discrimination can still rear its ugly head… In this context, the insertion of a Latin word in a couple of paragraphs may be a tiny step: but it is at least one in the right direction.

Zuska took offence, and I was a bit puzzled myself so I went and asked Maxine to clarify:

This decision puzzles me. Why not simply change the wording (s/’Scientific men’/scientists) and say “we’ve updated the statement to better reflect our modern aims”?
Mission statements that date to 1869 are pretty damn cool, I’ll grant you — but it seems that here tradition is trumping concerns (which NPG obviously shares!) about inclusive language. Why take a “tiny step… in the right direction” when the whole step is so easy to take instead?

Maxine’s response:

We did update our mission statement years ago, and I’ve added a link to the newer version (on the “about the journal” page in my post above, in light of your comment.
What the Editorial said was that the “original” mission statement would contain this correction, on any future occasions where we reprint it. It did not mean to imply that we had not updated our mission statement since 1869.

So that makes more sense; but as Zuska points out, there is some confusion over which statement is going to appear where. So, being a scientist — we learn by doing — I went and looked.
Online: I started by typing in www.nature.com and looked around the page for some kind of “about Nature” resource. The first thing I found was About NPG under “Information” at the bottom of the page — since I was actually at the Nature Publishing Group homepage, Nature the journal being actually at www.nature.com/nature.
On the About NPG page, under “Browse”, “Company Information”, there’s a link to mission, whereat we find the original in all its sexist glory.
From www.nature.com/nature (the journal itself), the obvious place to look is the About the journal link, which goes to the modern mission statement and includes a clearly labeled link to the same 1869 version as “mission” above.
In meatspace: I went to our little library here at work and picked up a physical copy of Nature for the first time in probably ten years. (Full disclosure, or something: it was the chimp genome issue, vol 437 issue 7055, Sept 2005.) The first five pages are full-page ads, and then comes the table of contents. In a sidebar on the left hand side is the following quote from the original mission statemtent, under the heading “NATURE’S MISSION, 1869:”; I’ve used a scan of the sidebar as a sort of sidebar for this entry. Note that this is not quite the same as, but not substantively different from, the online version.
So now at least I know what it is that I disagree with. I don’t think NPG should link to the 1869 statement, at least not without going through the modern version, as Nature (the journal site) does. I think the print journal should print the modern mission statement — with, if they want a nod to their impressive history, a comment to the effect that apart from updating sexist and exclusive language, not much has changed from the original (which is visible on our website, etc etc).

What do we mean by open science?

(Addressed in absentia to “Tools for Open Science”, Second Life, Aug 20 2007.  I am sorry I could not be there.)

I think we all know what we want, and I think we all want much the same thing, which boils down to just this: cooperation.  A way forward for science, a way out of the spiralling inefficiency of patent thickets, secret experiments and dog-eat-dog competition.  But we use a variety of terms, and probably mean slightly different things even when we use the same terms.  It might — I am not sure — be useful at this point to come together on an agreed definition for an agreed term or set of terms  — something equivalent to the Berlin/Bethesda/Budapest Open Access Declarations.

If this does not seem like a “tool for open science”, consider what the BBB definition has done for Open Access.  It provides cohesion, a point of reference and a standard introduction for newcomers, and acts as a nucleation center for an effective movement with clear and agreed goals.  Since this SL session takes off from SciFoo, and SciFoo is by all accounts very good at converting brainstorming sessions into practical outcomes, I thought perhaps the idea of a definition or declaration of Open Science might be a suitable topic.  In what I hope is the spirit of SciFoo, here are some ideas that might be useful in such a discussion.


Whatever this thing is, what should we call it?  There are a number of terms in use:

  • Open Science — has the weight of Creative Commons/Science Commons behind it, via iCommons
  • Open Source Science — Jamais Cascio, Chemists Without Borders
  • Open Source Biology — Molecular Biosciences Institute
  • I think “biology” too narrow — there seems little point in Open Chemistry, Open Microbiology, Open Foo all having different names.  I think Open Source Foo too likely to lead to confusion with software initiatives, and too likely to lead to pointless arguments about what the “source code” is.
  • That leaves Open Science, which would be my choice for an umbrella term.  A case can be made, though, for Open Research, on the same basis on which I argue against Open Biology etc — see this comment from Matthias Röder
  • Another “inclusive” possibility is to focus on information — Open Data, as per PMR’s wikipedia entry, or the broader Open Content.  In the same vein, the Open Knowledge Foundation provides a fairly comprehensive definition of Open Knowledge.
  • I have seen “Science 2.0” around quite a bit lately, though it’s a bit too marketing-speak for my taste
  • Open Notebook Science is a very specific subset of Open Science: if your notebook is open to the world, there’s not much confusion about access barriers!  It even comes with its own motto: “no insider information”.  This is as Open as Open gets.

Sources and Models

We don’t have to re-invent the wheel:


We don’t want to start a cult, and we don’t want to bog anyone down in semantics.  There’s no purity test or loyalty oath.  My own view is that Open Science (or whatever we end up calling it) is not an ideology but an hypothesis: that openly shared, collaborative research models will prove more productive than the highly competitive “standard model” under which we now operate. 

Openness in scientific research covers a range of practices, from tentative explorations with a single small side-project all the way to Open Notebook Science á la Jean-Claude, and we should welcome every step away from the current hypercompetitive model.  Open Notebook Science provides a useful marker for the Open end of the spectrum; perhaps all a Declaration need do is identify the minimum requirements that mark the other end of the spectrum?


What standards must a research project or programme meet in order to be considered Open?

  • obvious: Open Access publication
  • equally crucial: Open Data, that is, raw data as freely available (inc
    luding machine access) as OA text
  • probably indispensable: Open Licensing so as to avoid confusion as to what is truly available and for what purposes; as per Peters Suber and Murray-Rust, this must be
    • explicit
    • conspicuous
    • machine-readable
  • Open Semantics: perhaps none of this will be much good without metadata and standards to allow interoperability and free flow of information
  • desirable: Free/Open Source Software
  • David Wiley: “four Rs” of Open Content (cf. Stallman’s four fundamental freedoms for software):
    • 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
  • OKF definition of Open Knowledge

inspiration series: Jacob Collins

untitled? landscape by Jacob CollinsI sometimes take photographs and write about things that aren’t Open Science, and although I am trying to do something somehow meaningful — and I even think I’m getting better at it — I have a very hard time saying just what that “meaning” might be.
I’m going to start collecting pictures and words that either resonate with me and whatever it is I’m trying to say with my own pictures and words — or that annoy me into talking about it. In the latter category, here’s Jacob Collins, from an article in Columbia Magazine (thanks, Abbas):

I always wanted to do two things: to be skillful and to make beautiful art. I never had any confusion. Not that I am so skillful. I’ve been looking at Holbein drawings, Diego Velásquez portraits, and ancient Greek sculptures my whole cogent life, and you can’t look at those things and really feel good about yourself. The other thing that interests me is to make things beautiful. Often, when you’re in art school you get people saying, ‘Sure, this is pretty, but let me see what your ideas are.’ When I was a kid I didn’t know why that bothered me, but later I realized that it’s based upon the fallacy that beauty isn’t an idea. Beauty is a set of ideas, it is vastly complicated, and to understand whether something is beautiful, you’re using anthropology and psychology, and culture and nature, and even biology. You have to understand what ‘beauty’ is to know why you think something is beautiful.

Foses, Jacob Collins 2003I have nothing against classicism or realism, but if the galleries on his site are anything to go by I don’t care for most of Collins’ work. I find it somehow — pedestrian; more conventional than classical. (I liked Maureen Mullarkey’s description of Collins’ nudes: “McNudes for the carriage trade… fastidious erotica to go with the Jado bidet and high-thread-count linens from Yves Delorme.”) I don’t know whether that bit about not feeling good about himself is false or real modesty, but take a look at his drawings. Lack of skill is not the problem, even if he’s right and doesn’t compare to the transcendent examples he chose. A large part of my reaction to Collins is his choice of subject — I like him best when he applies his “high art” methods to quotidian objects, or when he gets out of the way and lets a portrait speak for itself. I like him least when he is rehashing ideas of beauty that have been imitated so much that they have become stale.
I originally started writing this as the other kind of inspiration piece, on the basis of the quoted comments above. I like Collins’ idea that beauty is sufficient as an end, that it is a complex statement in and of itself. I just disagree with him on the particulars of which things are, in fact, beautiful. If there’s any point to saying more about art than “I like/don’t like that”, then I think Collins’ rather impersonal portrayals of rather standard subject choices must qualify only as pretty — decorative — and not really beautiful.
So, in writing this out, I find at least one thing I’m trying to do with what, if I were not intensely self-conscious about it, I would call “my art”: I want to make beautiful things, and I want to understand why they are beautiful to me. But that’s hardly satisfactory, being so broad a comment that it probably applies to anyone who makes anything. I’ll keep trying.
(Hat-tips: Andrew Walkingshaw, whose recent musings on creativity and compartmentalisation struck a chord with me; and my old friend Ralf, who always takes “my art” just seriously enough.)

Yale vs. BMC

Yale science Libraries have stopped paying the article processing charges for Yale faculty who publish in BioMed Central journals. Yale says:

Starting with 2005, BioMed Central article charges cost the libraries $4,658, comparable to single biomedicine journal subscription. The cost of article charges for 2006 then jumped to $31,625. The article charges have continued to soar in 2007 with the libraries charged $29,635 through June2007, with $34,965 in potential additional article charges in submission.

BMC responds:

The main concern expressed in the library’s announcement is that the amount payable to cover the cost of publications by Yale researchers in BioMed Central’s journals has increased significantly, year on year. Looking at the rapid growth of BioMed Central’s journals, it is not difficult to see why that is the case. BioMed Central’s success means that more and more researchers (from Yale and elsewhere) are submitting to our journals each year. […]
An increase in the number of open access articles being submitted and going onto be published does lead to an increase in the total cost of the open access publishing service provided by BioMed Central, but the cost per article published in BioMed Central’s journals represents excellent value compared to other publishers.

The increased cost arises because Yale researchers are submitting more and more work to BMC journals.  More manuscripts = higher costs, but if the cost per article has not gone up, then BMC’s model scales effectively.  Here are some other ways to look at the numbers:

  • For around $65K, Yale gets about 40 articles published OA, that is,available free to everyone everywhere forever, plus a “subscription” (that is, Open Access, like everyone else) to 179 journals.  Theaverage biomed journal subscription is around $1000-1500/yr; choosing the lower figure to be conservative, those subscription-equivalents are worth $179K/yr.  Even if Yale only wanted to subscribe to around a third of the BMC journals, that would still cost about the same as the OA charges –and this comparison ignores the page, color and miscellaneous charges that many journals levy.  (An example: PNAS charges $70 per printed page, plus $325 for each color figure or table; $150 for each replacement or deletion of a color figure or table.)
  • Yale could publish those 40 articles elsewhere without paying anything (again, ignoring page etc. charges).  Assuming they don’t subscribe to any of the journals they publish in, though, every time any Yale employee wants to read one of those articles they’re on the hook for somewhere around $30; so it only takes 2166 person-articles, or an average of about 50 employees wanting to read each article, to get back to $65K — without the benefit of OA.
  • Yale spent about $7.7 million on subscriptions in 2005-6; converted to OA author-side charges at $1600/article, that’s about 4800 articles.  A PubMed search on “Yale” gives 2272 hits; “Yale in title/abstract” gives 131, leaving 2141 papers where “Yale” is probably in an author’s address.  I can’t find a quick way to break out Yale’s subscription expenditure by field, so what proportion of the $7.7mil goes to biomed journals I couldn’t say (though STM titles are the most expensive subscriptions for any academic library). If PubMed-indexed journals make up 44% (2141/4800) of Yale’s subscription costs, which does not seem unlikely, then they’re already paying $1600/article — without the benefit of OA.

A quick fiddle with biology + medicine data from theJournal Cost-Effectiveness database gives an average price per article of around $12 for toll-access journals, but that’s (one subscription)/(total no. articles).  The question is, how many subscriptions do they sell — that is, what is their income/article?  We know what BMC makes per article: about $1600 on average.  If an average toll-access journal sells just 135 subscriptions per year, they’re bringing in more per article than BMC.

There’s more, but that’ll do for now.  Two questions arising:

1. what’s the average page/colour/misc charge levied by toll-access journals?
2. how many subscriptions does an average journal sell each year?

An appendix of sorts: the BMC cost structure

Article Processing Charges

standard charge = $1600 (129 journals)

alternative charges: $2410 (2 journals)
$2310 (1 journal)
$2170 (1 journal)
$2010 (2 journals)
$1710 (1 journal)
$1970 (2 journals)
$1910 (4 journals)
$1810 (2 journals)
$1710 (5 journals)
$1505 (11 journals)
$1455 (1 journal)
$1305 (5 journals)
$1205 (2 journals)
$1005 (2 journals)
$805 (1 journal)
$725 (2 journals)
$500 (1 journal)
no charge (5 journals)

Supporter’s Membership

Supporter Members pay a flat rate annual Membership fee based on the number of biology, chemistry, physics and medical researchers and graduate students at the institution. Members of the institution are then given a 15% discount on the APC when publishing in our journals.

So if this fee is to be less than 15% of total APC, total APC must be at least the figure in column 3.  Since the average is likely to be close to $1600/article, dividing through gives the number of articles in column 4.

Postpay Membership

…group members are invoiced in arrears for articles authored by their members that have published in our journals since the last invoice date. Invoice schedules are set on a monthly or quarterly cycle.

Prepay Membership

…enables an organization to cover the whole cost of publishing for their investigators when publishing in our open access journals. No additional fees will be paid by individual authors. This is an advance payment system whereby customers pay upfront for accepted articles authored by their investigators to be processed and published. Upon publication, the full Article-Processing-Charge (APC) for the journal in question, minus a loyalty discount, will be deducted from the account.

The higher the amount paid in advance, the greater the loyalty discount given on each APC.

No numbers seem to be available for the “loyalty discount”.

brief idea/question

This reminded me of the famous psych experiments conducted by Milgram and Zimbardo, about which every thinking person spends some time wondering and which are more on the public mind than ever since Abu Ghraib. For some reason, this time it occurred to me, as it has not previously, that I’d like to hear from the subjects themselves. I found this account of the Milgram experiment by a participant, but nothing else like it. Does anyone know where I could find more such accounts?

Very small institution (21-500 faculty and postgraduate students in biology, chemistry and medicine) $1994 $13293 8.3
Small institution (501-1500 faculty etc.) $3987 $26580 16.6
Medium size institution (1501-2500 faculty etc.) $5980 $39867 24.9
Large institution (2501-5000 faculty etc.) $7974 $53160 33.2
Very large institution (5001-10000 faculty etc. $9967 $66447 41.5