Somehow this seems to have slipped under the radar: National Science Foundation announces plan for comprehensive public access to research results. They put it up on 18 March, two whole months ago, so our apologies for not having said anything until now!

This is the NSF’s rather belated response to the OSTP memo on Open Access, back in January 2013. This memo required all Federal agencies that spend $100 million in research and development each year to develop OA policies, broadly in line with the existing one of the NIH which gave us PubMed Central. Various agencies have been turning up with policies, but for those of us in palaeo, the NSF’s the big one — I imagine it funds more palaeo research than all the others put together.

So far, so awesome. But what exactly is the new policy? The press release says papers must “be deposited in a public access compliant repository and be available for download, reading and analysis within one year of publication”, but says nothing about what repository should be used. It’s lamentable that a full year’s embargo has been allowed, but at least the publishers’ CHORUS land-grab hasn’t been allowed to hobble the whole thing.

There’s a bit more detail here, but again it’s oddly coy about where the open-access works will be placed: it just says they must be “deposited in a public access compliant repository designated by NSF”. The executive summary of the actual plan also refers only to “a designated repository”

Only in the full 31-page plan itself does the detail emerge. From page 5:

In the initial implementation, NSF has identified the Department of Energy’s PAGES (Public Access Gateway for Energy and Science) system as its designated repository and will require NSF-funded authors to upload a copy of their journal articles or juried conference paper to the DOE PAGES repository in the PDF/A format, an open, non-proprietary standard (ISO 19005-1:2005). Either the final accepted version or the version of record may be submitted. NSF’s award terms already require authors to make available copies of publications to the Cognizant Program Officers as part of the current reporting requirements. As described more fully in Sections 7.8 and 8.2, NSF will extend the current reporting system to enable automated compliance.

Future expansions, described in Section 7.3.1, may provide additional repository services. The capabilities offered by the PAGES system may also be augmented by services offered by third parties.

So what is good and bad about this?

Good. It makes sense to me that they’re re-using an existing system rather than wasting resources and increasing fragmentation by building one of their own.

Bad. It’s a real shame that they mandate the use of PDF, “the hamburger that we want to turn back into a cow”. It’s a terrible format for automated analysis, greatly inferior to the JATS XML format used by PubMed Central. I don’t understand this decision at all.

Then on page 9:

In the initial implementation, NSF has identified the DOE PAGES system to support managing journal articles and juried conference papers. In the future, NSF may add additional partners and repository services in a federated system.

I’m not sure where this points. In an ideal world, it would mean some kind of unifying structure between PAGES and PubMed Central and whatever other repositories the various agencies decide to use.

Anyone else have thoughts?

Update from Peter Suber, later that day

Over on Google+, Peter Suber comments on this post. With his permission, I reproduce his observations here:

My short take on the policy’s weaknesses:

  • will use Dept of Energy PAGES, which at least for DOE is a dark archive pointing to live versions at publisher web sites
  • plans to use CHORUS (p. 13) in addition to DOE PAGES
  • requires PDF
  • silent on open licensing
  • only mentions reuse for data (pp. v, 18), not articles, and only says it will explore reuse
  • silent on reuse for articles even tho it has a license (p. 10) authorizing reuse
  • silent on the timing of deposits

I agree with you that a 12 month embargo is too long. But that’s the White House recommended default. So I blame the White House for this, not NSF.

To be more precise, PAGES favors publisher-controlled OA in one way, and CHORUS does it in another way. Both decisions show the effect of publisher lobbying on the NSF, and its preference for OA editions hosted by publishers, not OA editions hosted by sites independent of publishers.

So all in all, the NSF policy is much less impressive than I’d initially thought and hoped.

Matt drew my attention to an old paper I’d not seen before: Riggs (1903) on the vertebral column of Brontosaurus. The page I linked there shows only the first page (which in fact is half a page, since Riggs’ work is only in the right column).

Why only the first page? As Matt put it, “It’s been 110 years, just give us the PDF already. And they wonder (do they wonder?) why people don’t rush to embrace their stumbling broken halting limping steps toward OA.”

That’s exactly right. AAAS allows anyone to read the old Science papers anyway (good for them, as far as it goes), so why all the poxing about with registration? Just make it actual open access, as if you were good guys.

So, two observations, as promised.

First, here’s Matt’s observation: even making users register betrays a way of thinking wrongly about the material. It says, “This is ours but you can see it if you’ll jump through our hoops. Because it is ours.” Whereas real OA outlets say, “Hey, this is yours now, do what you want.”

And here’s mine: I sometimes wonder whether we’re headed for a world where the meaningful scientific literature is going to be from 1660-1923 and from 2010 onwards, with a big gap from 1924 to 2009 that just gets ignored. Because it’s the literature not old enough to be out of copyright but not new enough to be OA.

fat-necked-apatosaurs-make-the-world-go-round

The first hypothesis is that, contra Elk (1972), all Brontosauruses were rather fat at one end, then much fatter in the middle, then thin at the other end.

The second theory is that Diplodocus was dumb. Evidence is here presented in the form of an important new life restoration by Matthew Taylor.

derpolodocus

References

  • Elk, Anne. 1972. Anne Elk’s Theory on Brontosauruses. Reprinted in: Chapman, G., Cleese, J., Gilliam, T., Idle, E., Jones, T. and Palin, M. (eds). Just the Words, Volume 2. Methuen, London, 118-120.

AMNH 460 skeleton model 2

In a recent post I showed some photos of the mounted apatosaurine at the American Museum of Natural History in New York, AMNH 460, which Tschopp et al. (2015) regarded as an indeterminate apatosaurine pending further study.

A lot of museums whose collections and exhibits go back to the late 19th and early 20th centuries have scale model skeletons and sculptures that were used to guide exhibit design. I have always been fascinated by these models, partly because they’re windows into another era of scientific research and science communication, and partly because they’re just cool – basically the world’s best dinosaur toys – and I covet them. In my experience, it is very, very common to find these treasures of history buried in collections, stuck up on top of specimen cabinets, or otherwise relegated to some out-of-the-way corner where they won’t be in the way. I know that exhibit space is always limited, and these old models often reflect ideas about anatomy, posture, or behavior that we now know to be mistaken. But I am always secretly thrilled when I see these old models still on exhibit.

AMNH T rex skeleton model

The AMNH has a bunch of these things, because Henry Fairfield Osborn was crazy about ’em. He not only used 2D skeletal reconstructions and 3D model skeletons to guide exhibit design, he published on them – see for example his 1898 paper on models of extinct vertebrates, his 1913 paper on skeleton reconstructions of Tyrannosaurus, and his 1919 paper with Charles Mook on reconstructing Camarasaurus. That genre of scientific paper seems to have disappeared. I wonder if the time is right for a resurgence.

So in a glass case at the feet of AMNH 460 is a model – I’d guess about 1/12 or 1/15 scale – of that very skeleton. You can tell that it’s a model of that particular skeleton and not just some average apatosaur by looking carefully at the vertebrae. Apatosaurines weren’t all stamped from quite the same mold and the individual peculiarities of AMNH 460 are captured in the model. It’s an amazing piece of work.

AMNH 460 skeleton model

The only bad thing about it is that – like almost everything behind glass at the AMNH – it’s very difficult to photograph without getting a recursive hell of reflections. But at least it’s out where people can see and marvel at it.

Oh, and those are the cervical vertebrae of Barosaurus behind it – Mike and I spent more time trying to look and shoot past this model than we did looking at it. But that’s not the model’s fault, those Barosaurus cervicals are just ridiculously inaccessible.

So, memo to museums: at least some of us out here are nuts about your old dinosaur models, and where there’s room to put them on exhibit, they make us happy. They also give us views of the skeletons that we can’t get otherwise, so they serve a useful education and scientific purpose. More, please.

References

Osborn, H. F. (1898). Models of extinct vertebrates. Science, New Series, 7(192): 841-845.

Osborn, H.F. (1913). Tyrannosaurus, restoration and model of the skeleton. Bulletin of the American Museum of Natural History, 32: 91-92, plates 4-6.

Osborn, H. F., & Mook, C. C. (1919). Characters and restoration of the sauropod genus Camarasaurus Cope. From type material in the Cope Collection in the American Museum of Natural History. Proceedings of the American Philosophical Society, 58(6): 386-396.

In response to my post Copyright from the lens of reality and other rebuttals of his original post, Elseviers General Counsel Mark Seeley has provided a lengthy comment. Here’s my response (also posted as a comment on the original article, but I’m waiting for it to be moderated.)


 

Hi, Mark, thanks for engaging. You write:

With respect to the societal bargain, I would simply note that, in my view, the framers believed that by providing rights they would encourage creative works, and that this benefits society as a whole.

Here, at least, we are in complete agreement. Where we part company is that in my view the Eldred v. Ashcroft decision (essentially that copyright terms can be increased indefinitely) was a travesty of the original intent of copyright, and clearly intended for the benefit of copyright holders rather than that of society on general. (I further note in passing that those copyright holders are only rarely the creative people, but rights-holding corporations whose creative contribution is negligible.)

You continue:

[Journal] services and competencies need to be supported through a business model, however, and in the mixed economy that we have at the moment, this means that many journals will continue to need subscription and purchase models.

This is a circular argument. It comes down to “we use restrictive copyright on scholarly works at present, so we therefore need to continue to do so”. In fact, this this is not an argument at all, merely an assertion. If you want it to stick, you need to demonstrate that the present “mixed economy” is a good thing — something that is very far from evident.

The alternatives to a sound business model rooted in copyright are in my view unsustainable. I worry about government funding, patronage from foundations, or funding by selling t-shirts—I am not sure that these are viable, consistent or durable. Governments and foundations can change their priorities, for example.

If governments and foundations decide to stop funding research, we’re all screwed, and retention of copyright on the papers we’re no longer able to research and write will be the least of our problems. The reality is that virtually everyone in research is already dependent on governments and foundations for the 99% of their funding that covers all the work before the final step of publication. Taking the additional step of relying on those same sources for the last 1% of funding is eminently sensible.

On Creative Commons licences, I don’t think we have any material disagreement.

Now we come to the crucial question of copyright terms (already alluded to via Eldred v. Ashcroft above). You content:

Copyright law was most likely an important spur for the author or publisher to produce and distribute the work [that is now in the public domain] in the first place.

In principle, I agree — as of course did the framers of the US Constitution and other lawmakers that have passed copyright laws. But as you will well know, the US’s original copyright act of 1790, which stated its purpose as “encouragement of learning”, offered a term of 14 years, with an optional renewal of a further 14 years if the author was still alive at the end of the initial term. This 14-year was considered quite sufficient to incentivise the creation of new works. The intent of the present law seems to be that authors who have been dead for 70 years still need to receive royalties for their works, and in the absence of such royalties would not have created in the first place. This is self-evident nonsense. No author in the history of the world every said “I would have written a novel if I’d continued to receive royalties until 70 years after my death, but since royalties will only last 28 years I’m not going to bother”.

But — and this can’t be stated strongly enough — even if there were some justification for the present ridiculous copyright terms in the area of creative works, it would still say nothing whatsoever about the need to copyright scientific writing. No scientific researcher ever wrote a paper who would not have written it in the absence of copyright. That’s what we’re talking about here. One of the tragedies of copyright is that it’s been extruded from a domain where it has some legitimate purpose into a domain where it has none.

The Budapest Open Access Initiative said it best and most clearly: “the only role for copyright in this domain [scholarly research] should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited“. (And several of the BOAI signatories have expressed regret over even the controlling-integrity-of-the-work part of this.)


 

See also David Roberts’ response to Seeley’s posting.

AMNH 460 left anterolateral view

Apatosaurines on the brain right now.

I’ve been thinking about the question raised by Jerry Alpern, a volunteer tour guide at the AMNH, regarding the recent Tschopp et al. (2015) diplodocid phylogeny. Namely, if AMNH 460 is now an indeterminate apatosaurine, pending further study, what should the museum and its docents tell the public about it?

Geez, Apatosaurus, it’s not like we’re married!

I think it’s a genuinely hard problem because scientific and lay perspectives on facts and hypotheses often differ. If I say, “This animal is Apatosaurus“, that’s a fact if I’m talking about YPM 1860, the genoholotype of Apatosaurus ajax; it would continue to be a fact even if Apatosaurus was sunk into another genus (as Brontosaurus was for so long). We might call that specimen something else, but there would always be a footnote pointing out that it was still the holotype of A. ajax, even if the A. part was at least temporarily defunct – the scientific equivalent of a maiden name.* For every other specimen in the world, the statement, “This animal is Apatosaurus” is a hypothesis about relatedness, subject to further revision.

* This is going to sound kinda horrible, but when one partner in a marriage takes the other’s surname, that’s a nomenclatural hypothesis about the future of the relationship.

Apatosaurine cervicals are the best cervicals.

Apatosaurine cervicals are the best cervicals.

Fuzzy science

Things that look fairly solid and unchanging from a distance – specifically, from the perspective of the public – often (always?) turn out to be fairly fuzzy or even arbitrary upon closer inspection. Like what is Apatosaurus (beyond the holotype, I mean) – or indeed, what is a planet.** There is no absolute truth to quest for here, only categories and hypotheses that scientists have made up so that we can have constructive conversations about the crazy spectrum of possibilities that nature presents us. We try to ground those categories and hypotheses in evidence, but there will always be edge cases, and words will always break down if you push them too hard. Those of us who work on the ragged frontier of science tend to be fairly comfortable with these inescapable uncertainties, but I can understand why people might get frustrated when they just want to know what the damned dinosaur is called.

** Triton, the largest body orbiting Neptune, is almost certainly a captured Kuiper Belt object, and it’s bigger than Pluto. Moon or planet? Probably best to say a former dwarf planet currently operating as a satellite of Neptune – but that’s a mouthful (and a mindful, if you stop to think about it), not a short, convenient, easily-digestible label. Any short label is going to omit important information. This is related to the problem of paper title length – below some threshold, making something shorter means making it incomplete.

What I would say

I suppose the short version that is most faithful to the Tschopp et al. results is:

This skeleton (AMNH 460) might be Apatosaurus or Brontosaurus or a third, new thing – scientists aren’t sure yet.

A reasonable follow-up sentence – and an answer to the inevitable “Why not?” – would be:

They have to look at 477 anatomical details for lots of skeletons and weigh all the evidence, and that takes time.

Personally, if I was talking to museum visitors I would lean in conspiratorially and say:

If you want to call it Apatosaurus or Brontosaurus, go ahead – those are both ‘live’ hypotheses, and even the world’s experts on this problem can’t tell you that you’re guessing the wrong way – at least not yet.

And if there was a kid in the group, I’d add:

Maybe you’ll be the one to figure it out!

What would you say?

My neck is fat.

My neck is fat.

P.S. I wouldn’t change the signage. It could still turn out to be Apatosaurus, and the Tschopp et al. results do not lend themselves to easy label-ification.

P.P.S. With some modification for taxonomy, all of this applies to the Field Museum diplodocid FMNH P25112 as well.

Reference

Tschopp E, Mateus O, Benson RBJ. (2015) A specimen-level phylogenetic analysis and taxonomic revision of Diplodocidae (Dinosauria, Sauropoda) PeerJ3:e857 https://dx.doi.org/10.7717/peerj.857

This post is a response to Copyright from the lens of a lawyer (and poet), posted a couple of days ago by Elsevier’s General Counsel, Mark Seeley. Yes, I am a slave to SIWOTI syndrome. No, I shouldn’t be wasting my time responding to this. Yes, I ought to be working on that exciting new manuscript that we SV-POW!er Rangers have up and running. But but but … I can’t just let this go.

duty_calls

Copyright from the lens of a lawyer (and poet) is a defence of Elsevier’s practice of having copyright encumber scientific publishing. I tried to read it in the name of fairness. It didn’t go well. The very first sentence is wrong:

It is often said that copyright law is about a balance of interests and communities, creators and users, and ultimately society as a whole.

No. Copyright is not a balance between competing interests; it’s a bargain that society makes. We, the people, give up some rights in exchange for incentivising creative people to make new work, because that new work is of value to society. To quote the US constitution’s helpful clause, copyrights exist “To promote the Progress of Science and useful Arts” — not for authors, but for wider society. And certainly not of publishers who coerce authors to donate copyright!

(To be fair to Seeley, he did hedge by writing “It is often said that copyright law is about a balance”. That is technically true. It is often said; it’s just wrong.)

Well, that’s three paragraphs on the first sentence of Elsevier’s defence of copyright. I suppose I’d better move on.

The STM journal publishing sector is constantly adjusting to find the right balance between researcher needs and the journal business model, as refracted through copyright.

Wrong wrong wrong. We don’t look for a balance between researchers needs (i.e. science) and the journal business model. Journals are there to serve science. That’s what they’re for.

Then we have the quote from Mark Fischer:

I submit that society benefits when the best creative spirits can be full-time creators and not part-timers doing whatever else (other than writing, composing, painting, etc.) they have to do to pay the rent.

This may be true. But it is totally irrelevant to scholarly copyright. That should hardly need pointing out, but here it is for those hard of thinking. Scholars make no money from the copyright in the work they do, because (under the Elsevier model) they hand that copyright over to the publisher. Their living comes in the form of grants and salaries, not royalties.

Ready for the next one?

The alternatives to a copyright-based market for published works and other creative works are based on near-medieval concepts of patronage, government subsidy […]

Woah! Governments subsidising research and publication is “near-medieval”? And there we were thinking it was by far the most widespread model. Silly us. We were all near-medieval all this time.

Someone please tell me this is a joke.

Moving swiftly on …

Loud advocates for “copyright reform” suggest that the copyright industries have too much power […] My comparatively contrarian view is that this ignores the enormous creative efforts and societal benefits that arise from authoring and producing the original creative work in the first place: works that identify and enable key scientific discoveries, medical treatments, profound insights, and emotionally powerful narratives and musical experiences.

Wait, wait. Are we now saying that … uh, the only reason we get scientific discoveries and medical treatment because … er … because of copyright? Is that it? That can’t be it. Can it?

Copyright has no role in enabling this. None.

In fact, it’s worse than that. The only role of copyright in modern scholarly publishing is to prevent societal benefits arising from scientific and medical research.

The article then wanders off into an (admittedly interesting) history of Seeley’s background as a poet, and as a publisher of literary magazines. The conclusion of this section is:

Of course creators and scientists want visibility […] At the very least, they’d like to see some benefit and support from their work. Copyright law is a way of helping make that happen.

This article continues to baffle. The argument, if you want to dignify it with that name, seems to be:

  • poets like copyright
  • => we copyright other people’s science
  • => … profit!

Well, that was incoherent. But never mind: finally we come to part of the article that makes sense:

  • There is the “idea-expression” dichotomy — that copyright protects expression but not the fundamental ideas expressed in a copyright work.

This is correct, of course. That shouldn’t be cause for comment, coming from a copyright lawyer, but the point needs to be made because the last time an Elsevier lawyer blogged, she confused plagiarism with copyright violation. So in that respect, this new blog is a step forward.

But then the article takes a sudden left turn:

The question of the appropriateness of copyright, or “authors’ rights,” in the academic field, particularly with respect to research journal articles, is sometimes controversial. In a way quite similar to poets, avant-garde literary writers and, for that matter, legal scholars, research academics do not rely directly on income from their journal article publishing.

Er, wait, what? So you admit that scholarly authors do not benefit from copyright in their articles? We all agree, then, do we? Then … what was the first half of the article supposed to be about?

And in light of this, what on earth are we to make of this:

There is sometimes a simplistic “repugnance” about the core publishing concept that journal publishers request rights from authors and in return sell or license those rights to journal subscribers or article purchasers.

Seeley got that much right! (Apart from the mystifyingly snide use of “simplistic” and the inexplicable scare-quotes.) The question is why he considers this remotely surprising. Why would anyone not find such a system repugnant? (That was a rhetorical question, but here’s the answer anyway: because they make a massive profit from it. That is the only reason.)

Well, we’re into the final stretch. The last paragraph

Some of the criticism of the involvement of commercial publishing and academic research is simply prejudice, in my view;

Yes. Some of us are irrationally prejudiced against a system where, having laboriously created new knowledge, it’s then locked up behind a paywall. It’s like the irrational prejudice some coal-miners have against the idea of the coal they dig up being immediately buried again.

And finally, this:

Some members of the academic community […] base their criticism on idealism.

Isn’t that odd? I have never understood why some people consider “idealism” to be a criticism. I accept it as high praise. People who are not idealists have nothing to base their pragmatism on. They are pragmatic, sure, but to what end?

So what are we left with? What is Seeley’s article actually about? It’s very hard to pick out a coherent thread. If there is one, it seems to be this: copyright is helpful for some artists, so it follows that scholarly authors should donate their copyright to for-profit publishers. That is a consequence that, to my mind, does not follow particularly naturally from the hypothesis.

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