July 19, 2012
In a comment on the previous post, Steve P. asked whether “Apatosaurus” minimus might not be a Apatosaurus specimen after all — particularly, an Apatosaurus ajax individual resembling NSMT-PV 20375, the one in the National Science Museum, Tokyo, that Upchurch et al. (2005) so lavishly monographed.
Initially, I dismissed this idea out of hand, because the “Apatosaurus” minimus sacrum-pelvis complex is so very different to that of the “Brontosaurus” illustrated by Hatcher (1903: fig. 4), as seen in an earlier post. But on going back to the Upchurch et al. monograph I realised that their sacrum-ilium complex is very different from Hatcher’s. Here it is, cleaned up from scans and re-composed in the same format as the Camarasaurus and “Apatosaurus” minimus from last time, for easy comparison.
Sacrum and fused ilia of Apatosaurus ajax NSMT-PV 20375. Top row: dorsal view with anterior to left. Middle row, left to right: anterior, right lateral (reversed), posterior. Bottom row: ventral view with anterior to left. Modified from Upchurch et al. (2005: plate 4 and text-figure 9).
Here’s Hatcher’s “Brontosaurus” illustration (from his plate 4) again:
I’m not sure what to make of this. The Tokyo Apatosaurus seems to be intermediate in some respects between Hatcher’s specimen and “Apatosaurus” minimus.
One important difference is that the neural spines are much taller in Hatcher’s illustration than in the Tokyo Apatosaurus. Could that be ontogenetic? (IIRC the Tokyo individual is subadult). Or are they in fact different species? Or is it just individual variation?
I don’t know. Anyone?
- Hatcher, J.B. 1903. Osteology of Haplocanthosaurus with description of a new species, and remarks on the probable habits of the Sauropoda and the age and origin of the Atlantosaurus beds; additional remarks on Diplodocus. Memoirs of the Carnegie Museum 2:1-75.
- Upchurch, Paul, Yukimitsu Tomida, and Paul M. Barrett. 2005. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs No.26. Tokyo.
Upchurch et al. (2005)
July 18, 2012
This is the sacrum of Camarasaurus supremus AMNH 5761. Top row: dorsal view, with anterior to left. Middle row, from left to right: anterior, left lateral and posterior views. Bottom row: ventral view, with anterior to left. Modified from Ostrom and Mook (1921:figs. 43-44).
It’s instructive to compare with the “Apatosaurus” minimus sacrum. Direct comparison is somewhat hindered for two reasons: first, the ilia are fused to that sacrum but not to this; and second, different views are available, so I put the composites together differently. We can’t do anything about the ilia. But to facilitate comparison, here is a reworked version of the “Apatosaurus” minimus illustration with the right-lateral view discarded, a ventral-view silhouette added, and the composition mirroring that of Osborn and Mook’s Camarasaurus:
One thing is for sure: whatever else “Apatosaurus“ minimus might be, it ain’t Camarasaurus.
A couple of weeks ago we tried to work out what it costs the global academic community when you publish a paper behind an Elsevier paywall instead of making it open access. The tentative conclusion was that it’s somewhere between £3112 and £6224 (or about $4846-9692), which is about 3.6-7.2 times the cost of publishing in PLoS ONE.
That calculation was fraught with uncertainty, because it’s so difficult to get solid numbers out of Elsevier. So let’s try a simpler one.
In 2009, The STM report: an overview of scientific and scholarly journal publishing reported (page 5) that:
The annual revenues generated from English-language STM journal publishing are estimated at about $8 billion in 2008, up by 6-7% compared to 2007, within a broader STM publishing market worth some $16 billion.
There were about 25,400 active scholarly peer-reviewed journals in early 2009, collectively publishing about 1.5 million articles a year.
8 billion dollars divided by 1.5 million articles yields a per-article revenue to the STM industry of $5333. And since publisher revenue is the same as academia’s expenditure on publishing, that is the per-article cost to Academia.
(What about the articles currently published as gold open access? Don’t they cut down the number that are being bought through subscriptions, and so raise the average price of a paywalled article? Yes, but not by much: according to page 7 of the report, “about 2% of articles are published in full open access journals” — a small enough proportion that we can ignore it for the purposes of this calculation.)
What can we make of this $5333 figure? For a start, it’s towards the bottom of the $4846-9692 Elsevier range — only 10% of the way up that range. So the balance of probability strongly suggests that Elsevier’s prices are above the industry-wide average, but not hugely above — somewhere between 10% below and 80% above the average.
More importantly, each paywalled article costs the world as much as four PLoS ONE articles. In other worlds, if we all stopped submitted to paywalled journals today and sent all our work to PLoS ONE instead, the total scholarly publishing bill would fall by 75%, from $8 billion to $2 billion.
Why am I comparing with PLoS ONE’s $1350? There are other comparisons I could use — for example, the average cost of $906 calculated by of Solomon and Björk across 100,697 open-access articles in 1,370 journals. But that figure is probably propped up by journals that are deliberately being run at a loss in order to gain visibility or prestige. PLoS ONE is a more conservative comparison point because we know its $1350 is enough for it to run at a healthy operating profit. So we know that a switch to PLoS ONE and similar journals would be financially sustainable.
But there’s certainly no reason to think that PLoS ONE’s price of $1350 is as low as you can go and still have good-quality peer-reviewed gold open access. For example, PLoS ONE’s long-time Editor-in-Chief, Pete Binfield, thinks that it can be done, at a profit, for $99 — a staggering 92% price-cut from the $1350 figure we’ve been using. If he’s right — and he’s betting his mortgage that he is — then we could have 54 per-reviewed articles in PeerJ for every one that goes behind a paywall.
It’s too early to know whether PeerJ will work (and I’ll talk about that more another time). But the very fact that someone as experienced and wily as Binfield thinks it will — and was able to attract venture capital from a disinterested and insightful party — strongly indicates that this price-point is at least in the right ballpark.
Which is more than can be said for the Finch Report’s ludicrous over-estimate of £1500-£2000.
July 17, 2012
Mathematician David Roberts has pointed me to a useful new five-part series by Martin Paul Eve, entitled Starting an Open Access Journal. It’s well worth a look, for how it engages with so many practicalities and how tractable he makes it all seem.
- Part 1 — planning and social issues.
- Part 2 — Open Journal Systems, ISSNs, DOIs, CLOCKSS
- Part 3 — Launching, editorial/review procedures
- Part 4 — Copyediting, proofreading, typesetting
- Part 5 — After you publish the first issue
We’re actually pretty well served for open-access journals in our field (Acta Palaeontologica Polonica, Palaeontologia Electronica, PalArch’s journal of vertebrae palaeontology, soon PaleoBios, and of course PLoS ONE). But for scientists in other fields that have fewer options, starting their own journal may well be the single most effective thing they can do to advance open access. (It’s going to look pretty good on the CV, too!)
July 16, 2012
July 16, 2012
This is the Brontosaurus that I grew up with:
It’s by Kenyon Shannon, found on page 14 of The How And Why Wonder Book of Dinosaurs (Geis 1960). I call it Brontosaurus rather than Apatosaurus because this outdated rendition is forever tied to the outdated name in my mind.
It would be terribly easy to pick holes in this representation — the completely wrong head, the bizarre croc-like eyes, the incorrect attitude of the head, the tubular shape and much too thin profile of the neck, the full set of manual unguals and so on. But the part that’s most shocking to me is just how darned fat it is.
Even given that Apatosaurus was among the most robustly build of sauropods — certainly the most robust diplodocoid — how wrong is that super-fat forearm? Here, for comparison, is an Apatosaurus humerus:
And here is the lower arm:
Put them together and you can get some impression of the proportions of the complete forelimb:
In short: it’s a solidly build animal; but the Shannon depiction that we started with is not merely solid, it’s what we refer to as “a lardy bloater”. Just say no.
- Geis, Darlene. 1960. The How and Why Wonder Book of Dinosaurs. Price Stern Sloan, Los Angeles. 48 pages. ISBN: 0-8431-4250-2.
- Upchurch, Paul, Yukimitsu Tomida, and Paul M. Barrett. 2005. A new specimen of Apatosaurus ajax (Sauropoda: Diplodocidae) from the Morrison Formation (Upper Jurassic) of Wyoming, USA. National Science Museum Monographs No. 26. Tokyo. ISSN 1342-9574.
July 14, 2012
More goodness from Osborn and Mook’s (1921) gargantuan Camarasaurus monograph, again prepared largely for comparison with “Apatosaurus” minimus. Last time, I showed you one of O&M’s pubis illustrations. Now an ischium:
This shows the left ischium AMNH 576o’/Is.4. Left column: proximal aspect. Middle column, from top to bottom: medial, lateral, posterior (no dorsal view was provided). Right column: distal. Heavily modified from Osborn and Mook (1921: fig. 101) — cleaned up, lettering and lines removed, recomposed in a more informative layout, views rescaled to better match each other, and tweaked for colour.
As usual, click through for full resolution (only 989 x 978 this time).
It’s interesting to compare this with the similarly composed illustration of the “Apatosaurus” minimus ischium from last week.
July 13, 2012
(First of all, for anyone who’s not familiar with the plural of “pubis”, it’s spelled “pubes” but pronounced “pyoo-bees”. Stop sniggering at the back.)
As Matt and I struggle to figure out the partial pubis that is one of the elements of the “Apatosaurus” minimus specimen AMNH 675, one of the most helpful references is Osborn and Mook’s (1921) epic monograph on Camarasaurus. It’s not that 675 particularly resembles Cam — it doesn’t. It’s just that Osborn and Mook is very lavishly illustrated, so that it is (as far as I know) the only published paper in the history of sauropod studies to have shown a sauropod pubis in more than one aspect.
Here is one of the two pubes that they illustrated in the six cardinal aspects:
This shows the left pubis AMNH 5761/Pb.2. Top row: proximal aspect, with anterior to left. Middle row, from left to right: anterior, lateral, posterior, medial. Bottom row: distal, with anterior to left. Heavily modified from Osborn and Mook (1921: fig. 102) — cleaned up, lettering and lines removed, recomposed in a more informative layout, views rescaled to better match each other, and tweaked for colour.
As usual, click through for full resolution (only 1159 x 940 this time).
As you can see, the pubis is a very strangely shaped bone, twisted and with odd rugosities everywhere. If you’re very lucky, we’ll discuss these in more detail later. For now, the take-home message is that sauropod pubes are very weird and confusing, and the simple lateral view that’s typically all you ever see is terribly misleading.
July 12, 2012
Section 4 (What needs to be done, on page 7) begins as follows:
Implementing our recommendations will require changes in policy and practice by all stakeholders. More broadly, what we propose implies cultural change: a fundamental shift in how research is published and disseminated.
This is a crucial point. Cultural change is exactly what’s needed — not just in how research is published, as noted in the report, but even more importantly in how it’s evaluated. In particular, we’re going to have to stop assessing research by what journal it’s published in, and start looking at the value of the actual research.
This is already important — it always has been, because the use of journal reputation as a proxy for research quality has always been appallingly error-prone and misleading. But it’s going to become more and more important as open access grows more prevalent and a greater proportion of research moves into OA megajournals such as PLoS ONE, Sage Open and NPG’s Scientific Reports. These things are just too darned big to have a meaningful reputation. If you try to judge a PLoS ONE paper on the basis of the journal’s impact factor (4.411), you’ll quickly run aground: that’s a weak IF for a medic, but very strong for a palaeontologist. PLoS ONE is increasingly one of the journals of choice for palaeo papers, but it’s looked down on in astronomy. A question like “what’s the quality of PLoS ONE papers” is as about as meaningful as “what’s the price of property in London?” It depends on whether you’re talking about Knightsbridge or Peckham.
This is one of the fringe benefits of the shift towards megajournals: it’s going to make everyone see just how fatuous judgement by impact factor is. We’re going to see the end of comments on Guardian articles that say “my department actively discourages us from publishing in journals with IF less then 6.0″.
Unilateral action by the UK
Well, I seem to have gone off on a bit of a tangent there. Back to the Finch Report, pages 7 and 8:
Key actions: overall policy and funding arrangements
v. Renew efforts to sustain and enhance the UK’s role in international discussions on measures to accelerate moves towards open access.
This is also important. I like it that the Finch Report seems generally to advocate that we in the UK should lead the way in open access. But it’s also true that if we push on ahead of other countries, implementing mandatory open access unilaterally, we’ll be at a disadvantage compared with other countries: they will get our research for free, but we won’t get theirs till they follow suit.
And I am fine with that. Obviously it can’t continue indefinitely, but if taking a short-term financial hit is what it takes to get the world onside, that’s cool. Doing science costs money. And you haven’t done science till you’ve published your result. And you haven’t really published it until everyone can get it.
Now we come to a part of the report that I am really unhappy with. This is from the list in the section Key actions: publication in open access and hybrid journals, on page 8:
x. Extend the range of open access and hybrid journals, with minimal if any restrictions on rights of use and re-use for non-commercial purposes.
There’s that non-commercial clause again. This is worrying. If the Finch Report really is about what’s best for the country and for the world, there is no justification for NC. We want businesses to thrive as well as universities. And there are more businesses in the world than publishers! Cameron Neylon said this best in his Finch Report review, Good steps but missed opportunities:
This fudge risks failing to deliver on the minister’s brief, to support innovation and exploitation of UK research. This whole report is embedded in a government innovation strategy that places publicly funded knowledge creation at the heart of an effort to kick start the UK economy. Non-commercial licences can not deliver on this and we should avoid them at all costs.
That’s exactly right.
I will have more to say on this in a future post.
The role of repositories
There is a section headed Key actions: repositories on page 9. Tellingly, it has only two points, compared with 5, 6 and 5 for the other three key actions sections. Here is the second of those points:
xviii. Consider carefully the balance between the aims of, on the one hand, increasing access, and on the other of avoiding undue risks to the sustainability of subscription-based journals during what is likely to be a lengthy transition to open access. Particular care should be taken about rules relating to embargo periods. Where an appropriate level of dedicated funding is not provided to meet the costs of open access publishing, we believe that it would be unreasonable to require embargo periods of less than twelve months.
Who is the “we” that believes a six-month embargo period would be “unreasonable”?
Obviously not Research Councils UK, who recently stated “Ideally, a paper should become Open Access as soon as it is published. However [...] the Research Councils will accept a delay of up to six months in the case where no ‘Article Processing Charge’ is paid.”
Obviously not the Wellcome Trust, whose policy states that it: “requires electronic copies of any research papers that have been accepted for publication in a peer-reviewed journal, and are supported in whole or in part by Wellcome Trust funding, to be made available through PubMed Central (PMC) and UK PubMed Central (UKPMC) as soon as possible and in any event within six months of the journal publisher’s official date of final publication”.
No. “We” can only mean the publishers’ lobby. They hate repositories, and were somehow allowed to nobble all references to Green OA in the report. Don’t believe me? Search for the word “green” in the executive summary: zero hits in eleven pages. Try it in the main report? Three hits in 140 pages: one on page 16, parenthetical (“… a version of a publication through a repository (often called green open access)”), one on page 120, a repeat (“… a version of a publication via a repository, often after an embargo period. This strand is often called green open access”) and one on page 130 (an unrelated mention of the HM Treasury Green Book).
This is one of the most disturbing aspects of the report, and I can see why Stevan Harnad is irate.
Let us move on to happier matters.
Transparency and competition
From page 10:
One of the advantages of open access publishing is that it brings greater transparency about the costs, and the price, of publication and dissemination. The measures we recommend will bring greater competition on price as well as the status of the journals in which researchers wish to publish. We therefore expect market competition to intensify, and that universities and funders should be able to use their power as purchasers to bear down on the costs to them both of APCs and of subscriptions.
I think this is a very important and much neglected point, and it makes me want to write a blog on why author-pays is inevitably more economical than reader-pays. (Short version: granularity of transactions is smaller, so the market is efficient and real competition comes into play, as we are seeing with the launch of PeerJ.)
From page 10:
Our best estimate is that achieving a significant and sustainable increase in access, making best use of all three mechanisms, would require an additional £50-60m a year in expenditure from the HE sector: £38m on publishing in open access journals, £10m on extensions to licences for the HE and health sectors and £3-5m on repositories.
*Cough* *splutter* Hey, what now?
So let’s get this straight. Transitioning from subscription to open access is going to cost us £10M more on licences than we’re already paying? Rather than, say, £10M less, as we start cancelling subscriptions we don’t need?
This seems to be pure fantasy on the part of the publishers.
Not only that, the £38M is based on an “average APC” of … get ready … £1,500. (This is not stated in the executive summary, but it’s on page 61 of the full report.) That number is a frankly ludicrous over-estimate, being nearly double the $1350 =~ £870 charged by PLoS ONE, and nearly three times as much as the $906 =~ £585 found as the average of 100,697 articles in 1,370 journals by Solomon and Björk (2012).
So based on this a more realistic APC, the £38M comes down to £14.8M. Throw out the absurd extra £10M that publishers want for extra subscription licences, and the total cost comes from from “£50-60M per year” to about £19M. Still not chicken-feed, but a lot less painful, even in the short term.
And finally …
The report finishes on an upbeat note (page 10) and so do we:
We believe that the investments necessary to improve the current research communications system will yield significant returns in improving the efficiency of research, and in enhancing its impact for the benefit of everyone in the UK.
Yes. Absolutely right. Even if we only thought about academia, the financial case for open access would be unanswerable. But there is more to the world than academia, and the real benefits will be seen elsewhere.
Anyone who is not yet heartily sick of the Finch Report can read lots more analysis in the articles linked from Bjorn Brembs’s article The Finch Report illustrates the new strategy wars of open access at the LSE’s Impact blog.