Illustration talk slide 13

Illustration talk slide 14

Illustration talk slide 15

Somewhat lamely, this is the only slide I had in about lighting. I left it up while I talked about the most important points, which are:

  • Don’t use a flash unless you absolutely have to.
  • If you can swing it, the common convention is to have specimens illuminated from the upper left.*
  • If you have the time, it’s not a bad idea to bracket your Goldilocks shot with brighter and darker photos, by fiddling with your camera settings.

* I happily violate this convetion if illumination from another angle shows the specimen to better advantage–and if I have any control over illumination. Working with big bones in some collections, you basically have overhead florescent lights and that’s it. The NHM shot above may look not-so-hot, but there we at least had a desk lamp we could move around. In a lot of places I’ve worked, I didn’t have even that.

The other posts in this series are here.

In a comment on the previous post, Steve P. asked whether “Apatosaurusminimus 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 “Apatosaurusminimus 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 “Apatosaurusminimus 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 “Apatosaurusminimus.

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?

References

  • 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)

Thanks to the wonder of Osborn and Mook (1921), we have already seen multiview illustrations of the pubis and ischium of Camarasaurus. Now we bring you their Camarasaurus sacrum.

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 “Apatosaurusminimus 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 “Apatosaurusminimus 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.

References

More of my thoughts on the Finch Report; you may wish to read part 1 first. As before I will be quoting from the executive summary (11 pages) rather than the full report (140 pages).

Changing culture

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.

Non-commercial use

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.)

Costs

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.

Epilogue

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.

Here is another illustration that I prepared for the forthcoming “Apatosaurusminimus redescription. Compare this with the sacrum and fused ilia from the previous post.

Left ischium of AMNH 675, “Apatosaurusminimus. Left column: proximal. Middle column, top to bottom: medial (inverted), dorsal, lateral, ventral (all with proximal to left). Right column, distal. Click through for very high resolution (4810 x 5229).

Can you tell what it is yet?

By the way, I’d appreciate some advice on the directional nomenclature here. Since I’ve illustrated the lateral view with the long axis horizontal, I’m referring to the margin that’s closest to the tail as “dorsal” and the margin closest to the ground as “ventral”. But since the ischium is directed more or less posteroventrally, I guess you could equally make a case for designating those two aspects as “posterior” and “anterior” respectively. The third alternative is to embrace the diagonality and call them “posterodorsal” and “anteroventral”. Is one of these schemes conventional?

 

I mentioned a few posts ago that Matt and I are working on a redescription of AMNH 675, a sauropod specimen referred by Mook (1917) to “Apatosaurusminimus, but which everyone knows is not Apatosaurus. We plan to share the illustrations from this in-progress paper as we prepare them, so here is perhaps the key one:

Sacrum and fused ilia of AMNH 675, “Apatosaurus” minimus. Top row: left lateral and right lateral; middle row: dorsal, with anterior to top; bottom row, anterior and posterior. Scale bar = 1 m. Click through for very high resolution (6283 x 6479).

The other material comprising this specimen consists of a partial pubis and two ischia, one of which is complete. We’ll show you these once we’ve prepared the illustrations.

What actually is it? Well, we don’t know yet. it has a strange mix of advanced diplodocoid and advanced macronarian features. A preliminary phylogenetic analysis is inconclusive. We have some more approaches to follow up before we’re ready to nail a conclusion to the door.

Reference

Mook, Charles C. 1917. Criteria for the determination of species in the Sauropoda, with description of a new species of Apatosaurus. Bulletin of the American Museum of Natural History 38:355-360.

From the collections of the American Museum of Natural History, I give you the sacrum and fused ilia of “Apatosaurusminimus AMNH 675, as correctly identified by Steve P in a comment to the previous post:

"Apatosaurus" minimus sacrum with fused ilium, right lateral view

As Steve P rightly pointed out, AMNH 675 was designated as Brontosaurus sp. by Osborn (1904), and made the type of Apatosaurus minimus by Mook (1917).

It’s been known for some time that whatever this is, it’s not Apatosaurus — see for example McIntosh (1990a:398), McIntosh (1990b:59) and Upchurch et al. (2004:298). But what actually is it? Well, at the moment, no-one knows. Matt and I now have a manuscript in prep that we hope will somewhat elucidate this question. More to come on this specimen, most likely.

References

McIntosh, John S. 1990a. Sauropoda. In The Dinosauria, pp. 345–401. Berkeley and Los Angeles: University of California Press.

McIntosh, John S. 1990b. Species Determination in Sauropod Dinosaurs with Tentative Suggestions for the Their Classification. In Dinosaur Systematics: Approaches and Perspectives, pp. 53–69. Cambridge: Cambridge University Press.

Mook, Charles C. 1917. Criteria for the determination of species in the Sauropoda, with description of a new species of Apatosaurus. Bulletin of the American Museum of Natural History 38:355-360.

Osborn, Henry F. 1904. Manus, sacrum, and caudals of Sauropoda. Bulletin of the American Museum of Natural History 20:181-190.

Upchurch, Paul, Paul M Barrett, and Peter Dodson. 2004. Sauropoda” In The Dinosauria, 2nd Edition, pp. 259–322. Berkeley and Los Angeles: University of California Press.