CalAcad Skulls - wall of voodoo

Back in the early aughts Cal Acad did a huge exhibit simply titled, “Skulls”. It was extremely rad, and I could have been running a separate blog this whole time with nothing but photos from that exhibit. (Update: the website for the exhibit is still going. Check it out.) I was just sorting through some old folders and found some favorites. The photo above is the wall of California sea lion skulls, 900-odd in all, arranged from the biggest, gnarliest males on one end to the most gracile females on the other end.

CalAcad Skulls - sad sea lions

They also had quite a few pathological sea lion skulls. Here are two that haunted me–they got tangled up in fishing lines that slowly sawed through their skulls and into their brains, killing them.

CalAcad Skulls - sad elk

This elk had a pretty funky growth on its right dentary.

CalAcad Skulls - sad deer

But easily the most “Naw!”-inducing pathology in the whole exhibit was this poor deer, which has a pathological growth the size and shape of a big pastry where its right eye used to be. I don’t know if it’s just a coincidence that its antlers are all wonky, too–maybe Darren will show up and enlighten us.

So if you’re feeling down, you can at least console yourself that you don’t have a flyblown, pus-leaking cinnamon roll of pathological bone growing on your face. Have a nice day!

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[Introduction from Mike. I’m on the OKFN’s open-access mailing list, where we’re currently embroiled in a rather tedious reiteration of the debate about the merits of the various open-access licences. On Monday, veteran of the OA wars Jan Velterop posted a message so perfect that I immediately asked him for permission to re-publish it as a guest post here on SV-POW!. He kindly agreed, so over to Jan for the rest of this post. The only changes I’ve made are to highlight what I consider the key passages.]

I’ve been following this discussion with increasing bemusement. Frankly, it’s getting ridiculous, at least in my humble opinion. A discussion such as this one about licensing and copyright only serves to demonstrate that copyright, once conceived as a way to stimulate and enable science and the arts, has degenerated into a way to frustrate, derange and debilitate knowledge exchange.

I’m not the first one to point out that absolutely anything, under any copyright licence or none, could be abused for evil purposes or, in more mild circumstances, lead to misunderstandings and accidental abuse. I agree with all those who said it.

The issue here is what science and scientific results stand for. Their purpose is emphatically not “to be copyrightable items”. Copyright, invented to combat commercial abuse, has become a means of commercial abuse. The purpose of science and scientific results is to enrich the world’s knowledge. Any commercial advantage – appropriate for industrially funded research – can be had by 1) keeping results secret (i.e. not publishing them), or 2) getting a patent. Science, particularly modern science, is nothing without a liberal exchange of ideas and information.

Ideally, scientific publications are not copyrightable at all, and community standards take care of proper acknowledgement. We don’t live in an ideal world, so we have to get as close as we can to that ideal, and that is by ameliorating the insidious pernicious effects of copyright with CC-Zero and CC-BY licences.

The existence of the NC rider or stipulation for CC licences is unfortunate and quite damaging. Mainly because of the vagueness and ambiguity of what ‘commercial use’ means. Ideas in published articles can be freely used for commercial purposes of any kind, as ideas are not copyrightable. Only “the way the ideas have been formulated” is covered by copyright, and thus by the NC clause in copyright licences. In my interpretation that means that most usage of published material that is not a straightforward selling of text or images can be freely done. But that’s my interpretation. And that’s exactly where it rubs, because all the NC clause does is introduce hypothetical difficulties and liabilities. As a result of which, NC practically means: “stay away from using this material, because you never know with all those predatory legal eagles around”. In other words, it’s virtually useless for modern, sophisticated scientific knowledge discovery, which doesn’t just consist of reading papers any longer, but increasingly relies on the ability to machine-process large amounts of relevant information, as human ocular reading of even a fraction of the information is not possible anymore. At least not in most fast-moving areas of the sciences. Read this article, or similar ones, if you want to be convinced: On the impossibility of being expert, BMJ 2010; 341  (Published 14 December 2010 – unfortunately behind a paywall).

The taxpayer angle (“must be open because the taxpayer paid for it”), leading to Kent Andersonian notions of knowledge protectionism (“results of research paid by US taxpayers should not be available to non-US citizens unless they pay for it”), is a most unfortunate, visceral and primitive reaction and a complete red herring. For many reasons, not least because the taxpayer, or vicariously the taxman, isn’t the party that pockets any money payed for paywalled information. Besides, how far do you go? Americans not being allowed to stay alive due to a cure that was developed with public money in Switzerland unless they pay through the nose for it to the Swiss tax authorities? The “as-long-as-I-am-well-the-rest-of-you-can-go-to-hell” personality disorder. The whole idea is so against the ethos of science that those even thinking in that direction must be taken to be utterly and entirely unsuitable to any role in the scientific community.

Access control and restriction via copyright was at best a necessary evil in the print era; the ‘necessary’, though, has disappeared in the web environment.

Have a nice day!

Jan Velterop

Following on from Matt’s post about the difficulty of photographing big specimens without distortion, I thought I’d have a play with our best Sauroposeidon C8 photo, which I think is this one:

sauroposeidon-c8-alone

(That’s been the basis for classic SV-POW! posts such as Your neck is pathetic and Darren’s new indeterminate Wealden maniraptoran is inadequate.)

I was motivated by Andy Farke’s comment:

Another–and perhaps more important–area where surface models excel is when you can remove colors on the original specimen that wash out relevant details…I bet this is probably the case for the example vertebra of Sauroposeidon. How many fossae and foramina just don’t show up well on the photos above?

Andy was talking about completely colourless 3d surface models, in which the 3d shape allows a render to make shadows that bring out the subtle shapes. But it made me wonder whether we could get anywhere just by washing out the most prevalent colour in the photo.

I started by doing a big, fat Gaussian blur on a duplicate layer — 500 pixels in each direction — and sampling the colour in the middle, to get a rough-and-ready average. (There may be a better way — please shout if you know one.) That average colour was#7e6b2f. I used it to run Colour To Alpha on another duplicate of the original layer, so that we’d be left with only residual colours. Here’s the result:

sauroposeidon-c8-alone-colour-completely-removed

I’m in two minds about this. It may be informative, but it sure is ugly. To compromise, I reinstated the original layer underneath this mostly-transparent one, and turned its opacity down to 75%. Here’s the result — a nice compromise:

sauroposeidon-c8-alone-colour-removed

Of course, there are endless other approaches you can take — that’s the blessing and the curse of image-editing programs like GIMP. For example, here’s what I got doing a simple Colours → Auto → White Balance:

sauroposeidon-c8-alone-whitebalanced

I’m not sure that isn’t the best of the bunch, in terms of informativeness.

I also tried something else — not amazingly successfully, but I think it’s worth seeing. Since the two photos that Matt showed in the previous post were evidently taken from somewhat different angles, I thought I’d have a go at compositing them into a red-cyan anaglyph. Because the variation in camera position is mostly dorsoventral rather than anteroposterior, the vert has to be pointed upwards for the two eyes to see the two versions from different horizontal points. Here’s the best I could do:

c8-anaglyph

I would say this is of some value; but it’s nowhere near as good as, for example, the anaglyph of Cervical S of the Archbishop. I could sit and look at that one all day. The problems with this one arise for three reasons.

First, I had to reduce both parts of the Sauroposeidon anaglyph to monochrome (since one was already in that form), so all colour information was lost.

Second, I had to scale the high-resolution picture to the same size as the lower-resolution one, throwing away more detail.

Finally, and most important, the two photos were not taken with the intention that they should be used to make an anaglyph. To work well, this has to be done with the images taken under the same lighting conditions, at the same distance from the specimen, from perspectives differing by about the distance between the pupils of the viewer, and with the camera-position difference being perfectly in the plane of the specimen. Needless to say, none of these conditions was met in this case, so it’s actually quite impressive that it works as well as it does.

We have a lot of options for illustrating specimens these days. Postage-stamp-sized greyscale photos really don’t cut it any more.

Here are two photos of what I infer to be C8 of OMNH 53062, the holotype of Sauroposeidon. The top one was taken by Mike during our visit to the OMNH in 2007. If you’re a regular you may recognize it from several older posts: 1, 2, 3. The bottom one was taken by Mike Callaghan, the former museum photographer at the OMNH, sometime in 1999 or 2000. I used it in Wedel et al. (2000) and Wedel and Cifelli (2005).

Sauroposeidon OMNH 53062 C8 photos compared

You’ll notice that the two photos are far from identical. In both cases, the photographers were up on ladders, as far above the vertebra as they could get, and there are still significant perspective effects. That’s just a fact of life when you’re taking photos of a vertebra that is 1.4 meters long, from anything lower than a helicopter. In Mike Taylor’s shot, the neural spine looms a little too large; in Mike Callaghan’s shot, the prezygapophysis looks a little too small, probably because it was curving off at the edge of the shot. So neither photograph is “right”; both distort the morphology of the specimen in different ways. Here’s how the two images stack up, with the outlines scaled to the same length:

Sauroposeidon OMNH 53062 C8 outlines compared

When I ran a draft of this post past Mike, he wrote (with permission to post):

I think the current draft misses an important point: the warning. We really can’t trust photos, however carefully taken, and however beautifully composited into TNFs*. You’re welcome to quote me as having said I’d have assumed the two C8s were different vertebrae. For that matter, I bet I could have worked up several taxonomically significant characters to distinguish them. Yikes.

* TNF = Taylor Normal Form, i.e., making multi-view photos like the ones here and here.

So the moral is, photos of big specimens almost always involve some distortion. This is clearly not ideal. But I have a plan for fixing it. I am hoping to get back to the OMNH this spring, and the next time I’m there, I’m going to take photos of this vertebra from a zillion angles and make a 3D model through photogrammetry. Happily, Heinrich Mallison has been producing a very helpful series of tutorials on that very topic over at dinosaurpaleo: 1, 2, 3, 4, with more on the way (I’ll update the links here later). Update: Don’t forget to check out Peter Falkingham’s (2012) paper in PE on making photogrammetric models with free software.

Armed with that model, it should be possible to produce a perspective-free lateral view image of the vertebra, to which all of the previous photos can be compared. I can’t use CT data because this vertebra has never been CTed; it’s too big to fit through a medical CT scanner, and probably too fragile to be packed up and shipped to an industrial CT machine like they used on Sue (not to mention that would require a significant chunk of money, which is probably not worth spending on a problem that can be solved in other ways).

So, photogrammetry to the rescue, or am I just deluding myself? Let me know what you think in the comments.

Finally, I should mention that the idea of superseding photographs with 3D photogrammetric models is not original. I got religion last week while I was having beers with Martin Sander and he was showing me some of the models he’s made. He said that going forward, he was going to forbid his students to illustrate their specimens only with photographs; as far as he was concerned, now that 3D models could be cheaply and easily produced by just about everyone, they should be the new standard. Inspiring stuff–now I must go do likewise.

Some previous posts on Sauroposeidon:

References

My thanks to Steve Wang for pointing out that The Paleontological Society (in the USA, not to be confused the UK’s Palaeontological Association) has a new open access policy. The highlights are:

The Journal of Paleontology and Paleobiology now offer two options for Open Access publishing […]

Gold Open Access: authors or their institution may purchase Gold OA for their article by paying an Article Processing Fee (APC) of $2,500 ($1,500 for Society members). […] Gold Open Access articles will be published under the terms of the CC-BY-NC 3.0 license by default or CC-BY 3.0 license upon request.

Green Open Access: Authors of all articles published in the Journal of Paleontology or Paleobiology may freely post (e.g., to personal and institutional web sites) and distribute freely the final accepted manuscript file (not the pdf of the published article) under Green Open Access, 12 months after its publication.

Positives

It’s good to see this real step forwards, and a lot of people are going to be particularly pleased that both Gold and Green are on offer.

The Gold APC, especially for members, is noticeably cheaper than at most of the legacy publishers. (It’s $2500 for non-members, but they can join the society for $55 to take advantage of the lower price.) Elsevier, Springer, Wiley and Taylor and Francis have all spontaneously arrived at APCs at or very close to $3000 (and I’m quite sure there was no illegal price-fixing involved.) Members pay half of that — which is in the same ball-park as PLOS ONE’s long-established benchmark of $1350.

It’s excellent that there is an option to make the Gold articles true, BOAI-compliant open access by using the CC By licence.

It’s good that the Green OA embargo is no longer than 12 months.

Negatives

While $1500 is half the price of legacy publishers’ OA offerings, it still feels like a previous-generation APC. PeerJ, Ubiquity and Magnolia Press among others have raised the bar (or do I mean lowered it?) by charging APCs an order of magnitude less. It’s a shame that the Paleontological Society haven’t opted to go with a next-gen publisher such as Ubiquity, who publish quite a few society journals at good prices.

The default to the CC By-NC licence is unfortunate, as it will prevent legitimate scholarly uses including re-use of figures in commercial journals, uses in teaching at universities that charge tuition, and use in Wikipedia. We can hope that most authors will choose CC By, which suffers from none of these drawbacks; but experience shows that most authors’s immediate reaction, before they’ve thought it through in detail, is to err towards imposing more rather than less restrictions. The Society could have set expectations differently by using CC By except where authors request CC By-NC.

It’s odd that the policy stipulates that version 3.0 of the CC licences is used, when the current version is 4.0, but it’s not a big deal.

The imposition of the Green OA embargo is unfortunate (All Green-OA embargoes are iniquitous). Not only that, but 12 months exceeds the 6 months suggested by the better, earlier version of the RCUK policy and some others.

Nothing at all is said about the licence under which Green OA manuscripts should be made available. This is a missed opportunity, since in the absence of a clear statement of what is allowed, potential users will err on the side of safety — so, for example, PaleoSoc Green papers are likely to be omitted from content-mining projects.

Summary

This policy represents a valuable step forward for the Society; but it’s not all it could have been.

Some of the limitations have been imposed by the Society for its own benefit, which one can understand: the highish APC, the embargo (though of course there is no evidence that embargo-less Green affects subscription revenue).

But other limitations could easily be fixed at no cost to the Society. In particular, I would like to see them reverse the CC By/By-NC option, so that the more open option is the default; and I’d like them to make it clear that Green OA papers may be (and should preferentially be) provided under CC By, too.

“Look at all the things you’ve done for me
Opened up my eyes,
Taught me how to see,
Notice every tree.”

So sings Dot in Move On, the climactic number of Stephen Sondheim’s Pulitzer Prize-winning music Sunday in the Park with George, which on the surface is about the post-impressionist painter Georges Seurat, but turns out to be a study of obsession and creativity.

xx

Un dimanche après-midi à l’Île de la Grande Jatte – 1884 [A Sunday Afternoon on the Island of La Grande Jatte – 1884]

“Taught me how to see”? What kind of talk is that? One the surface, it seems silly — we all know how to see. We do it constantly, without thinking. Yet it’s something that artists talk about all the time. And anyone who’s sat down and seriously tried to paint or draw something will have some understanding of what the phrase means. We have such strong implicit ideas of what things look like that we tend to reproduce what we “know” is there rather than what’s actually there. Like I said, we see without thinking.

In fact, the psychology of perception is complicated and sophisticated, and the brain does an extraordinary amount of filtering of the visual signals we get, to save us the bother of having to consciously process way too much data. This is a whole scientific field of its own, and I’m going to avoid saying very much about it for fear of making a fool of myself — as scientists so often do when wandering outside their own field. But I think it’s fair to say that we all have a tendency to see what we expect to see.

xx

Phylogeny of Sauropoda, strict consensus of most parsimonious trees according to Wilson (2002:fig. 13a)

In the case of sauropods, this tendency has meant that we’ve all been startlingly bad at seeing pneumaticity in the caudal vertebrae of sauropods. Because the literature has trained us to assume it’s not there. For example, in the two competing sauropod phylogenies that dominated the 2000s, both Wilson (2002) and Upchurch et al. (2004) scored caudal pneumaticity as very rare: Wilson’s character 119, “Anterior caudal centra, pneumatopores (pleurocoels)”, was scored 1 only for Diplodocus and Barosaurus; and  Upchurch et al. (2004:286) wrote that “A few taxa (Barosaurus, Diplodocus, and Neuquensaurus) have pleurocoel-like openings in the lateral surfaces of the cranial [caudal] centra that lead into complex internal chambers”. That’s all.

And that’s part of the reason that every year since World War II, a million people have walked right past the awesome mounted brachiosaur in the Museum Für Naturkunde Berlin without noticing that it has pneumatic caudals. After all, we all knew that brachiosaur caudals were apneumatic.

But in my 2005 Progressive Palaeontology talk about upper limits on the mass of land animals estimated through the articular area of limb-bone cartilage, I included this slide that shows how much bigger the acetabulum of Giraffatitan is than the femoral head that it houses:

Screenshot from 2014-01-24 17:30:30

And looking at that picture made me wonder: those dark areas on the sides of the first few caudals (other than the first, which is a very obvious plaster model) certainly look pneumatic.

Then a few years later, I was invited to give a talk at the Museum Für Naturkunde Berlin itself, on the subject “Brachiosaurus brancai is not Brachiosaurus“. (This of course was drawn from the work that became my subsequent paper on that subject, Taylor 2009) And as I was going through my photos to prepare the slides of that talk, I thought to myself: darn it, yes, it does have pneumatic caudals!

So I threw this slide into the talk, just in passing:

Screenshot from 2014-01-24 17:32:06

Those photos were pretty persuasive; and a closer examination of the specimen on that same trip was to prove conclusive.

Meanwhile …

Earlier in 2009, I’d been in Providence, Rhode Island, with my Index Data colleagues. I’d managed to carve a day out of the schedule to hope along the coast to the Yale Peabody Museum in New Haven, Connecticut. My main goal was to examine the cervicals of the mounted Apatosaurus (= “Brontosaurus“) excelsus holotype (although it was also on that same trip that I first saw the Barosaurus holotype material that we’ve subsequently published a preprint on).

The Brontosaurus cervicals turned out to be useless, being completely encased in plaster “improvements” so that you can’t tell what’s real and what’s not. hopefully one day they’ll get the funding they want to take that baby down off its scaffold and re-prep the material.

But since I had the privilege of spending quality time with such an iconic specimen, it would have been churlish not to look at the rest of it. And lo and behold, what did I see when I looked at the tail but more pneumaticity that we thought we knew wasn’t there!

Wedel and Taylor (2013b: Figure 10).

An isolated pneumatic fossa is present on the right side of caudal vertebra 13 in Apatosaurus excelsus holotype YPM 1980. The front of the vertebra and the fossa are reconstructed, but enough of the original fossil is visible to show that the feature is genuine. (Wedel and Taylor 2013b: Figure 10).

What does this mean? Do other Giraffatitan and Apatosaurus specimens have pneumatic tails? How pervasive is the pneumaticity? What are the palaeobiological implications?

Stay tuned! All will be revealed in Matt’s next post (or, if you can’t wait, in our recent PLOS ONE paper, Wedel and Taylor 2013b)!

References

Mummified mouse - closeup

Here’s a nice thing: friends and relatives just assume (correctly) that I will want whatever dead animals they find. So I was not completely surprised when I got a call from my brother Ryan (pillager of the Earth) asking if I wanted a dead mouse he’d found mummified at the back of an unused cupboard. Happily this was over the holidays so I could get the specimen in person and not have to deal with mailing it.

This was not destined to be my mummified mouse, however. My son, London, has started a collection of his own. One of the first real skulls in his collection was that of a rat that we found dead in our front yard last year. I cut off its head and we boiled and cleaned the skull together (I still need to post about that). Then we mounted it in a clear plastic bottle that had previously contained toothpicks, so he could take it for show-and-tell. Last fall a second rat turned up dead in the yard; that one is still in the freezer, awaiting complete skeletonization. The mystery of the plague of dead rats was solved when we got home one evening and found our cat, Moe, in the front yard with only the hind leg of a third rat hanging out of his mouth. If I could just train him to kill them and not eat them, we could make a rat army

Funny side-note: we keep Skulls Unlimited catalogs around for leisure reading. London was looking through one not long after we prepped his rat skull and he saw that you could get a fully-prepared natural bone skull for about twenty bucks. That price seems about right to me, given the amount of work and care that has to go into cleaning, but London was outraged: “Why would people pay TWENTY DOLLARS for a rat skull when they could just clean their own!?”

That’s my boy! I didn’t have the heart to tell him that some people don’t have a ready supply of rats lying around. He’s not old enough to understand that level of deprivation.

Mummified mouse - in box

So, obviously the mummified mouse was going to show-and-tell. But I didn’t want it to get destroyed. My cheap and low-tech solution was to get a rigid plastic display box from the local hobby store ($5.99 for a two-pack) and stuff it with cotton balls. We cleared some of the cotton around the skull first so it would be more visible. Knowing how third-graders can be when exciting things get passed around, I also glued the lid on. The mouse and the cotton balls are completely immobile even when violently shaken, and hopefully they’ll stay that way indefinitely. I forgot to include a scale bar in either of these photos or to measure my damned murine, but the box lid is 5 inches on side. HeroClix Knifehead showed up because kaiju are notorious attention hogs.

Now, to see if Mousenkhamun can survive the rigors of third grade. I’ll keep you posted.