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Brian Engh (bottom left, enthusing about the Ceratosaurus just off-screen) and I are recently returned to civilization after a stint of fieldwork in Utah. On the way home, we made a detour to Salt Lake to visit the new Natural History Museum of Utah.

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The NHMU is one of the nicest museums I’ve ever had the pleasure of roaming through. They have a ton of stuff on display, including lots of real fossils and quite a few touchable specimens, with an understandably heavy emphasis on Utah’s extensive paleontological record.

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The museum is also beautifully laid out – you can walk around almost all of the mounts and see most of them from multiple levels of elevation. The signage hits a new high for being both discreet and informative. Almost everything on display is clearly identified either as a cast or by specimen number (or maybe both), and the real specimens typically list both the discoverer and the preparator. I’ve never seen that before, and I like it a lot.

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I suppose I should say a few words about the Barosaurus mount. It’s pretty cool – you can get very close to it, walk all the way around the body, and – crucially for a true sauropod lover – count vertebrae. They gave it 16 cervicals and 9 dorsals, just as hypothesized by McIntosh (2005), and unlike the AMNH Barosaurus, which has the neck cheated out by one extra cervical.

On the left in the photo above is the famous wall of ceratopsian skulls. More about that next time.

Reference

McIntosh, J.S. 2005. The genus Barosaurus Marsh (Sauropoda, Diplodocidae); pp. 38-77 in Virginia Tidwell and Ken Carpenter (eds.), Thunder Lizards: the Sauropodomorph Dinosaurs. Indiana University Press, Bloomington, Indiana, 495 pp.

I just read this on The Scholarly Kitchen and nearly fell out of my seat:

In an era with more access given to less qualified people (laypeople and an increasingly unqualified blogging corps presenting themselves as experts or journalists), not to mention to text-miners and others scouring the literature for connections, the obligation to better manage these materials seems to be growing. We can no longer depend on the scarcity of print or the difficulties of distance or barriers of professional expertise to narrow access down to experts with a true need.

I think this may be the most revealing thing ever written on The Scholarly Kitchen. It’s hard to see a way of reading it that isn’t contemptuous of everyone outside the Magic Circle. Ideally, the great unwashed should be excluded altogether; but if we can’t do that, then at least we must tell when what to read and how to use it. Heaven forfend that we let Ordinary People make such decisions for themselves. That is for the priestly caste to do.

Last week I went to Halifax, Nova Scotia, for the twice-yearly meet-up with my Index Data colleagues. On the last day, four of us took a day-trip out to Peggy’s Cove to eat lunch at Ryer Lobsters.

We stopped off at the Peggy’s Cove lighthouse on the way, and spotted a vertebrate, which I am pleased to present:

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It’s a whale skull, but I have no idea what kind. Can anyone help out?

So much for vertebrates — it was really all about the inverts. Here are six of them:

mike-with-lobster

I have a 2lb lobster here; my colleague Jakub went for two 1lb lobsters, as did Jason and Wolfram (not pictured). That’s Wolfram’s lobster closest to the camera, giving a better impression of just what awesome beasts these were.

Peggy’s Cove: recommended. For vertebrates and inverts.

(Thanks to Wolfram Schneider for these photos.)

 

Aquilops tattoo

My 40th birthday present from Vicki. I commissioned the art from Brian Engh. I bow to no one in my love for his original Aquilops head reconstruction:

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

Life restoration of Aquilops by Brian Engh. Farke et al. (2014: fig. 6C). CC-BY.

BUT it’s waaay too detailed for a tattoo unless I wanted a full back piece. I sent Brian this sketch to convey what I wanted – to emphasize the strong lines of the piece, punch up the spines and spikes, basically shift it toward a comic book style without devolving into caricature:

Aquilops tattoo - Matt sketch raw

Originally I was going to have Aquilops‘ name and year of discovery in the tat. I decided to drop the lettering, for several reasons. One, it won’t hold up as well over the next few decades. Two, if someone is close enough to read it, we’ll probably be talking about the tattoo already. Third, the tattoo is a better conversation starter without a caption. First I get to tell people what Aquilops is, then I get to explain what ‘fourth author‘ means. ;-)

As he did for the original Aquilops head recon, Brian sent a selection of possible color schemes, mostly based on those of extant lizards. I couldn’t decide which I liked best, so I talked it over with my tattoo artist, Tanin McCoe at Birch Avenue Tattoo in Flagstaff, Arizona. I wasn’t just interested in what looks good on paper, but what would work well with my skin tone and still look good 20 years from now. Tanin really liked the earth-tone color scheme with the dark stripe across the eye, so that’s how we went. The tattoo Aquilops is facing left instead of right because it’s on my left shoulder – my right deltoid was already occupied.

They do good work at Birch Avenue – Vicki’s gotten three pieces there, including this skeleton key that was also done by Tanin:

Vicki skeleton key tattoo - 1200

Yes, the key’s bit is a human sphenoid – that was my idea.

Anyway, I’m super-happy with the tattoo, and I’m glad it’s healed enough to show off. Thanks, Brian and Tanin!

The longest cell in Andy Farke is one of the primary afferent (sensory) neurons responsible for sensing vibration or fine touch, which runs from the tip of his big toe to his brainstem. (NB: I have not actually dissected Andy to confirm this, or performed any viral neuron tracing on him, this is assumed based on comparative anatomy.) Here’s a diagram:
Longest cell in Andy Farke

This is what happens when (a) I need to create a diagram to illustrate the longest cell in the human body for my students, and (b) my friends put stuff online with a CC-BY license.

Found this while I was checking out Aquilops art online:

Aquilops_scale

It’s a derivative work by Andy IJReid, from this Wikimedia page, based on two PhyloPic silhouettes Andy created (go here for the pathetically tiny lower vertebrate and here for Aquilops).

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From there it was pretty straighforward to mash up Andy’s silhouette with the nerve stuff from Wedel (2012: fig. 2).

So if you want the full deets on licensing – which I am obligated to provide whether you want them or not – the image up top is a derivative image by me, based on work by Andy published at PhlyoPic under the Creative Commons Attribution 3.0 unported (CC-BY 3.0) license, and based on my own image published in Acta, also under a CC-BY license.

If you’d like to know more about the science behind very long nerves in vertebrates, please see these posts:

Also, keep making stuff and putting it online under a license people can actually use. It’s beneficial for science and education, and hugely entertaining for me.

Reference

Wedel, M.J. 2012. A monument of inefficiency: the presumed course of the recurrent laryngeal nerve in sauropod dinosaurs. Acta Palaeontologica Polonica 57(2):251-256.

We as a community often ask ourselves how much it should cost to publish an open-access paper. (We know how much it does cost, roughly: typically $3000 with a legacy publisher, or an average of $900 with a born-open publisher, or nothing at all for many journals.)

We know that peer-review is essentially free to publishers, being donated free by scholars. We know that most handling editors also work for free or for peanuts. We know that hosting things on the Web is cheap (“publishing [in this sense] is just a button“).

Publishers have costs associated with rejecting manuscripts — checking that they’re by real people at real institutions, scanning for obvious pseudo-scholarship, etc. But let’s ignore those costs for now, as being primarily for the benefit of the publishers rather than the author. (When I pay a publisher an APC, they’re not serving me directly by running plagiarism checks.)

The tendency of many discussions I’ve been involved with has been that the main technical contribution of publishers is the process that is still, for historical reasons, known as “typesetting” — that is, the transformation of the manuscript from from an opaque form like an MS-Word file (or indeed a stack of hand-written sheets) into a semantically rich representation such as JATS XML. From there, actual typesetting into HTML or a pretty PDF can be largely automated.

So: what does it cost to typeset a manuscript?

First data point: I have heard that Kaveh Bazargan’s River Valley Technologies (the typesetter that PeerJ and many more mainstream publishers use) charges between £3.50 and £9 per page, including XML, graphics, PDF generation and proof correction.

Second data point: in a Scholarly Kitchen post that Kent Anderson intended as a criticism of PubMed Central but which in fact makes a great case for what good value it provides, he quotes an email from Kent A. Smith, a former Deputy Director of the NLM:

Under the % basis I am using here $47 per article. John [Mullican, a program analyst at NCBI] and I looked at this yesterday and based the number on a sampling of a few months billings. It consists on the average of about $34-35 per tagged article plus $10-11 for Q/A plus administrative fees of $2-3, where applicable.

Using the quoted figure of $47 per PMC article and the £6.25 midpoint of River Valley’s range of per-page prices (= $9.68 per page), that would be consistent with typical PMC articles being a bit under five pages long. The true figure is probably somewhat higher — maybe twice as long or more — but this seems to be at least in the same ballpark.

Third data point: Charles H. E. Ault, in a comment on that Scholarly Kitchen post, wrote:

As a production director at a small-to-middling university press that publishes no journals, I’m a bit reluctant to jump into this fray. But I must say that I am astonished at how much PMC is paying for XML tagging. Most vendors looking for the small amount of business my press can offer (say, maybe 10,000 pages a year at most) charge considerably less than $0.50 per page for XML tagging. Assuming a journal article is about 30 pages long, it should cost no more than $15 for XML tagging. Add another few bucks for quality assurance, and you might cross the $20 threshold. Does PMC have to pay a federally mandated minimum rate, like bridge construction projects? Where can I submit a bid?

I find the idea of 50-cent-per-page typesetting hard to swallow — it’s more than an order of magnitude cheaper than the River Valley/PMC level, and I’d like to know more about Ault’s operation. Is what they’re doing really comparable with what the others are doing?

Are there other estimates out there?

 

Re-reading an email that Matt sent me back in January, I see this:

One quick point about [an interesting sauropod specimen]. I can envision writing that up as a short descriptive paper, basically to say, “Hey, look at this weird thing we found! Morrison sauropod diversity is still underestimated!” But I honestly doubt that we’ll ever get to it — we have literally years of other, more pressing work in front of us. So maybe we should just do an SV-POW! post about the weirdness of [that specimen], so that the World Will Know.

Although as soon as I write that, I think, “Screw that, I’m going to wait until I’m not busy* and then just take a single week* and rock out a wiper* on it.”

I realize that this way of thinking represents a profound and possibly psychotic break with reality. *Thrice! But it still creeps up on me.

(For anyone not familiar with the the “wiper”, it refers to a short paper of only one or two pages. The etymology is left as an exercise to the reader.)

It’s just amazing how we keep on and on falling for this delusion that we can get a paper out quickly, even when we know perfectly well, going into the project, that it’s not going to work out that way. To pick a recent example, my paper on quantifying the effect of intervertebral cartilage on neutral posture was intended to be literally one page, an addendum to the earlier paper on cartilage: title, one paragraph of intro, diagram, equation, single reference, DONE! Instead, it landed up being 11 pages long with five illustrations and two tables.

I think it’s a reasonable approximation to say that any given project will require about an order of magnitude more work than we expect at the outset.

Even as I write this, the top of my palaeo-work priority list is a paper that I’m working on with Matt and two other colleagues, which he kicked off on 6 May, writing:

I really, really want to kill this off absolutely ASAP. Like, seriously, within a week or two. Is that cool? Is that doable?

To which I idiotically replied:

IT SHALL BE SO!

A month and a bit later, the answers to Matt’s questions are clear. Yes, it’s cool; and no, it’s not doable.

The thing is, I think that’s … kind of OK. The upshot is that we end up writing reasonably substantial papers, which is after all what we’re meant to be trying to do. If the reasonably substantial papers that end up getting written aren’t necessarily the ones we thought they were going to be, well, that’s not a problem. After all, as I’ve noted before, my entire Ph.D dissertation was composed of side-projects, and I never got around to doing the main project. That’s fine.

In 2011, Matt’s tutorial on how to find problems to work on discussed in detail how projects grow and mutate and anastamose. I’m giving up on thinking that this is a bad thing, abandoning the idea that I ought to be in control of my own research program. I’m just going to keep chasing whatever rabbits look good to me at the time, and see what happens.

Onwards!

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