How can it be?

IMG_0517

All credit to the Yale Peabody Museum for having the courage to display this historically important object in their public gallery instead of hiding it in a basement. It’s the skull from the original mount of the Brontosaurus (= Apatosaurus) excelsus holotype YPM 1980.

Needless to say, it bears no resemblance at all to the actual skull of Apatosaurus, and the one they now have on the mount is much, much better:

IMG_0500-skull

But how did the YPM people ever arrive at this double-plus-ugly skull above? We see a similar skull in Marsh’s (1891) second attempt at restoring the skeleton of Brontosaurus:

Marsh1891-plateXVI-Apatosaurus-skull

But even this is not as ugly and Just Plain Wrong as the physical model they made. (Marsh’s first restoration of the Brontosaurus skeleton, in 1893, had a much less clear skull.)

So how did the YPM come to make such a monstrosity? What was it based on? Tune in next time for the surprising details!

Bizarrely, we’ve never really featured the  YPM 1980 mount here on SV-POW! — we’ve often shown individual bones, but the mounted skeleton appears only in the background of the much less impressive Morosaurus (= Camarasaurus) lentus mount. We’ll fix that real soon.

 

Five days ago, I released a program for drawing comparative figures of vertebral columns, such as this one from our neural-spine bifurcation paper. With my idiot computer-scientist hat on, I gave that program the startlingly unmemorable name vcd2svg — the reasoning being that it takes Vertebral Column Descriptions and translates them into Scalable Vector Graphics.

In a comment on that post, Vertebrat rightly noted:

The name is a bit opaque. It sounds like a tool for people who have VCD files and want to convert them to SVG. Maybe this means extracting frames from Video CD files as SVG (a rather inappropriate format)? :)

Your target users don’t have VCD files, don’t want to convert anything, and have little or no preference for SVG. They want to make diagrams of vertebrae.

A fair point. Accordingly, I have renamed the program VertFigure — a name chosen in part because Google doesn’t know of anything else with the same name. The canonical GitHub page is now http://github.com/MikeTaylor/VertFigure but the old address still works, and git checkouts made from the old name will also continue to work. The command-line program that does the conversion is now also named VertFigure.

 

Visiting relatives in Texas, just like last spring. Very distant relatives. And this happened:

Photobombing fawn

Here’s the culprit, with his sidekicks Monorail Badger, Trashbag Tortoise, and Kas-Tor, Last Beaver of Krypton. A disreputable bunch.

Dude I am so stuffed

The victim. Some call him the Winter Cervical. He was fast, strong–and he had a metal arm…ature.

Paluxysaurus vert

Meanwhile, in the back:

DinoMorph horse

I think it’s fair to say that this “bifurcation heat-map”, from Wedel and Taylor (2013a: figure 9), has been one of the best-received illustrations that we’ve prepared:

Wedel and Taylor 2013 bifurcation Figure 9 - bifurcatogram

(See comments from Jaime and from Mark Robinson.)

Back when the paper came out, Matt rashly said “Stand by for a post by Mike explaining how it came it be” — a post which has not materialised. Until now!

This illustration was (apart from some minor tweaking) produced by a program that I wrote for that purpose, snappily named “vcd2svg“. That name is because it converts a vertebral column description (VCD) into a scalable vector graphics (SVG) file, which you can look at with a web-browser or load into an image editor for further processing.

The vertebral column description is in a format designed for this purpose, and I think it’s fairly intuitive. Here, for example, is the fragment describing the first three lines of the figure above:

Taxon: Apatosaurus louisae
Specimen: CM 3018
Data: —–YVVVVVVVVV|VVVuuunnn-

Taxon: Apatosaurus parvus
Specimen: UWGM 155556/CM 563
Data: –nnn-VVV—V-V|VVVu——

Taxon: Apatosaurus ajax
Specimen: NMST-PV 20375
Data: –n–VVVVVVVVVV|VVVVYunnnn

Basically, you draw little ASCII pictures of the vertebral column. Other directives in the file explain how to draw the various glyphs represented by (in this case) “Y”, “V”, “u”, and “n”.

It’s pretty flexible. We used the same program to generate the right-hand side (though not the phylogenetic tree) of Wedel and Taylor (2013b: figure 2):

Wedel and Taylor (2013b: Figure 2).

Wedel and Taylor (2013b: Figure 2).

The reason I mention this is because I released the software today under the GNU General Public Licence v3.0, which is kind of like CC By-SA. It’s free for anyone to download, use, modify and redistribute either verbatim or in modified form, subject only to attribution and the requirement that the same licence be used for modified versions.

vcd2svg is written in Perl, and implemented in part by the SVG::VCD module, which is included in the package. It’s available as a CPAN module and on GitHub. There’s documentation of the command-line vcd2svg program, and of the VCD file format. Also included in the distribution are two documented examples: the bifurcation heat-map and the caudal pneumaticity diagram.

Folks, please use it! And feel free to contribute, too: as the change-log notes, there’s work still to be done, and I’ll be happy to take pull requests from those of you who are programmers. And whether you’re a programmer or not, if you find a bug, or want a new feature, feel free to file an issue.

A final thought: in academia, you don’t really get credit for writing software. So to convert the work that went into this release into some kind of coin, I’ll probably have to write a short paper describing it, and let that stand as a proxy for the actual program. Hopefully people will cite that paper when they generate a figure using the software, the way we all reflexively cite Swofford every time we use PAUP*.

Update (12 April 2014)

On Vertebrat’s suggestion, I have renamed the program VertFigure.

References

Illustration talk slide 61

Illustration talk slide 62

Illustration talk slide 63

Illustration talk slide 64

Illustration talk slide 65

Illustration talk slide 66

The rest of the series is here. As promised, here are the files for the talk, in PPT and PDF formats.

Wedel 2014 Photography and illustration lecture (PPT, ~53 Mb)

Wedel 2014 Photography and illustration lecture (PDF, ~21 Mb)

References

Illustration talk slide 58

Illustration talk slide 59

Illustration talk slide 60

The rest of the series.

References

This morning sees the publication of the new Policy for open access in the post-2014 Research Excellence Framework from HEFCE, the Higher Education Funding Council for England. It sets out in details HEFCE’s requirement that papers must be open-access to be eligible for the next (post-2014) Research Excellence Framework (REF).

Here is the core of it, quoted direct from the Executive Summary:

The policy states that, to be eligible for submission to the post-2014 REF, authors’ final peer-reviewed manuscripts must have been deposited in an institutional or subject repository on acceptance for publication. Deposited material should be discoverable, and free to read and download, for anyone with an internet connection [...]  The policy applies to research outputs accepted for publication after 1 April 2016, but we would strongly urge institutions to implement it now.

There are lots of ifs, buts and maybes, but overall this is excellent news, and solid confirmation that the UK really is committed to an open-access transition. Before we go into those caveats, let’s take a moment to applaud the real, significant progress that this policy represents. For the first time ever, universities’ funding levels, and so individual academics’ careers, will be directly tied to the openness of their output. Congratulations to HEFCE!

celebrate-2

Also commendable: the actual policy document is very carefully written, and includes details such as “Outputs whose text is encoded only as a scanned image do not meet the requirement that the text be searchable electronically.” It’s evident that a lot of careful thought has gone into this.

Now for those caveats:

The policy will not apply to monographs, book chapters, other long-form publications, working papers, creative or practice-based research outputs, or data.

This is a shame, but understandable, especially in the case of books. I would have hoped that chapters within edited volumes would have been included. But the main document notes that “Where a higher education institution (HEI) can demonstrate that it has taken steps towards enabling open access for outputs outside the scope of this definition, credit will be given in the research environment component of the post-2014 REF.”

Next disappointment:

The policy allows repositories to respect embargo periods set by publications. Where a publication specifies an embargo period, authors can comply with the policy by making a ‘closed’ deposit on acceptance. Closed deposits must be discoverable to anyone with an Internet connection before the full text becomes available for read and download (which will occur after the embargo period has elapsed). Closed deposits will be admissible to the REF.

I would of course have wanted all embargo periods to be eliminated, or at the very least capped at six months as in the old, pre-watering-down, RCUK policy. But that was too much to hope for in the political environment that publishers have somehow managed to create.

More positively, it’s a good sop that deposit must be made on acceptance — not when the embargo expires, or even on publication, but on acceptance. These “closed deposits” are like a formal promise of openness, with an automated implementation. We don’t have good experimental data on this, but it seems likely that this approach will result in much better compliance rates than just telling authors “you have to come back six to 24 months after publication and make a deposit”.

Third disappointment:

There are a number of exceptions to the various requirements that will be automatically allowed by the policy. These exceptions cover circumstances where deposit was not possible, or where open access to deposited material could not be achieved within the policy requirements. These exceptions will allow institutions to achieve near-total compliance, but the post-2014 REF will also include a mechanism for considering any other exceptional cases where an output could not otherwise meet the requirements.

The exceptions encourage weasel-wordage, of course, and some of the specific exceptions listed in Appendix C are particularly weak: “Author was unable to secure the use of a repository”, “Publication is print-only (no electronic version)”, and the lamentable “Publication does not offer a compliant green or gold option”, which really means “HEFCE authors should not be using this publication”.

But when you read into the details, this approach with specific exceptions is actually rather better than the alternative that had been on the table: a percentage-based target, where some specific proportion of REF submissions would need to be open access. Instead of saying “80% of submissions must be open access” (or some other percentage), HEFCE is saying that it wants them all to be open access except where a specific excuse is given. I’d like them to be much less accommodating with what excuses they’ll accept, but the important thing here is that they have set the default to open.

Now for the most regrettable part of the policy:

While we do  not request that outputs are made available under any particular licence, we advise that outputs licensed under a Creative Commons Attribution Non-Commercial Non-Derivative (CC BY-NC-ND) licence would meet this requirement.

I won’t rehearse again all the reasons that Non-Commercial and No-Derivatives clauses are poison, I’ll just note that works published under this licence are not open access according to the original definition of that term, which allows us to “use [OA works] for any other lawful purpose, without financial, legal, or technical barriers”.

Yet even here, the general tenor of the policy is positive. While it accepts NC-ND, the policy adds that “where an HEI can demonstrate that outputs are presented in a form that allows re-use of the work, including via text-mining, credit will be given in the research environment component of the post-2014 REF”.

One last observation: HEFCE should be commended on having provided an excellent, detailed explanation of feedback they received to their consultations. As always, reading such documents can be frustrating because they necessarily contain some views very different from mine; but it’s useful to see the range of opinions laid out so explicitly.

No open-access policy document I’ve ever seen has been perfect, and this one is no exception. But overall, the HEFCE open-access policy is a significant and welcome step forward, and carries the promise of further positive moves in the future.

 

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