As I was clearing out some clutter, I came across this hand-written list of projects that I wanted to get completed:

old-poop

Sadly, I didn’t put a date on the list. But I can estimate it as before 2013 (because of the reference of Why giraffes have short necks as a project still to be completed) but after 2011 (because the no necks for sex project is not listed.) So it’s probably from 2012, which means four years have passed since I wrote that list.

What have I achieved in that time? Not nearly enough.

  • ICZN checklist refers to the short set of name-a-new-animal instructions that I was crowdsourcing here on SV-POW!. We started this on 10 February 2011, had it nearly done less than two weeks later, then … stalled for no reason at all. Eighteen months later, the ICZN changed to allow electronic publication, instantly rendering the in-progress document obsolete. Now I don’t know whether to kill the project or update it. Should have just published it in 2011.
  • WTH (Why giraffes have short necks) was published in PeerJ, hurrah!
  • PBJ stands for “Pneumatic Butt on a JANGO“. It was published in the PLOS ONE’s sauropod gigantism collection, hurrah!
  • Archbishop is of course the Natural History Museum’s Tendaguru brachiosaur, which I have been planning to describe since 2004. Still not done. Shameful.
  • Apatosaurus” minimus is a descriptive project. Real work has been done, and I gave a talk about it at SVPCA in 2012. Not much progress since then. Lame.
  • Astrolembospondylus refers to the starship-shaped cervical vertebra of the Barosaurus holotype YPM 429. That project has seen daylight as both an SVPCA talk in 2013 and a PeerJ Preprint — which is great. But once the reviews were in, we should have turned it around and got it submitted as a proper paper. For some reason, we didn’t, and this project, too, is in limbo. Weak.
  • ODP is the Open Dinosaur Project. Do not get me started on that train-wreck.
  • Neck cartilage: giraffe, ostrich, croc. This refers to a comparative dissection project to determine whether sauropods had intervertebral discs. I proposed it as a Masters project twice, but no-one bit; then I offered to up to anyone who wanted it on SV-POW!, with the same (lack of) result. Looks like it’s not sexy enough for anyone to invest the time into, which is a shame because it’s important.
  • Limb cartilage limiting mass refers to the second talk I ever gave, at Progressive Palaeontology in 2004. It’s ridiculous that I never wrote this up. Ridiculous.
  • Haemodynamics refers to Matt’s and my looong-running plans to write up our thoughts about Roger Seymour’s work that suggests blood-circulation issues prevented sauropods from having habitually erect necks. I’m going to blame Matt for this one’s lack of progress. (Not because he’s any more to blame than I am — just because I’ve been taking all the blame so far, and I want to share it around a bit.)
  • Immature sauropods, pop. dynamics. Parts of this made it out in the recent Hone, Farke, and Wedel (2016) paper on dinosaur ontogenetic stages. Not as much as I’d have liked to see, but enough to make a dedicated paper about this not really feasible.
  • Ostrich skull atlas. I made lovely multi-view photos of nearly every bone in my ostrich skull. My plan was, and sort of still is, to publish them all in a text-light paper. No progress on this. I still have a few bones left to photograph, and may need to completely disarticulate the mandible before I can do that.
  • Wealden sauropod vert. analysis. I’d planned, going back to the earliest posts on this blog, to properly redescribe and analyse the many fascinating isolated sauropod vertebrae of the Wealden Formation. This is another one that I gave a ProgPal talk about before getting distracted. Not sure if this will ever happen: I’m still very interested in it, but even more interested in other things.
  • Fossils explained is a series of articles for geologists, explaining various fossil groups in laymen’s terms (here is an example). Darren’s done half a dozen of them. Once many years ago I expressed an interest in doing one on sauropods, and the editor liked the idea. Then … nothing. My bad.
  • Ventral compression bracing is a section that, heaven help us, we somehow decided we should remove from Why Giraffes Have Short Necks and make into its own paper. It got stalled on some croc-dissection work that Matt was doing with his student Vanessa and is now in limbo.

That’s fifteen projects that I had on the go, or planned to work on, four years ago. I make it that two of them (WTH and PBJ) have been published and one (Barosaurus) has made it as far as a the preprint stage. Three more are probably dead for various reasons, and that leaves nine where I’ve made woefully inadequate progress — in most cases, none at all.

Meanwhile, needless to say, I’ve added a bunch more projects to my To Do list since I scribbled this one out. (And to be fair to me, I’ve got a few other projects out in this time that weren’t mentioned in the note: neural spine bifurcation as Matt’s co-author, lead author on intervertebral cartilage and sole on its addendum; I slipped in as last author on Haestasaurus; and I wrote the SPARC briefing paper on evaluating researchers.)

What does all this mean?

I don’t know. Some of those no-progress yet projects are still very much alive in my mind — notably the Archbishop, of course. Others might never happen. Some are 90% done and I should just push them out the door.

One moral of this story is that I shouldn’t have burned 250 hours since Christmas playing Skyrim. But maybe a more constructive one is that it’s just really hard to know what projects are going to take wings and fly and which aren’t. My guess — and I’d love to hear some confirmation or denial in the comments — is that most researchers have a similar palette of half-done projects floating around their hindbrains, continually projecting low-level guilt rays. I guess I long ago gave up on the idea that I would ever finish all my projects, because the only way that would happen would be if I never started any more new ones — and that ain’t gonna happen.

Oh, here’s a better moral: ideas to work on are cheap. In fact Matt and I have so darned many that we sometimes just give them away here on SV-POW!. (I am pretty certain that there are lots more similar project-giveaway posts somewhere here, but we didn’t tag them at the time.)

Ideas are cheap; actual work is hard.

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I hate to keep flogging a dead horse, but since this issue won’t go away I guess I can’t, either.

1. Two years ago, I wrote about how you have to pay to download Elsevier’s “open access” articles. I showed how their open-access articles claimed “all rights reserved”, and how when you use the site’s facilities to ask about giving one electronic copy to a student, the price is £10.88. As I summarised at the time: “Free” means “we take the author’s copyright, all rights are reserved, but you can buy downloads at a 45% discount from what they would otherwise cost.” No-one from Elsevier commented.

2. Eight months ago, Peter Murray-Rust explained that Elsevier charges to read #openaccess articles. He showed how all three of the randomly selected open-access articles he looked at had download fees of $31.50. No-one from Elsevier commented (although see below).

3. A couple of days ago, Peter revisited this issue, and found that Elsevier are still charging THOUSANDS of pounds for CC-BY articles. IMMORAL, UNETHICAL , maybe even ILLEGAL.This time he picked another Elsevier OA article at random, and was quoted £8000 for permission to print 100 copies. The one he looked at says “Open Access” in gold at the top and “All rights reserved” at the bottom. Its “Get rights and content” link takes me to RightsLink, where I was quoted £1.66 to supply a single electronic copy to a student on a course at the University of Bristol:

Screenshot from 2014-03-11 09:40:35

(Why was I quoted a wildly different price from Peter? I don’t know. Could be to do with the different university, or because he proposed printing copies instead of using an electronic one.)

On Peter’s last article, an Elsevier representative commented:

Alicia Wise says:
March 10, 2014 at 4:20 pm
Hi Peter,

As noted in the comment thread to your blog back in August we are improving the clarity of our OA license labelling (eg on ScienceDirect) and metadata feeds (eg to Rightslink). This is work in progress and should be completed by summer. I am working with the internal team to get a more clear understanding of the detailed plan and key milestones, and will tweet about these in due course.

With kind wishes,

Alicia

Dr Alicia Wise
Director of Access and Policy
Elsevier
@wisealic

(Oddly, I don’t see the referenced comment in the August blog-entry, but perhaps it was on a different article.)

Now here is my problem with this.

First of all, either this is deliberate fraud on Elsevier’s part — charging for the use of something that is free to use — or it’s a bug. Following Hanlon’s razor, I prefer the latter explanation. But assuming it’s a bug, why has it taken two years to address? And why is it still not fixed?

Elsevier, remember, are a company with an annual revenue exceeding £2bn. That’s £2,000,000,000. (Rather pathetically, their site’s link to the most recent annual report is broken, but that’s a different bug for a different day.) Is it unreasonable to expect that two years should be long enough for them to fix a trivial bug?

All that’s necessary is to change the “All rights reserved” message and the “Get rights and content” link to say “This is an open-access article, and is free to re-use”. We know that the necessary metadata is there because of the “Open Access” caption at the top of the article. So speaking from my perspective as a professional software developer of more than thirty years’ standing, this seems like a ten-line fix that should take maybe a man-hour; at most a man-day. A man-day of programmer time would cost Elsevier maybe £500 — that is, 0.000025% of the revenue they’ve taken since this bug was reported two years ago. Is it really too much to ask?

(One can hardly help comparing this performance with that of PeerJ, who have maybe a ten-thousandth of Elsevier’s income and resources. When I reported three bugs to them in a course of a couple of days, they fixed them all with an average report-to-fix time of less than 21 hours.)

Now here’s where it turns sinister.

The PeerJ bugs I mentioned above cost them — not money, directly, but a certain amount of reputation. By fixing them quickly, they fixed that reputation damage (and indeed gained reputation by responding so quickly). By contrast, the Elsevier bug we’re discussing here doesn’t cost them anything. It makes them money, by misleading people into paying for permissions that they already have. In short, not fixing this bug is making money for Elsevier. It’s hard not to wonder: would it have remained unfixed for two years if it was costing them money?

But instead of a rush to fix the bug, we have this kind of thing:

I find that very hard to accept. However complex your publishing platform is, however many different modules interoperate, however much legacy code there is — it’s not that hard to take the conditional that emits “Open Access” in gold at the top of the article, and make the same test in the other relevant places.

As John Mark Ockerbloom observes:

Come on, Elsevier. You’re better than this. Step up. Get this done.

Update (21st March 2014)

Ten days layer, Elsevier have finally responded. To give credit where it’s due, it’s actually pretty good: it notes how many customers made payments they needn’t have made (about 50), how much they paid in total (about $4000) and says that they are actively refunding these payments.

It would be have been nice, mind you, had this statement contained an actual apology: the words “sorry”, “regret” and “apologise” are all notably absent.

And I remain baffled that the answer to “So when will this all be reliable?” is “by the summer of 2014”. As noted above, the pages in question already have the information that the articles are open access, as noted in the gold “Open Access” text at top right of the pages. Why it’s going to take several more months to use that information elsewhere in the same pages is a mystery to me.

Update 2 (24th March 2014)

As noted by Alicia in a comment below, Elsevier employee Chris Shillum has posted a long comment on Elsevier’s response, explaining in more detail what the technical issues are. Unfortunately there seems to be no way to link directly to the comment, but it’s the fifth one.

 

Better

AMNH T. rex mount, photo by Mike Taylor.

In a recent comment, Doug wrote:

If I want to be a truly educated observer of Tyrannosaurus rex mounts, what 5 things should I look for in a reconstruction to assess if it is true to our current scientific understanding? I’m not talking tail dragging/upright at this point…we are well past that I hope.

If he had asked about Apatosaurus, I could have written him a novel. But it is a point of pride with me not to contribute to the over-application of human attention to T. rex; not only would it be vulgar, it would also be a waste of resources, considering how many people already have that covered. So, you theropod workers and avocational “rexperts”, we’re finally inviting you to the high table. Please, tell us–and Doug–what separates the good T. rex mounts from the crappy ones. Big piles of SV-POW! bucks will be showered on whoever brings the most enlightenment, especially if you adhere to the requested List of 5 Things format.

The comment lines are open–go!

Suppose, hypothetically, that you worked for an organisation whose nominal goal is the advancement of science, but which has mutated into a highly profitable subscription-based publisher. And suppose you wanted to construct a study that showed the alternative — open-access publishing — is inferior.

What would you do?

You might decide that a good way to test publishers is by sending them an obviously flawed paper and seeing whether their peer-review weeds it out.

But you wouldn’t want to risk showing up subscription publishers. So the first thing you’d do is decide up front not to send your flawed paper to any subscription journals. You might justify this by saying something like “the turnaround time for traditional journals is usually months and sometimes more than a year. How could I ever pull off a representative sample?“.

Next, you’d need to choose a set of open-access journals to send it to. At this point, you would carefully avoid consulting the membership list of the Open Access Scholarly Publishers Association, since that list has specific criteria and members have to adhere to a code of conduct. You don’t want the good open-access journals — they won’t give you the result you want.

Instead, you would draw your list of publishers from the much broader Directory of Open Access Journals, since that started out as a catalogue rather than a whitelist. (That’s changing, and journals are now being cut from the list faster than they’re being added, but lots of old entries are still in place.)

Then, to help remove many of the publishers that are in the game only to advance research, you’d trim out all the journals that don’t levy an article processing charge.

But the resulting list might still have an inconveniently high proportion of quality journals. So you would bring down the quality by adding in known-bad publishers from Beall’s list of predatory open-access publishers.

Having established your sample, you’d then send the fake papers, wait for the journals’ responses, and gather your results.

To make sure you get a good, impressive result that will have a lot of “impact”, you might find it necessary to discard some inconvenient data points, omitting from the results some open-access journals that rejected the paper.

Now you have your results, it’s time to spin them. Use sweeping, unsupported generalisations like “Most of the players are murky. The identity and location of the journals’ editors, as well as the financial workings of their publishers, are often purposefully obscured.”

Suppose you have a quote from the scientist whose experiences triggered the whole project, and he said something inconvenient like “If [you] had targeted traditional, subscription-based journals, I strongly suspect you would get the same result”. Just rewrite it to say “if you had targeted the bottom tier of traditional, subscription-based journals”.

Now you have the results you want — but how will you ever get through through peer-review, when your bias is so obvious? Simple: don’t submit your article for peer-review at all. Classify it as journalism, so you don’t need to go through review, nor to get ethical approval for the enormous amount of editors’ and reviewers’ time you’ve wasted — but publish it in a journal that’s known internationally for peer-reviewed research, so that uncritical journalists will leap to your favoured conclusion.

Last but not least, write a press-release that casts the whole study as being about the “Wild West” of Open-Access Publishing.

Everyone reading this will, I am sure, have recognised that I’m talking about  John Bohannon’s “sting operation” in Science. Bohannon has a Ph.D. in molecular biology from Oxford University, so we would hope he’d know what actual science looks like, and that this study is not it.

Of course, the problem is that he does know what science looks like, and he’s made the “sting” operation look like it. It has that sciencey quality. It discusses methods. It has supplementary information. It talks a lot about peer-review, that staple of science. But none of that makes it science. It’s a maze of preordained outcomes, multiple levels of biased selection, cherry-picked data and spin-ridden conclusions. What it shows is: predatory journals are predatory. That’s not news.

Speculating about motives is always error-prone, of course, but it it’s hard not to think that Science‘s goal in all this was to discredit open-access publishing — just as legacy publishers have been doing ever since they realised OA was real competition. If that was their goal, it’s misfired badly. It’s Science‘s credibility that’s been compromised.

Update (9 October)

Akbar Khan points out yet more problems with Bohannon’s work: mistakes in attributing where given journals were listed, DOAJ or Beall’s list. As a result, the sample may be more, or less, biased than Bohannon reported.

 

 

 

No time for anything new, so here’s a post built from parts of other, older posts.

The fourth sacral centrum of Haplocanthosaurus CM 879, in left and right lateral view. This is part of the original color version of Wedel (2009: figure 8), from this page. (Yes, I know I need to get around to posting the full-color versions of those figures. It’s on my To Do list.)

Note the big invasive fossa on the right side of the centrum. The left side is waisted (narrower at the middle than the ends) like most vertebrae of most animals, but has no distinct fossa on lateral face of the centrum. What’s up with that? Here’s an explanation from an old post (about another sauropod) that still fits:

Now, this asymmetry is also weird, but it’s expected weirdness. Pneumaticity seems to just be inherently variable, whether we’re talking about human sinuses or the facial air sacs of whales or the vertebrae of chickens. It appears that the form of pneumatic features is entirely determined by local tissue interactions, with little or no genetic control of the specific form. Think of it this way: genes prescribe certain developmental events, and those events bring tissues into contact–such as pneumatic epithelium and bone. The morphology of the bone arises out of that interaction, and each interaction of bone and pneumatic epithelium has the potential to produce something new. In this case, the diverticula on the left side of the vertebral column come from the lungs or air sacs on the left, and those on the right side come from the lungs or airs sacs on the right, so it’s really two sets of diverticula contacting the bone independently. The wonder, then, is not that pneumatic bones are so variable, but that we see any regularities at all.

I do not dare behold it

January 14, 2011

By a curious coincidence, today’s Bob The Angry Flower cartoon is all about the Archbishop description.

Enjoy.

But, hey, at least I got my confession in early — I was officially the first participant to fail the 2010 Paleo Project Challenge.

THIS year, for sure!

 

Pimp my ‘pod 2: haids

December 13, 2010

Here’s another dual-purpose post (part 1 is here), wherein I use some of Brian Engh’s cool art to riff on a related topic (with kind permission–thanks, Brian!). Back when he was first planning his awesome Sauroposeidon life restoration, Brian sent these head studies:

(Note that Brian’s ideas were still evolving at this point, and he roofed the nasal chamber with a keratinous resonating chamber instead of the inflatable sac seen in the finished product. I think both are plausible [not likely, just plausible] and look pretty rad, although the latter is obviously a lot more metal.)

I think these are dynamite, because they show that you can avoid “shrink-wrapped dinosaur syndrome” (SWDS) and still make an anatomically detailed, realistic-looking life restoration. SWDS is what I call the common convention in paleo-art of simply draping the skeleton–and especially the skull–in Spandex and calling that a life restoration. I think it’s a popular technique because you can show off the skeleton inside the animal and thereby demonstrate that you’ve done your homework (especially to an audience that already knows the skeletons*). It gives artists an easy way to add detail to their critters; if you actually slab on realistic soft tissues and lose most of those skeletal and cranial landmarks, you have to come up with something else to make your animals look detailed and visually interesting. And by now it’s been going strong for several decades, so people expect it.

* Without harshing on anyone, I suspect that a lot of consumers of paleo-art have spent more time looking at dinosaur skeletons than looking at live animals and thinking about how much or little of their skeletal structure is visible in life, which may make them susceptible to mistaking “shows a lot of the bony structure” for “biologically realistic”. I suspect that because it was true of me for a good chunk of my life; as usual, the one ranting is ranting mostly at his former self. What cured me was dissecting animals and reading TetZoo–happily, two avenues of self-improvement that are open to everyone.

In the second image above (the one showing the innards) Brian kindly credited me for lending a little assistance. That assistance was mainly in forwarding him my full cranio-centric anti-SWDS rant, which I originally put together for a certain documentary that ended up using almost none of my ideas. I’ve been meaning to recycle it here for ages, and Brian’s new art is just the kick in the pants I needed. Without further ado:

“Sauroposeidon head suggestions no labels.jpg” [above] shows a mock-up of the skull, a traditional restoration of the head, the skull with accurate soft tissues, and an updated restoration. The traditional restoration looks like a lot of paleoart from the past two decades–it looks like someone shrink-wrapped the skull. But this is not what the heads of real animals look like at all. If you look at almost any animal, whether it is a lizard, croc,* turtle, snake, bird, cow, horse, rodent, or human, you can’t see the holes in the skull because they are filled with muscles or air sacs and smoothed over with skin. Here are the 8 specific features I fixed in the updated restoration:

* I got a little carried away here–some of the holes in croc skulls are not hard to make out, because their skin is unusually tightly bound to the very rugose skull. Most dinosaurs didn’t have that same skull texture, and there is little reason to think that their heads were similarly shrink-wrapped. Abelisaurs, maybe. Sauropods, not so much.

(1) the profile of the top of the head and start of the neck would have been smoothed out by jaw muscles bulging through holes in the top of the head (strange but true), and by neck muscles coming up onto the back of the skull.

(2) The fleshy nostril should be down on the snout at the end of the nasal troughs. The bony nostrils make that huge hump on top of the head, but they are continuous with these two grooves that run down the front of the face, and almost certainly the whole bony-nostril-plus-groove setup was covered by soft tissues and the actual air holes were down on the snout. That fleshy covering would have been propped up and not sucked down tight to the skull, so you wouldn’t be able to see the boundaries of bony nostrils from the outside. The fleshy nostril should also be fairly big; it is unlikely that a 50-ton animal with a head a yard long had nostrils the size of a horse’s.

(3) The holes in the skull should not be visible. The habit of drawing and painting dinosaurs with shrink-wrapped heads is so entrenched that smooth heads look undetailed and a little fake, but smooth heads are undoubtedly more accurate. The head wasn’t necessarily a completely smooth bullet–it probably had decorative scales and patches of color–but we can be fairly certain that the holes in the skull were not visible through the skin.

(4) The jaw joint is all the way at the back of the head, but past the tooth row the upper and lower jaws were bound together by jaw muscles.  When the jaws opened, as shown in the lower images, the muscles were covered by skin. This skin might have been outside the jaws and stretchy, as shown in the attached image “bird cheeks.jpg”, or it might have been tucked in between the jaws as shown in “croc cheeks.jpg” [below].

Another caveat in my own defense: I know that condors do not have muscular, mammal-style cheeks, so the “cheek” skin here is doing more than just covering jaw muscles (farther back on the  jaw the skin is covering jaw muscles). Remember that I was writing quick art suggestions for a less technically sophisticated audience, not a dissertation on condor heads. The take home point is that you can’t tell from looking at the condor below where the jaw muscles start or where the jaw joint is located (unless you already know something about bird skulls). Other than the  gross outline, there simply isn’t much osteology on display–and this is a naked head!

(5) The eyes are usually reconstructed as small, dull, and centered in the vertical middle of the eye socket. In fact the eyes were probably located toward the top end of the eye socket, they were probably colorful as in most reptiles and birds, and they may have been pretty big. [But not that big; see Mickey’s comment below, and note that Brian got it right anyway.]

(6) The external ear hole is usually left out. It should be behind the back of the skull and in front of the hindmost jaw muscles.

(7) The profile of the back of the head follows jaw muscles, not the boundaries of the skull bones.

(8) Sauropods had true flip-top heads. The skull of Giraffatitan looks like nothing so much as an upside down toilet bowl, with the toilet seat for the lower jaw. Sauropods probably used that big gape to shove in as much plant material as possible per unit time. Crocodiles and many birds have an extensible throat pouch that allows them to bolt larger bites than you’d think, and the same was probably true of most dinosaurs, especially sauropods. There may have been a visible division between the muscular neck and this fleshy “gullet”. See “croc throat.jpg” and “bird throat.jpg” [below].

After seeing one of the preliminary designs for the documentary Sauroposeidon–which sadly ended up being a Big Gray Pachyderm in the show–I sent the following. Even though they ignored it, and even though it appears here as a rehash of an argument I’ve made several times already, I’m still proud of it. Especially the concluding advice–potential artistic collaborators take note!
I think you could safely put on a lot more color. People are used to big animals being dull, but that’s because most big animals are mammals and, except for primates, all mammals are effectively colorblind. So big mammals are a horrible guide to how colorful other big animals might be. Komodo dragons and crocs are both fairly dull, but they’re all ambush predators and they have to be dull or they don’t eat. If I get inspired I might take your Sauroposeidon into Photoshop and color it up; otherwise maybe have your artists look at tropical birds, toss back a couple of stiff drinks, and throw caution to the wind.