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.

 

 

 

I started teaching fifteen years ago, as a graduate student at the University of Oklahoma in the spring of 1998. This document is a summary of everything I’ve learned about how students learn from then up until now. I’m setting it down in print because I found myself giving the same advice over and over again to students in one-on-one sessions—and at least for some of them, it’s made a difference.

Here’s the summary. The rationale for each point is explained in more detail below.

  1. Learn how you learn.
  2. Use your solo study time to build things.
  3. Use your group study time to explain things to other people, and to have them explain things to you.
  4. Focus on the stuff that scares you; use your fear as an ignorance-detector.
  5. Review everything on a regular basis—for a given exam, daily if possible.
  6. Spread out your study time so you don’t study past the point of diminishing returns.
  7. Spend as much time in lab as possible.
  8. Learn to ask for help.

1. Learn how you learn.

All of the rest of this advice will be many times more effective once you learn how you learn. Some people are visual learners, some verbal, some more narrative, some more spatial. I myself am visual all the way. I can really struggle with written descriptions, but if I draw something a couple of times, it will be in my head forever. I have a colleague who is just the opposite, and her preferred study method is to organize everything into giant tables. Now, I don’t know a ton about all the different learning modes, but other people do, and most schools have some kind of education, counseling, or student services office with people who can help you figure this out. If you don’t have access to resources like that, fear not: you can probably diagnose your strongest learning mode on your own, by straightforward experimentation. Observe your information consumption—what kinds of things do you gravitate toward, and what kinds of explanations do you struggle with?

2. Build things.

When you study, don’t just read your notes or watch videos. Build things. My very first question when students come to me about studying is, “What are you building when you study?” I don’t care if it is sketches or tables or flashcards or posters or interpretive dance—that’s for you to figure out (see point [1]). But whatever your preferred avenue of expression, if you spend at least part of your study time making things, you will engage your motor neurons, which is a way of coercing your interneurons into actually thinking about the output. And that will help fix the information in your brain. In short, active learning beats passive learning. And as a bonus, you’ll have your own customized notes that you can return to later (for example, when you’re studying for boards).

3. Study with a group, and explain things to each other.

In all of my time teaching anatomy at four different universities, it has always been true that the students who did the best were part of effective study groups. It’s not just autocorrelation, because struggling students improve when they join effective study groups. I think that this is because people in effective study groups spend their time asking each other questions, not just to quiz each other, but primarily in the vein of, “I don’t understand this, can you please explain it to me.” (Hint: if you don’t do that in your study group, maybe your group is not effective. The fix is obvious.) And when you try to explain something to someone else, you will rapidly find out what you actually understand versus what you only thought you understood. And when other people explain things to you, at best you are getting tutored, and at worst they are finding their own weaknesses, although ideally both things go on at once, and both parties benefit.

I reckon that about half of what I learned in graduate school, I learned from my fellow grad students. I am pretty sure that my advisors understood and anticipated that, and deliberately fostered environments in which peer-to-peer teaching could flourish. In small group work you can get more focused, individual attention than you can in a lecture hall with dozens or hundreds of other people. Don’t only study in groups—some solo study is necessary to firm things up for yourself, and to build your own tools (see point [2])—but don’t only study on your own, either.

4. Study what you’re afraid of.

Use fear and anxiety to your advantage: let them direct you to study what you’re afraid of. Think of your study time as a bug hunt, in which you systematically identify your weaknesses and deal with them. If  you know the lungs cold but the thought of cardiac autonomics causes your pulse to spike, then you already know where you need to put the time in. Use confusion and fear as diagnostics for areas you need to work on.

5. Review everything regularly.

Repetition beats cramming, for at least a couple of reasons. One is that anatomy, like most subjects dealing with nature, is a continuum. But you tend to get it delivered in 50-minute chunks, with the inherent continuity broken up into more-or-less arbitrary bins (“hip”, “thigh”, “knee”, etc.). One of your primary jobs, then, is to take this string of chunks and mentally turn it back into a continuum: to find the joins between adjacent lectures, and the overarching  principles that unite them all. The best way I know to do this is to review everything on a regular basis—daily, if possible. If you have two hours blocked out to study, spend the first 30 minutes going over your notes* from all of the previous lectures, then get on to the day’s topic. Next time, whatever you studied today will be another link in the chain. In time, you will see how today’s material links back to previous lectures, and forward to later ones.

* The whole point of notes (by which I mean sketches, flashcards, etc.—whatever it is that you are building during your study time) is to serve as a funnel between the course material and your brain. So useful notes have to package things so they are easier to understand. If the map is as complicated as the territory, it’s not really a map. It’s okay if your first set of notes is overly long and ugly, because your first set of notes should not be your only set. As your understanding improves, build new tools (i.e., make new notes) that reflect that.

6. Don’t study past the point of diminishing returns.

This is the other reason why repetition beats cramming. You need to revisit the material multiple times because the amount you can learn in one session is finite. There is a real biological basis for this: the neurotransmitters and receptors involved in shifting information from short-term memory to long-term memory need a certain amount of time to recharge, and that time is measured in hours, not minutes. Somewhere around the three hour mark, your brain will have absorbed as much as it can for that session. You can keep putting more stuff into short-term memory, but it won’t get copied to long-term memory. Get up and do something else, and come back to it that evening, or the next day. (“Do something else” can mean “do useful work for your other classes”, especially if the work for other classes is different in kind, like practicing techniques.) The more times you revisit the material, the more opportunities you have to successfully copy it into long-term memory, the more you actually learn.

This may sound crazy, because we have all had episodes of sustained effort lasting more than three hours, like a day at work. The difference is that at work, you’re not trying to remember everything, and when you study, that is precisely what you are trying to do. I have had students tell me that they are studying for six to eight hours at a time and they’re still not getting it. This is heartbreaking—such long uninterrupted sessions guarantee that at least half of that time is simply wasted. You absolutely can study effectively for six or eight hours a day, you just need to break up the time: two hours in the morning, three in the afternoon, another three in the evening, so your neurotransmitters can recharge in between. You will hear people say things like, “Study smarter, not harder.” Mostly this boils down to, “Study actively and more frequently, not passively or for too long at a stretch.”

7. Spend as much time as you can in the lab.

Spend as much time as you can in lab, not just on dissecting days, but anytime the lab is open. We have a saying, that you learn concepts in the lecture hall but you learn anatomy in the lab. The time with the cadavers is a gift, the only opportunity you will have for the rest of your career to spend dozens of hours getting tactile experience cutting on patients who don’t bleed and can’t code. Use it. “But what about my friends, family, pets, hobbies—my life?” Your life extends ahead of you for decades. Your time in the anatomy lab lasts for a few weeks at most.

8. Learn to ask for help.

The last thing I have to say is the most important: learn to ask for help. I am on one of the student performance committees at WesternU, where students end up when they fail courses. There are a constellation of things that may cause a student to fail a course, but one of the big ones is trying to bull through alone. I get it—you were hot stuff in high school, maybe college too, the big fish in the small pond, and you’re used to being the smartest person in the room. Well, now you’re in med school, and your previous specialness is now the default for everyone here. It is very likely that college did not prepare you to work anywhere near as hard as you will have to now. The good news is that you are therefore untested, so even you don’t know how much you are capable of. In the next few years, you will find reserves of strength that you did not know you possess—but you will not do it alone. Asking for help is not a sign of weakness. It means that you are strong enough to be honest about your limitations, which is the first step to overcoming them. In my experience, more people fail out of pride than from lack of ability.

Whom should you ask for help? It depends on your situation, but a short list includes peers, TAs, professors, student services, counselors, and the school administration. If you don’t know whom to ask, just ask someone, and they’ll probably point you in the right direction. Usually knowing whom to ask is not the hurdle—it’s being willing to ask in the first place. If you are struggling in a course and you haven’t been to talk to the instructor, then you’re not trying as hard as you could be. You have committed years of your life to this. Isn’t succeeding more important than polishing your pride while the ship sinks? Learn to ask for help.

OMNH baby Apatosaurus

I was at the Oklahoma Museum of Natural History in March to look at their Apatosaurus material, so I got to see the newly-mounted baby apatosaur in the “Clash of the Titans” exhibit (more photos of that exhibit in this post). How much of this is real (i.e., cast from real bones, rather than sculpted)? Most of the vertebral centra, a few of the neural arches, some of the limb girdle bones, and most of the long bones of the limbs. All of the missing elements–skull, neural arches, ribs, appendicular bits–were sculpted by the OMNH head preparator, Kyle Davies. Kyle is one of those frighteningly talented people who, if they don’t have what they need, will just freaking build it from scratch. Over the years he has helped me out a LOT with the OMNH sauropod material–including building a clamshell storage jacket for the referred scapula of Brontomerus so we could photograph it from the lateral side–so it’s about time I gave him some props.

Atlas-axis model with Kyle

Case in point: this sweet atlas-axis complex that Kyle sculpted for the juvenile Apatosaurus mount.

Atlas-axis model by Kyle Davies

Most fish, amphibians, and other non-amniote tetrapods only have a single specialized vertebra for attaching to the skull. But amniotes have two: a ring- or doughnut-shaped first cervical vertebra (the atlas) that articulates with the occipital condyle(s) of the skull, and a second cervical vertebra (the axis) that articulates with the atlas and sometimes with the skull as well. Mammals have paired occipital condyles on the backs or bottoms of our skulls, so our skulls rock up and down on the atlas (nodding “yes” motion), and our skull+atlas rotates around a peg of bone on the axis called the odontoid process or dens epistrophei (shaking head “no” motion). As shown in the photos and diagrams below, the dens of the axis is actually part of the atlas that fuses to the second vertebra instead of the first. Also, reptiles, including dinosaurs and birds, tend to have a single ball-shaped occipital condyle that fits into the round socket formed by the atlas, so their “yes” and “no” motions are less segregated by location.

Anyway, the whole shebang is often referred to as the atlas-axis complex, and that’s the reconstructed setup for a baby Apatosaurus in the photo above.  In addition to making a dull-colored one for the mount, Kyle made this festive version for the vert paleo teaching collection. Why so polychromatic?

Atlas-axis model key

Because in fact he built two: the fully assembled one two photos above, and a completely disassembled one, some of which is shown in this photo (I had to move the bigger bits out of the tray so they wouldn’t block the key card at the back). I originally composed this post as a tutorial. But frankly, since Kyle did all of the heavy lifting of (a) making the thing in the first place, (2) making a color-coded key to it, and (d) giving me permission to post these photos, it would be redundant to walk through every element. So think of this as a self-study rather than a tutorial.

UPDATE in December, 2019: oh heck with it, I’m very belatedly renaming this a tutorial, so I can tag on a follow-up post as Tutorial 36b and curate this where it belongs, on our Tutorials page. The URL will stay the same, like a digital fossil.

Atlas-axis model by Kyle Davies - labeled

Oh, all right, here’s a labeled version. Note that normally in an adult animal the single piece of bone called the atlas would consist of the paired atlas neural arches (na1) and single atlas intercentrum (ic1), and would probably have a pair of fused cervical ribs (r1). Everything else would be fused together to form the axis, including the atlas pleurocentrum (c1), which forms the odontoid process or dens epistrophei (etymologically the “tooth” of the axis).

Romer 1956 fig 119 atlas-axis complex

Here’s the complete Romer (1956) figure from the key card, with a mammalian atlas-axis complex  for comparison. Incidentally, the entire book this is drawn from, Osteology of the Reptiles, is freely available online.

Apatosaurus axis-atlas complex Gilmore 1936 figs 5 and 6

And here’s the complete Gilmore (1936) figure. Sorry for the craptastic scan–amazingly, this one is NOT freely available online as far as I can tell, and Mike and I have been trying to get good scans of the plates for years. Getting back on topic, single-headed atlantal cervical ribs have been found in several sauropods, especially Camarasaurus where several examples are known, so they were probably a regular feature, even though they aren’t always preserved.

Also, as noted in this post, it is odd that in this specimen of Apatosaurus the cervical ribs had not fused to the first two vertebrae, even though they normally do, and despite the fact that the vertebrae had fused to each other, even though they normally don’t. Further demonstration, if any were needed, that sauropod skeletal fusions were wacky.

Varanops atlas-axis complex Campione and Reisz 2011 fig 2C3

For comparison to the above images, here is the atlas-axis complex in the synapsid Varanops, from Campione and Reisz (2011: fig. 2C).

Those proatlas thingies are present in some sauropods, but that’s about all I know about them, so I’ll say no more for now.

There is a good overview of the atlas-axis complex with lots of photos of vertebrae of extant animals on this page.

Previous SV-POW! posts dealing with atlantes and axes (that’s right) include:

References

Readers with long memories might recall that, nearly two years ago, we published annotated skeletal reconstructions of Camarasaurus and of Tyrannosaurus, with all the bones labelled. At the time, I said that I’d like to do an ornithischian, too.

Well, here it is at last, based on Marsh’s (1891) classic reconstruction of Triceratops:

Marsh1891--Restoration-of-Triceratops--plate-XV

Click through for the full-sized version (2076 by 864 pixels), which — like the other two — you are welcome to print out and hang on your wall as a handy reference, or to use in teaching. (Marsh’s original is out of copyright; I hereby make my modified version available under the CC By 3.0 licence.)

As the conference season heaves into view again, I thought it was worth gathering all four parts of the old Tutorial 16 (“giving good talks”) into one place, so it’s easy to link to. So here they are:

  • Part 1: Planning: finding a narrative
    • Make us care about your project.
    • Tell us a story.
    • You won’t be able to talk about everything you’ve done this year.
    • Omit much that is relevant.
    • Pick a single narrative.
    • Ruthlessly prune.
    • Find a structure that begins at the beginning, tells a single coherent story from beginning to end, and then stops.
  • Part 2: The slides: presenting your information to be understood
    • Make yourself understood.
    • The slides for a conference talk are science, not art.
    • Don’t “frame” your content.
    • Whatever you’re showing us, let us see it.
    • Use as little text as possible.
    • Use big fonts.
    • Use high contrast between the text and background.
    • No vertical writing.
    • Avoid elaborate fonts.
    • Pick a single font.
    • Stick to standard fonts.
    • You might want to avoid Ariel.
    • Do not use MS Comic Sans Serif.
    • Use a consistent colour palette.
    • Avoid putting important information at the bottom.
    • Avoid hatching.
    • Skip the fancy slide transitions.
    • Draw highlighting marks on your slides.
    • Show us specimens!
  • Part 3: Rehearsal: honing the story and how it’s told
    • Fit into the time.
    • Become fluent in delivery.
    • Maintain flow and momentum.
    • Decide what to cut.
    • Get feedback.
  • Part 4: Delivery: telling the story
    • Speak up!
    • Slow down!
    • Don’t panic!

Also, some addenda written later:

  • Addendum 1: give a talk that holds attention!
    • Love your taxon.
    • Show us pictures of your taxon.
    • Engage with the audience.
    • Tell a story.
    • Talks are not papers.
  • Addendum 2: giving talks: what to leave out
    • Don’t start by saying the title.
    • Don’t introduce yourself.
    • Don’t reiterate your conclusions at the end.
    • Don’t say “thanks for listening”.
    • Don’t read the acknowledgements out loud.
    • Don’t say “I’ll be happy to take questions”.
  • Addendum 3: giving talks: some more positive thoughts
    • Offer lots of jump-back-on points.
    • Anticipate possible objections and meet them in advance.
    • Do the work to make it worth the audience’s while.
    • Efficiently introduce a taxon and make it interesting before launching into details.

 

There’s an awful lot of talk about “predatory open access publishers” recently. So much talk that I can’t help wondering whether the phrase is being pushed by barrier-based publishers in another attempt to smear open access. (Hey, they have previous.)

Anyway, for anyone who is worried that they might be tricked into giving their work to one of these low-quality predatory publishers that accepts anything and only cares about the fee, here is my guide to avoiding this scenario.

So. Imagine you have an article ready to go, when you receive an invitation to submit it to a journal that you’ve never heard of before. How do you decide whether to send it to them?

Do not send it to them.

Problem solved.

Sheesh.

There are probably many ways of getting a “90% complete” paper finished and ready for submission, but here’s the way that works for me. (It’s working for me right now: I’m in the middle of the process, and broke off to write this just for a a break.)

You will need:

  • A printed copy of your manuscript
  • A red pen
  • A CD of Dar Williams songs that you know inside out
  • A bottle of red wine
  • A bar of white chocolate (optional)

Method:

Take the printed copy of the manuscript. read it through, with the Dar Williams CD on in the background. Every time you see anything you don’t like, scribble on the printed copy with the red pen. It might a typo, a misspelling, an infelicitous phrasing, a missing reference, a taxonomic name needing italics; or it might be something bigger, like two sections that need to be swapped.

Do you really need a printed copy for this? YES YOU DO! Can’t you just do it on the screen? NO YOU CAN’T! For one thing, you’ll keep breaking off to read email, which is a complete killer. For another, you’ve been working on this manuscript on screens for months already. Your poor brain is inoculated against its on-screen appearance. You need the mental jolt that a shift of format gives you. And you need the freedom to scribble. When I do this, I often write in suggestions to myself of what alternative wording to use, but I feel free to ignore them when I come to make the edits.

Do you really need a Dar Williams CD? I am prepared to concede it doesn’t necessarily have to be Dar Williams. But it does need to be something that you know so well that it won’t surprise you, it won’t grab your attention away from the work you’re doing. Much as I love Dream Theater, their music is really not the way to go for this. What you want is music that will keep feeding you without distracting you.

Do you really need the red wine and the white chocolate? Perhaps not, but you don’t want this to be a boring, unpleasant process, do you? Treat yourself. (DISCLOSURE: I have moved on to beer.)

What next?

As soon as I’m done posting this, I’ll be going to Step 2, which is to go through the manuscript, making edits on the master copy. Most of them are trivial to do. A few are going to need real work. For these, I just leave a marker in the master copy, “###” and a note saying what needs doing. I will later search for these and do the work. But not tonight.

The goal of this process is to capture all the information that you wrote on the printed copy, so that you can throw it away and move on with your life.

That’s it — it’s all you need to do. For the record, I expect to submit in the  next three or four days.

For a paper that I and Matt are preparing, we needed to measure the centrum length of a bunch of turkey cervicals. That turns out to be harder than you’d think, because of the curious negative curvature of the articular surfaces.

turkey-cervical-c7-white

Above is a C7 from a turkey: anterior view on the left; dorsal, left lateral and ventral views in the middle row; and posterior on the right. As you can see from the anterior, dorsal and ventral views, the anterior articular surface[1] is convex dorsoventrally  but concave transversely; and as you can see from the lateral view, the posterior face is concave dorsoventrally and convex transversely.

This means you can’t just put calipers around the vertebra. If you approach the vertebra from the top or bottom, then the upper or lower lip of the posterior articular surface will protrude past the centre of the saddle, and give you too long a length. If you approach from the side, the same will happen with the left and right lips of the anterior articular surface.

What are we trying to measure anyway?

But this raises the question of what it is we’re trying to measure. I said “we needed to measure the centrum length of a bunch of turkey cervicals”, but what exactly is centrum length? Why shouldn’t the upper and lower lips of the posterior articular surface count towards it?

What does centrum length mean?

The problem doesn’t only arise with bird cervicals. The same issue arises in measuring more sensible and elegant vertebrae, such as our old friend HMN SII:C8, or MB.R.2181:C8 as we must now learn to call it.

Janensch1950-fig43-sii-c8-MEASUREMENTS

Although the back of the vertebra is nice and simple here — it’s obvious what line we’re measuring to at the back — we have three choices of where the “front” of the vertebra is, and a case can be made for any of them as being “the length of the vertebra”.

The longest measurement (here marked “T” for “total length”) goes to the front of the prezygapophyseal rami. The next one (“C” for “centrum length”) goes to the anteriormost point of the condyle. The distinction is important: as noted recently, the longest vertebra in the world belongs to Sauroposeidon if we use total length, but to Supersaurus if we use centrum length.

But in life, most of the condyle would be buried in the cotyle of the preceding vertebra. So should it count towards the length of the vertebra? If you consider a string of articulated vertebrae, the buried condyles don’t contribute to the overall length of the neck. So Matt and I call the length from the posterior margin of the condyle to the posterior margin of the cotyle the functional length (marked “F” above), which I believe is a new term.

Another way to think of the functional length is the distance from a given point on a vertebra (in this case the posterior margin of the cotyle) to the same point on the adjacent vertebra:

Janensch1950-fig43-sii-c8-MEASUREMENTS2

For our current project, Matt and I are interested in how the lengths of individual vertebrae contribute to total neck length, so for our purposes, functional length is definitely what we want.

By the way, Janensch is the only author I know of to have even recognised the importance of functional length. The measurement tables on pages 39 and 44 have columns for “Gesamtlänge des Wirbels ab Vorderende per Präzygapophyse”, “Gesamtlänge der Wirbel-Körpers in 1/2 Höhe” and “Länge der Wirbel-körpers ohne Condylus in 1/2 Höhe” — that is, “Total length of the vertebra from the anterior end of the prezygapophysis”, “Total length of the centrum measured at mid-height” and “Length of the centrum minus condyle at mid-height”. This is typical of his careful and methodical approach. Kudos!

Hey! I thought this was about turkeys

And so it is. Here is the functional length measurement for a turkey cervical:

turkey-cervical-c7-white-MEASUREMENT

It’s the shortest anteroposterior distance between the two articular surfaces.

Measuring functional length

Matt and I chatted about this at some length, and I am ashamed to say that we thought through all sorts of complicated solution involving subtracting measurements from known scaffold length and suchlike.

It took us a stupidly long to to arrive at the very obvious solution, which is just to modify the calipers to have a “tooth” that can protrude into the concavity of the anterior articulation between its left and right lips. Easily done with a flat-ended screw and a blob of wood glue:

IMG_1000

With the measurements of all the vertebrae in my series, I can now fairly confidently expect that the sum of the individual lengths will come out at about the length of the complete neck.

You know, unless intervertebral cartilage turns out to be important or something.

References

  • Janensch, Werner. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3:27-93.

 

Footnotes

1. Matt and I are so used to opisthocoelous sauropod presacrals that when we’re talking about vertebrae — any vertebrae — we tend to say “condyle” and “cotyle” for the anterior and posterior articular surfaces, no matter what their morphology. When talking about crocodile cervicals or titanosaur caudals, we’re even likely to say ridiculous things like “the condyle is concave and the cotyle is convex”. Nonsense, of course: condyle means “A rounded prominence at the end of a bone, most often for articulation with another bone.” What we should say is “the condyle is at the back and the cotyle is in front”.

I’ve measured a few necks in my time, including the neck of a baby giraffe. I can tell you from experience that necks are awkward things to measure, even if they have been conveniently divested of their heads and torsos. They have a tendency to curl up, which impedes attempts to find the straight-line length. Even when you manage to hold them straight, you want them maximally compressed end-to-end rather than stretched out, which is hard to achieve without buckling them out of the straight line. And then you need to measure between perpendiculars in a straight line.

Awkward.

Tonight, I needed to measure the mass and length of seven turkey necks. (Never mind why, all will become clear in time.) And I found a way to do it that works much better than anything I’ve done before.

Here’s the equipment:

IMG_0961-equipment

You will need:

  • Kitchen scales (for weighing the necks)
  • Small numbered labels (for the sandwich bags that the necks will go into for the freezer once they’ve been measured)
  • Pen and paper to take down the measurements
  • Translucent ruler
  • Saucepan full of turkey necks
  • Slightly less than one half of a birthday cake decorated like a map of Middle-earth [optional]
  • A Duplo baseboard (double-sized Lego) and about fifteen 4×2 bricks

Use the bricks to build an L-shaped bracket on the board — about half way back, so that can rest your hand in front of it.

IMG_0963-straightened

Now you can push the neck into the angle of the bracket. By keeping it pressed firmly against the back wall (yellow in my construction), you can keep it straight. I find the best way to get the neck exactly abutting the left (red) wall is to start with the neck in its natural position, with the anterior and posterior ends curving towards you, then sort of unroll it against the back wall, and finally push the posterior end into place with your little finger (see below). There is a satisfying moment– almost a click — as the back end pops into place and the neck slides along a little to right as necessary to accommodate the added length.

IMG_0966-blocked

Now use another brick (blue in this photo) as a bracket: slide it along the back wall from right to left until it’s solidly abutting the anteriormost vertebra. If you do this right, there is very little travel: the entire series of vertebrae is lined up and solidly abutted, with bone pushing against the left wall and your new brick. I find there’s less than half a millimeter of variation between the length under gentle-but-firm pressure (which is what I measured) and under the very strongest force you can exert without buckling the neck.

IMG_0967-measured

Once you have found the blue brick’s correct position, you need to hold it firmly in place and measure its position relative the the left wall. (It doesn’t matter if you let the neck re-curl at this point, so long as the blue brick doesn’t shift.)

You need a translucent ruler so that you can lay it across the neck and see where blue brick falls under the scale. (My ruler’s zero is, rather annoyingly, 5 mm from the end; so I needed to subtract 5 mm from the lengths I measured.)

IMG_0969-bagged

Finally, I bagged up each neck in its own sandwich bag, ready for the freezer. Each neck is labelled with a number so that when I take it out for dissection, I will be able to relate the measurements and observations that I make back to these initial measurements.

For the record, here are the measurements:

  • Neck 1: 154 g, 179.5 mm.
  • Neck 2: 122 g, 151 mm.
  • Neck 3: 154 g, 199.5 mm.
  • Neck 4: 133 g, 162.5 mm.
  • Neck 5: 142 g, 169 mm.
  • Neck 6: 80 g, 167 mm.
  • Neck 7: 70 g, 169 mm.

As expected, there is some correlation between neck mass and length; but not as much as you might expect. Naively (i.e. assuming isometric similarity) mass should be proportional to length cubed, but there is a lot of scatter about that line. I don’t know whether that is due to individual variation, or merely because the various necks — all of them incomplete — are different sections of the full neck. Hopefully I will be able to confirm or rule out that possibility when I’ve dissected down to naked vertebrae.

The best open-access publishers make their articles open from the get-go, and leave them that way forever. (That’s part of what makes them best.) But it’s not unusual to find articles which either start out free to access, then go behind a paywall; or that start out paywalled but are later released; or that live behind a paywall but peek out for a limited period.

Let’s talk about these.

Initial “open access”

You’ll sometimes come across journals where articles are free to read for some initial period after their publication. For example, the announcement of the Journal of Photonics for Energy says “The journal will be available as open access for the first year”; and the 2008/9 progress report for the Journal of Nutrition says “We will continue to restrict open access for one year, as per current procedure”.

Despite the good intentions of the journals, these articles are not open access in any useful sense. The point of an open-access article is that it’s there when you need it. If it’s there this week, but I need to read and cite it next week when I can’t get it any more, then that’s no good.

Of course, this doesn’t mean that publishers have a mandate to keep articles up on their web-sites forever (although we would prefer that they do). What it means is that, if they want to be open access, they can’t prohibit others from mirroring and archiving those papers, and continuing to make them available after they’ve disappeared from the publisher’s site.

Note that any article published with a Creative Commons licence — even the most restrictive of those licences — is safe from this kind of disappearance. Those licences guarantee third parties’ rights to archive, replicate and redistribute the articles.

Delayed open access

it’s probably more common to take the opposite approach. Some journals, including Science and Proceedings B, make articles free to read, and so “gratis open access”, after an embargo period during which they are available only to subscribers.  This period is one year in the case of both these journals; that seems to be typical.

Are such journals open access? I would say that the journals themselves are not open access, but that the articles become open access once they cross the release line. So for example, Raichlen and Polk’s new neurobiology paper in Proc B. is not open access, but Anderson et al.’s seed-dispersal paper (which is a year older) is. On that basis you might choose to refer to Proc B. as a “delayed open access” journal.

[Unfortunately, Science is not truly open access even for older articles such as Stevens and Parrish’s DinoMorph. That’s because it requires registration/login before you can get to the papers. The BOAI FAQ does not accept registration-required content as open access, specifying “without financial, legal, or technical barriers other than those inseparable from gaining access to the internet itself”.]

Transitory “open access”

And then you have the worst of both worlds. Every now an then a journal or a publisher has a special offer where they open up access to their articles for a limited period — for example, this one where the Royal Society opened up all their content for two weeks, or this where an issue of European Physical Journal D was opened for a week.

It seems churlish to criticise a generous action like this, but I find it close to useless, and I think most other researchers will, too. When I am working on a paper, I don’t choose what to cite based on which journal or publisher the papers are from: I would never think, “Oh, let’s see, European Physical Journal D is open at the moment, I’ll cite something from there”. I cite what’s relevant and appropriate, irrespective of its source; and if I can’t get the papers I need at that time there’s a problem.

I sometimes wonder what publishers think will be the result of this kind of limited-time-only offer. One obvious outcome is that people will batch-download the transitorily available content — either to store up for themselves in case they even happen to need it (which is wasteful of both bandwidth and storage); or to post openly elsewhere for permanence (which is usually a violation of copyright).

To summarise: I think that making articles open access after a delay is a good thing (though obviously not as good as making them open access immediately!). But that making them free to read for a limited time — either when first published or as part of some special event later — is of very limited value, and can’t really be described as open access.