I got in a conversation recently with a friend who is about to have his first paper published. It’s been through review and is now accepted at a well-respected old-school journal owned by a legacy publisher. It’s not an open-access journal, and he asked my advice on how he could make the paper open access.

We had a fruitful discussion, and we agreed that I’d write up the conclusions for this blog.

First, you can pay the publisher to open-access your paper. That’s a legitimate option at “hybrid OA” journals, which by this point is pretty much all paywalled journals. But even when the journal invites it, that’s not always possible. In this case, my friend has no institutional funds available, and really isn’t in a position to bung the publisher $3000 out of his own pocket.

The second option is to write to the journal saying that you select the OA option, but that since you have no institutional support you have to ask for a waiver. Will this work? It’s impossible to tell unless you try it. Some journals might have an absolutely-no-waiver policy; heck, some might have a “we always give waivers but don’t advertise the fact” policy. My guess is that most have no policy at all, but that editors (who are nearly all researchers themselves) will tend to be sympathetic, and support your case. Anyway, it can’t hurt to politely ask.

If that fails, the the third approach is to use the SPARC Author Addendum. Using this legal instrument (which is freely available), you do not transfer copyright to the publisher, as they usually request, but instead give them a non-exclusive right to publish — which of course is all they actually need. That leaves you legally free to post the accepted (peer-reviewed) version of the manuscript elsewhere: in an institutional repository, your own web-site or wherever. (I’ve never used this myself, but I hear it’s widely accepted.)

If the publisher is intransigent enough to reject the SPARC Addendum, the fourth approach is to dedicate your manuscript to the public domain (for example by posting it on arXiv with the CC Public Domain Declaration). Then return the copyright transfer form to the publisher, saying truthfully that there is no copyright to transfer. Publishers are used to dealing with submissions that have no copyright: for example, everything authored by U.S. federal employees is in the public domain. Their copyright forms usually already have a section for declaring public domain.

Finally if somehow all of the above tactics fail — if the journal flatly refuses to give an APC waiver, won’t accept the SPARC addendum, and rejects works that are in the public domain though not written by US Government employees — and if despite their evident hostility to science you still want to stick with the journal that accepted your paper — then you have one final option. You can just go ahead and give them the copyright, but then post the final PDF on your own web-site anyway. Of course, you are not technically allowed to do that, but historically it’s never been a problem. It’s very widely done — especially by old-school professors, because it would never even occur to them that sharing their own work could be a problem.

To be clear, I am not advocating the last of these. The four preceding approaches are better because they are fully in compliance with copyright law. But when dealing with a publisher that is simply determined to prevent your work from being read, then you have to weigh for yourself whether you’re more interested in respecting copyright, or doing what’s right.

This is the situation with several of my own old papers, which in my young and stupid days I signed over to publishers without giving it any thought at all. Having got myself into that situation, it seems to me that making those papers available anyway is the least bad of several bad options. But I would never choose that approach now, since I publish exclusively in open-access venues.

Summary

Option zero (not discussed here) is to use an open-access venue to start with: then none of these issues even arise. But failing that:

  1. If you have funds, use them to pay the publisher an APC to make the article open access.
  2. Ask the journal for an APC waiver.
  3. Use the SPARC Author Addendum to retain copyright and give the journal a licence to publish.
  4. Dedicate the manuscript to the public domain and tell the publisher there is no copyright to transfer.
  5. If all else fails, just post the paper publicly anyway.

In his post on Vicki’s new book Broken Bones, Matt told us his twelve-step process for producing stippled illustrations like this one of a crushed skull, which became the cover image of the book:

Skull drawing - F1 - original on white

As soon as I saw that, I found myself thinking that it would look nice with some shading of the bone. Of course the existing stippling is a perfect guide to how dense the shading should be at each point, so I figured there had to be an easy way to do this automatically. There is, and this is what I whipped up in five minutes:

skull-drawing-f1-original-on-white-50px-blur

Here’s how I did it.

  1. I loaded Matt’s image into the GIMP, my image editor of choice.
  2. For some reason the crucial next step doesn’t work with greyscale images, so I converted it to RGB (Image → Mode  RGB)
  3. I removed the white background, leaving it transparent (Colours → Colour to Alpha… and click OK on the default colour, white)
  4. I added a new all-white background layer.
  5. I duplicated the skull layer, and named it “shading”
  6. I blurred the shading layer by 50 pixels (Filters → Blur → Gaussian Blur…, set the blur radius to 50 pixels and hit OK.) That gives you the shading you want, but it smudges out past the outline of the skull, hence the last two steps:
  7. I went back to the skull layer, and using the Fuzzy Select Tool (magic wand) selected the contiguous transparent area outside the skull parts.
  8. I went back to the shading layer and cut the selected area, leaving only that shading that’s inside the boundary of the skull.

As always with Gimp tutorials, it takes about ten times as long to explain as to actually do.

When I showed this to Matt, I rather immodestly said I was “super-happy with it”. Matt said he was “super-happy with the idea, but only regular happy with this specific execution”. He felt that the blurring was too strong, and that it should be backed off by 30-40%. So I made a new shading layer in the same way as above, but this time blurring by only 30 pixels. Here’s the resulting image:

skull-drawing-f1-original-on-white-30px-blur

It’s quite a subtle difference, but clear if you flip back and forth between the images (which you can most easily do by putting them in adjacent tabs of your browser). Personally, I think I prefer the 50-pixel version, since I think the shading clings rather too closely to the lines in this one, but YMMV.

Since I had both blur layers right there in the image, I thought it might be interesting to see how they look together. Here’s the result:

skull-drawing-f1-original-on-white-30+50px-blur

I’m actually rather fond of this version, but it’s a long way from the crisp, clinical feel of the original.

You can thicken up the shading by duplicating one or both of the shading layers as many times as you wish (or or course thin it out by sliding down the opacity level). Its also easy to make the shading coloured: just use Colours  → Levels, select the individual colour channels, and bring up their bottom levels to taste.

Putting all that together, here’s one I made with very dense, yellowish (bone-coloured) shading. I did it starting with the 50-pixel shading layer, upping the red output level to 200 and the green to 150, then duplicating that layer, and reducing the 30-pixel shading layer to 50% opacity.

skull-drawing-f1-original-on-white-yellow

You can play for hours with all these sliders, tweaking as you wish, thanks to the magic of layers. It’s well worth investing a bit of time to learn some of the capabilities of a program like GIMP. Matt and I are very far from wizards, but we have at least got a bit past just using it to cut out backgrounds, and it opens up possibilities.

If the internet has any underlying monomyth, or universally shared common ground, or absolute rule, it is this:

People love to see the underdog win.

This rule has a corollary:

When you try to censor someone, they automatically become the underdog.

I say “try to censor” someone, because on the internet that is remarkably difficult to achieve. I’m not going to argue that the attention paid to the range of stories told on the internet is fairly distributed–being published is not the same as being read, and people seem to prefer cat pictures to reading about genocide. But it’s awfully hard to shut someone up, and any attempt to do so may backfire spectacularly.

If you work for an organization of any size, or have amassed any considerable power, reputation, or influence personally, you need to keep that at the forefront of your mind in every interaction you ever have with anyone, anywhere, ever. The reason for this constant attention is to keep you from becoming the overdog and thereby making an ass of yourself (and your organization, if you belong to one). Go read about the Streisand Effect and think proactively about how to keep that from happening to you.

Now, for the purposes of this tutorial I am going to arbitrarily sort the full range of possible messages into four bins:

  1. Those that make the teller look good.
  2. Those that make the teller look bad.
  3. Those that make someone else look good.
  4. Those that make someone else look bad.

Two and three are dead easy and often go hand in hand. If you want to spread messages of that type, all you have to do is find someone with less power, reputation, or influence–a prospective underdog, in other words–and be a jerk to them, thus turning them into an actual underdog. Coercion, threats, employment termination–these are all pretty good and may eventually pay off. But if you really want to look like a complete tit, and make the other party an instant hero, you gotta go for censorship. Out here in bitspace, it is the ne plus ultra of suicidal moves. It’s like Chuck Norris winding up for a roundhouse kick to someone’s face, only somehow his foot misses the other person’s face and hits him right in the junk instead. We will click and tap on that until they pry the mice and touchscreens from our cold, dead hands.

The first one–positive messages about yourself–is tricky. You can’t just go around telling people that you’re awesome. Anyone with any sense will suspect advertising. The only sure-fire method I know of is to do good work where people can see it. One thing you will just have to accept is that reputations are slow-growing but fast-burning. So, again, try to avoid burning yours down.

The last one–making someone else look bad–is also surprisingly tricky. If you just broadcast negatives to the world, that will probably backfire. At the very least, people start thinking of you as a negative force rather than a positive one. If the person you want to make look bad has ever lied or falsified data or oppressed anyone, use that. If they’ve ever tried to censor someone, or are actively trying to censor you, rejoice, they’ve done most of the work for you.

The upside of that last one is that, provided you’re not actively nasty, it is hard for others to hurt your reputation. If they just spew vitriol, it will probably backfire. If they lie about you, it will definitely backfire. About the only way to really trash your reputation is through your own actions. Your fate is in your own hands.

———–

So, this is transparently a meditation on the DNLee/Biology Online/Scientific American story.

I would really like to know the backstory. Did someone at Biology Online contact SciAm and ask them to take down DNLee’s post? If so, well, geez, that was stupid. Why does anyone ever expect this to work anymore? I mean, the actual event from which the Streisand Effect got its name happened a decade ago, which may seem short in human terms but is an eternity online (it’s two-thirds of the lifespan to date of Google, for example).

If someone at SciAm did it unilaterally to protect their valued financial partner, it was doubly stupid, because not only did the censorship act itself fail, but now people like me are wondering if Biology Online asked for that “protection”. In other words, people are now suspecting Biology Online of something they might not have even done (although what they did do–what their employee did on their behalf, which amounts to the same thing–was bad enough).

So all in all the affair is like a tutorial on how to royally cock things up on the internet. And in fact it continues to be–Mariette DiChristina’s “apology” is a classic non-apology, that uses a torrent of words to say very little. Her self-contradictory tweets are much more revealing, despite being under 140 characters each. And in fact her loudest message is the complete lack of communication with DNLee before she pulled the post. So meaning scales inversely with message length for DiChristina–not a great quality in an Editor-In-Chief. And, OMG does she need to learn about the Asoh defense.

In the end, the whole thing just saddens me. I’m sad that SciAm made the wrong call immediately and reflexively. It says to me that they don’t care about transparency or integrity. They may say otherwise, but they are belied by their actions.

I’m sad that, having not even known that Biology Online exists, my perception of them now starts from a position of, “Oh, the ones that called that science writer a whore.” (If you’re a BO fan, please don’t write in to tell me how wonderful BO actually is; doing so is just admitting that you didn’t read this post.)

I’m sad that this happened to DNLee. I hope that going forward her reputation is determined by the quality of her work and the integrity of her actions, and not by words and circumstances inflicted on her by others.

… I wonder if I could make it as a corporate consultant if I put on a suit, walked into rooms full of pointy-haired bosses, and just explained the Streisand Effect and the Asoh Defense as if they were novel insights. I’ll bet I could make a killing.

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.

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.
    • [You want to end up with] 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!

Enjoy!

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.

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