Last night, I did a Twitter interview with Open Access Nigeria (@OpenAccessNG). To make it easy to follow in real time, I created a list whose only members were me and OA Nigeria. But because Twitter lists posts in reverse order, and because each individual tweet is encumbered with so much chrome, it’s rather an awkward way to read a sustained argument.

So here is a transcript of those tweets, only lightly edited. They are in bold; I am in regular font. Enjoy!

So @MikeTaylor Good evening and welcome. Twitterville wants to meet you briefly. Who is Mike Taylor?

In real life, I’m a computer programmer with Index Data, a tiny software house that does a lot of open-source programming. But I’m also a researching scientist — a vertebrate palaeontologist, working on sauropods: the biggest and best of the dinosaurs. Somehow I fit that second career into my evenings and weekends, thanks to a very understanding wife (Hi, Fiona!) …

As of a few years ago, I publish all my dinosaur research open access, and I regret ever having let any of my work go behind paywalls. You can find all my papers online, and read much more about them on the blog that I co-write with Matt Wedel. That blog is called Sauropod Vertebra Picture of the Week, or SV-POW! for short, and it is itself open access (CC By)

Sorry for the long answer, I will try to be more concise with the next question!

Ok @MikeTaylor That’s just great! There’s been so much noise around twitter, the orange colour featuring prominently. What’s that about?

Actually, to be honest, I’m not really up to speed with open-access week (which I think is what the orange is all about). I found a while back that I just can’t be properly on Twitter, otherwise it eats all my time. So these days, rather selfishly, I mostly only use Twitter to say things and get into conversations, rather than to monitor the zeitgeist.

That said, orange got established as the colour of open access a long time ago, and is enshrined in the logo:

OAlogo

In the end I suppose open-access week doesn’t hit my buttons too strongly because I am trying to lead a whole open-access life.

… uh, but thanks for inviting me to do this interview, anyway! :-)

You’re welcome @MikeTaylor. So what is open access?

Open Access, or OA, is the term describing a concept so simple and obvious and naturally right that you’d hardly think it needs a name. It just means making the results of research freely available on the Internet for anyone to read, remix and otherwise use.

You might reasonably ask, why is there any other kind of published research other than open access? And the only answer is, historical inertia. For reasons that seemed to make some kind of sense at the time, the whole research ecosystem has got itself locked into this crazy equilibrium where most published research is locked up where almost no-one can see it, and where even the tiny proportion of people who can read published works aren’t allowed to make much use of them.

So to answer the question: the open-access movement is an attempt to undo this damage, and to make the research world sane.

Are there factors perpetuating this inertia you talked about?

Oh, so many factors perpetuting the inertia. Let me list a few …

  1. Old-school researchers who grew up when it was hard to find papers, and don’t see why young whippersnappers should have it easier
  2. Old-school publishers who have got used to making profits of 30-40% turnover (they get content donated to them, then charge subscriptions)
  3. University administrators who make hiring/promotion/tenure decisions based on which old-school journals a researcher’s papers are in.
  4. Feeble politicians who think it’s important to keep the publishing sector profitable, even at the expense of crippling research.

I’m sure there are plenty of others who I’ve overlooked for the moment. I always say regarding this that there’s plenty of blame to go round.

(This, by the way, is why I called the current situation an equilibrium. It’s stable. Won’t fix itself, and needs to be disturbed.)

So these publishers who put scholarly articles behind paywalls online, do they pay the researchers for publishing their work?

HAHAHAHAHAHAHAHAHAHA!

Oh, sorry, please excuse me while I wipe the tears of mirth from my eyes. An academic publisher? Paying an author? Hahahahaha! No.

Not only do academic publishers never pay authors, in many cases they also levy page charges — that is, they charge the authors. So they get paid once by the author, in page-charges, then again by all the libraries that subscribe to read the paywalled papers. Which of course is why, even with their gross inefficiencies, they’re able to make these 30-40% profit margins.

So @MikeTaylor why do many researchers continue to take their work to these restricted access publishers and what can we do about it?

There are a few reasons that play into this together …

Part of it is just habit, especially among more senior researchers who’ve been using the same journals for 20 or 30 years.

But what’s more pernicious is the tendency of academics — and even worse, academic administrators — to evaluate research not by its inherent quality, but by the prestige of the journal that publishes it. It’s just horrifyingly easy for administrators to say “He got three papers out that year, but they were in journals with low Impact Factors.”

Which is wrong-headed on so many levels.

First of all, they should be looking at the work itself, and making an assessment of how well it was done: rigour, clarity, reproducibility. But it’s much easier just to count citations, and say “Oh, this has been cited 50 times, it must be good!” But of course papers are not always cited because they’re good. Sometimes they’re cited precisely because they’re so bad! For example, no doubt the profoundly flawed Arsenic Life paper has been cited many times — by people pointing out its numerous problems.

But wait, it’s much worse than that! Lazy or impatient administrators won’t count how many times a paper has been cited. Instead they will use a surrogate: the Impact Factor (IF), which is a measure not of papers but of journals.

Roughly, the IF measures the average number of citations received by papers that are published in the journal. So at best it’s a measure of journal quality (and a terrible measure of that, too, but let’s not get into that). The real damage is done when the IF is used to evaluate not journals, but the papers that appear in them.

And because that’s so widespread, researchers are often desperate to get their work into journals that have high IFs, even if they’re not OA. So we have an idiot situation where a selfish, rational researcher is best able to advance her career by doing the worst thing for science.

(And BTW, counter-intuitively, the number of citations an individual paper receives is NOT correlated significantly with the journal’s IF. Bjorn Brembs has discussed this extensively, and also shows that IF is correlated with retraction rate. So in many respects the high-IF journals are actually the worst ones you can possibly publish your work in. Yet people feel obliged to.)

*pant* *pant* *pant* OK, I had better stop answering this question, and move on to the next. Sorry to go on so long. (But really! :-) )

This is actually all so enlightening. You just criticised Citation Index along with Impact Factor but OA advocates tend to hold up a higher Citation Index as a reason to publish Open Access. What do you think regarding this?

I think that’s realpolitik. To be honest, I am also kind of pleased that the PLOS journals have pretty good Impact Factors: not because I think the IFs mean anything, but because they make those journals attractive to old-school researchers.

In the same way, it is a well-established fact that open-access articles tend to be cited more than paywalled ones — a lot more, in fact. So in trying to bring people across into the OA world, it makes sense to use helpful facts like these. But they’re not where the focus is.

But the last thing to say about this is that even though raw citation-count is a bad measure of a paper’s quality, it is at least badly measuring the right thing. Evaluating a paper by its journal’s IF is like judging someone by the label of their clothes

So @MikeTaylor Institutions need to stop evaluating research papers based on where they are published? Do you know of any doing it right?

I’m afraid I really don’t know. I’m not privy to how individual institution do things.

All I know is, in some countries (e.g. France) abuse of IF is much more strongly institutionalised. It’s tough for French researchers

What are the various ways researchers can make their work available for free online?

Brilliant, very practical question! There are three main answers. (Sorry, this might go on a bit …)

First, you can post your papers on preprint servers. The best known one is arXiv, which now accepts papers from quite a broad subject range. For example, a preprint of one of the papers I co-wrote with Matt Wedel is freely available on arXiv. There are various preprint servers, including arXiv for physical sciences, bioRxiv, PeerJ Preprints, and SSRN (Social Science Research Network).

You can put your work on a preprint server whatever your subsequent plans are for it — even if (for some reason) it’s going to a paywall. There are only a very few journals left that follow the “Ingelfinger rule” and refuse to publish papers that have been preprinted.

So preprints are option #1. Number 2 is Gold Open Access: publishing in an open-access journal such as PLOS ONE, a BMC journal or eLife. As a matter of principle, I now publish all my own work in open-access journals, and I know lots of other people who do the same — ranging from amateurs like me, via early-career researchers like Erin McKiernan, to lab-leading senior researchers like Michael Eisen.

There are two potential downsides to publishing in an OA journal. One, we already discussed: the OA journals in your field may not be be the most prestigious, so depending on how stupid your administrators are you could be penalised for using an OA journal, even though your work gets cited more than it would have done in a paywalled journal.

The other potential reason some people might want to avoid using an OA journal is because of Article Processing Charges (APC). Because OA publishers have no subscription revenue, one common business model is to charge authors an APC for publishing services instead. APCs can vary wildly, from $0 up to $5000 in the most extreme case (a not-very-open journal run by the AAAS), so they can be offputting.

There are three things to say about APCs.

First, remember that lots of paywalled journals demand page charges, which can cost more!

But second, please know that more than half of all OA journals actually charge no APC at all. They run on different models. For example in my own field, Acta Palaeontologica Polonica and Palaeontologia Electronica are well respected OA journals that charge no APC.

And the third thing is APC waivers. These are very common. Most OA publishers have it as a stated goal that no-one should be prevented from publishing with them by lack of funds for APCs. So for example PLOS will nearly always give a waiver when requested. Likewise Ubiquity, and others.

So there are lots of ways to have your work appear in an OA journal without paying for it to be there.

Anyway, all that was about the second way to make your work open access. #1 was preprints, #2 is “Gold OA” in OA journals …

And #3 is “Green OA”, which means publishing in a paywalled journal, but depositing a copy of the paper in an open repository. The details of how this works can be a bit complicated: different paywall-based publishers allow you to do different things, e.g. it’s common to say “you can deposit your peer-reviewed, accepted but unformatted manuscript, but only after 12 months“.

Opinions vary as to how fair or enforceable such rules are. Some OA advocates prefer Green. Others (including me) prefer Gold. Both are good.

See this SV-POW! post on the practicalities of negotiating Green OA if you’re publishing behind a paywall.

So to summarise:

  1. Deposit preprints
  2. Publish in an OA journal (getting a fee waiver if needed)
  3. Deposit postprints

I’ve written absolutely shedloads on these subjects over the last few years, including this introductory batch. If you only read one of my pieces about OA, make it this one: The parable of the farmers & the Teleporting Duplicator.

Last question – Do restricted access publishers pay remuneration to peer reviewers?

I know of no publisher that pays peer reviewers. But actually I am happy with that. Peer-review is a service to the community. As soon as you encumber it with direct financial incentives, things get more complicated and there’s more potential for Conflict of interest. What I do is, I only perform peer-reviews for open-access journals. And I am happy to put that time/effort in knowing the world will benefit.

And so we bring this edition to a close. We say a big thanks to our special guest @MikeTaylor who’s been totally awesome and instructive.

Thanks, it’s been a privilege.

tiny brontosauruses

October 17, 2014

tiny brontosauruses

This arrived on my Facebook wall, courtesy of Raul Diaz. For a split second I really did think the one second from the right was an older-model Carnegie Brachiosaurus toy.

I assume that, like me, you have people in your life that you don’t correspond with very often, and when you remember that they exist, it just makes you happy. Like, yeah, there’s a slightly higher chance that our species is going to make it, just because that person is out there in the world, doing what they do. Raul is in that category for me. He’s a herpetologist, but that term doesn’t really do him justice; Raul is into herps like Genghis Khan was into real estate acquisition.

Now he’s an Assistant Professor at La Sierra University and also teaches at the Loma Linda University School of Medicine (Raul, that is, not Genghis Khan). But I’ve known him since he was an undergrad. He was a student in one of my discussion sections for the evolution course at Berkeley. I had a tradition in all the classes I taught as a grad student: on the last class meeting I’d have people bring food and we’d have a little potluck. Raul showed up with a six-pack of Pabst Blue Ribbon. No-one else was partaking, so Raul and I spent 50 minutes drinking PBR and talking about descent with modification. Good times.

Oh, and the “tiny brontosauruses” are actually coatis, genus Nasua, raccoon relatives that range from the southwestern US to northern South America. Surprisingly, I don’t think that Darren has ever covered coatis in detail at TetZoo; maybe this will spur him into action.

After the sheep skull ten days ago, here is Logan the wallaby in all his glory:

wallaby-skull-multiview

As always, click through for the full-sized version (6833 × 5082).

 

Remember I picked up those three sheep skulls (and some other bones, including a complete neck) from a shallow pit in a field near where we live? Here is first first of the skulls, cleaned up and photographed in orthogonal views.

sheep-skull-composite

It’s interesting to compare it to the pig skull from way back:

pig-skull-white

Sheep and pigs are both perfectly well-behaved artiodactyls, but their skulls are dramatically different. The pig is extraordinarily more robust, and has absolutely massive jaw-muscle fossae.

The sheep would have been difficult to prepare by the usual simmer-and-slice method — too easy to damage, especially inside the nasal cavity, where the respiratory turbinates are very fragile. The pig is a much easier proposition. I was able to clean out its nasal cavity just by running water through it at fairly high pressure, without doing any damage.

For anyone who wants to get into skull preparation, I definitely recommend starting with a pig.

Just over a year ago, in his write-up of the Edinburgh SVPCA, Matt included a photo of me standing in front of a Giant Irish Elk (Megaloceros), positioned so that the antlers seem to be growing out of my head. Matt finished his post with a background-free version of that photo, and commented:

… so he can be dropped right into posters, slide shows, and other works of science and art. I really, really hope that he turns up in conference talks and other presentations in the months and years to come. If so, send us a photo documenting his miraculous apparition and we’ll show it to the world.

It has come to pass.

Last week, Vladimir Socha gave a presentation about “famous paleontologists” during the “Night of the Scientists” event:

X-277

(I think that’s Bakker on the left of the slide.)

Here’s one of his slides:

X-265

Yep. That’s the Queen of England at the top, and me, her subject, beneath. With antlers.

Here’s a cleaner version of the slide that Vladimir sent me:

vladimir-socha-slide

Apparently the text translates as:

Paleontologists should have a sense of humour, too. On the internet, this is largely shown for example by british computer programmer and sauropod expert Michael P. Taylor (*1968).

So there you go. I made it into “famous paleontologists”, ahead of a vast number of far worthier candidates, because of my antlers.

I think there’s a lesson there for all of us.

But I’m darned if I know what it is.

Just a quick photo-post today. A couple of months ago, walking around the fields near our house, I found a broad shallow pit with a lot of a sheep skeletal elements in it. I took my youngest son out on an expedition, and we rescued the good material. I’ve cleaned up the first two (of three) skulls. Here is the smaller of the two — which is also more complete, and the big one has lost its nasals.

IMG_1707-oblique

Click through for glorious high-resolution (4000 x 3000, and not a pixel wasted).

I took a nice set of orthogonal-view photos of this skull. When I have time, I will clean them up and composite them as I did with my pig-skull, which I’m sure you all remember:

pig-skull-white

(Well … I call it my pig skull, but it’s not mine any longer. I donated it as the prize for winning the TetZooCon quiz, and it is now the proud possession of Kelvin Britton. But I have another one, so that’s all right.)

 

Internal Iliac Arteries - MJW 2011

Here’s a thing I put together to help my students understand the many branches of the internal iliac artery in humans. In the image above, we’re looking in superomedial view into the right half of the sacrum and pelvis. Bones are white, ligaments blue, the piriformis muscle sort of meat-colored, and arteries red (for a tour of the pelvis identifying all of this stuff, see my pelvic foramina slideshow). At the top is a big inverted Y-shape: the common iliac arteries branching from the abdominal aorta, which continues on, much reduced, as the median sacral artery. The right common iliac artery is shown bifurcating into the external iliac artery, which continues on out of the pelvis to become the femoral artery, and the internal iliac artery, source of much fear and doubt.

The first thing to understand is that any particular branching pattern of the internal iliac arteries, whether in an anatomical altas, a lecture, revealed in a dream, or even in your own body, will probably have no bearing whatsoever on the branching pattern in the next person you encounter, alive or dead. Furthermore, the variation between right and left in a single person can be as great as that among different people. The branches to pelvic viscera are particularly fiendish; they sometimes travel far into the pelvis as a common trunk and then “starburst” near their target organs, making identification almost impossible. Do not waste your time trying to memorize any particular branching sequence. Instead, concentrate on matching the arteries to their targets; you will discover the identities of the branches by seeing where they are going, not the order in which they branch.

There are typically 10 named branches of the internal iliac artery. Authorities quibble on the details, as we’ll see in a moment, but if you know these 10, you’ll be fine for almost any conceivable purpose. A simple scheme of my own devising for remembering them is 2-4-4:

TWO to the back body wall:

  1. iliolumbar A—may arise from external or common iliac AA; sometimes double
  2. lateral sacral A—note branches to anterior sacral foramina and anastomoses with median sacral A

FOUR leaving the pelvis entirely:

  1. obturator A—often arises from the external iliac A instead, exits pelvis through obturator canal
  2. superior gluteal A—exits pelvis through suprapiriform foramen
  3. inferior gluteal A—exits pelvis through infrapiriform foramen, with internal pudendal A
  4. internal pudendal A—exits pelvis through infrapiriform foramen, with inferior gluteal A

FOUR to pelvic viscera:

  1. superior vesical A—usually the dominant artery of the anterior trunk, this is the patent part of the obliterated umbilical artery, which survives as the medial umbilical ligament
  2. inferior vesical A (males) / vaginal A (females)—may branch off uterine A (females) or superior vesical A (both)
  3. uterine A (females)—major artery to uterus, approaches laterally within the broad ligament
    A to ductus deferens (males)—extremely small and difficult to trace
  4. middle rectal A—usually the most inferior branch of the entire internal iliac tree (at least inside the pelvis)

My way to explain those last four is to extend my index finger and say, “Everybody has to pee, so up front we have superior vesical.” Then extend my pinky and say, “And everyone has to poop, so in back we have middle rectal.” Then extend digits three and four and explain that the identity of the middle two arteries varies between the sexes (but that the inferior vesical artery of males and the vaginal artery of females are basically the same vessel).

There is a LOT of variation in the descriptions of the internal iliac artery branches among different sources — almost as much variation as there is in the arteries themselves.

  • ​The Thieme Atlas of Anatomy, 2nd Ed (Gilroy et al. 2009), Table 19.1 on p. 254, includes the inferior vesical artery for both sexes. The artery to ductus deferens is listed as a branch of the superior vesical artery, and the uterine and vaginal arteries are listed separately, bringing the total for females to 11.
  • Clinically Oriented Anatomy, 7th Ed (Moore et al. 2013), Table 3.4 and pp. 350-355, lists the 10 branches I went through above. Moore et al. explicitly say that the vaginal artery is the female homolog of the inferior vesical artery (p. 351).
  • Gray’s Anatomy, 40th Ed (Standring et al. 2008), pp. 1085-1089, splits the difference. The artery to ductus deferens is not listed; instead, the ductus deferens is said to be supplied by the inferior vesical A (in contrast to Thieme, which has it is supplied by the superior vesical A). Both the vaginal and inferior vesical arteries are listed, but the vaginal artery is said to frequently replace the inferior vesical artery.

The upshot is that pretty much all of these sources agree on how the blood is getting distributed, there are just some minor differences over what we call certain vessels. I have never personally seen a dissection detailed enough to allow an interior vesical artery to be recognized separately from the vaginal artery — the vagina lies so close behind the bladder that whatever you call the artery that runs lateral to them, it could easily be supplying both structures, and probably does. As far as I’m concerned, the inferior vesical artery in males and the vaginal artery in females are the same artery, in that they both supply the inferior portion of the bladder. I think it’s just a historical hiccup that we call them by different names, possibly perpetrated by smelly, lonely, vagina-obsessed men of centuries past.

A final note, added in revision: some sources refer to two trunks or divisions of the internal iliac artery: a posterior trunk that gives rise to the iliolumbar, lateral sacral, and superior gluteal arteries, and an anterior trunk that gives rise to everything else. If that’s what your professor tells you, smile and nod and keep your heretical thoughts to yourself. Personally, I regard the notion of trunks of the internal iliac artery alongside phlogiston, luminiferous aether, and snorkeling sauropods, as romantic nonsense at best. I have seen an obturator artery arise from a superior gluteal artery and a pudendal artery arise from a superior vesical artery. In a world where variants like those can and do turn up frequently, the stability and reason implied by regular trunks is illusory.

References

  • Gilroy, A., MacPherson, B., and Ross, L. (eds.) 2009. Atlas of Anatomy, 2nd ed. Thieme, Stuttgart.
  • Moore, K.L., Dalley, A.F., and Agur, A.M. 2013. Clincially Oriented Anatomy, 7th ed. Lippincott Williams & Wilkins, Philadelphia.
  • Standring, S. 2008. Gray’s Anatomy, 40 ed. Churchill Livingstone, London.
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