I just gave an answer to this question on Quora, and it occurred to me that I ought to also give it a permanent home here. So here it is.


This is a great example of a question that you’d think would have a simple, clear answer, but doesn’t. In fact, as a palaeontologist specialising in dinosaur gigantism, I have an abiding fear of being asked this question in a pub quiz, and not being able to produce the name that’s written on the quizmaster’s answer sheet.

First, what do we mean by “biggest”? Diplodocus was longer than Apatosaurus, but Apatosaurus was heavier. Giraffatitan was taller than either. Let’s simplify and assume we want to know the heaviest dinosaur.

Second, estimating the masses of extinct animals is incredibly hard even when we have a pretty complete skeleton. For example, the gigantic mounted brachiosaur skeleton in Berlin (which used to be called “Brachiosaurus” brancai but is now recognised as the separate genus Giraffatitan) has been subject to at least 14 estimates in the published scientific literature, as summarised here. They vary from 13,618 kg to 78,258 kg — a factor of 5.75 for the same individual. That’s like looking at a human skeleton and not knowing whether its from Kate Moss or Arnold Schwazenegger. (There are reasons for this and I urge you to read the linked article.)

Third, the big dinosaurs tend to be very poorly represented. Giraffatitan is probably the heaviest dinosaur known from a more or less complete skeleton (though even that is put together from several different individuals) so I could give that as the answer to the hypothetical pub-quiz — though the answer sheet would probably be out of date and call it Brachiosaurus.

Fourth, which individual of a given species do we mean? I said Giraffatitan is known from a more or less complete skeleton. And my best guess is that that individual massed, say, 30,000 kg. But an isolated fibula of the same species is known that’s 12.6% longer than the one in the skeletal mount. That suggest an animal that masses 1.126^3 = 1.43 times as massive as the mounted skeleton — say 43,000 kg. There might be yet bigger Giraffatitan individuals. On the other hand, there is some evidence that Apatosaurus, which is usually thought of as not being so big, might have got even bigger.

Fifth, the very biggest specimens tend to be known from only a handful of bones. A good example here is the titanosaur Argentinosaurus, which is known from several vertebrae and a few limb bones, but not all from the same individual. It’s a good bet that it massed 60-70 tonnes — so maybe about twice as much as Giraffatitan, but much less than the often-cited 100 tonnes. Other, more recently discovered, titanosaurs seem to be in the same size class: Puertasaurus, Futalognkosaurus, Dreadnoughtus and more. They they are hard to compare directly due to the paucity of overlapping material, or at least described overlapping material. (Scientists are working on getting more of this stuff properly described in the literature, which will help.)

But, sixth, the very biggest dinosaurs tend to be apocryphal. There’s Amphicoelias fragillimus, known only from E. D. Cope’s drawing of the upper half of a single vertebra. This may have been 50 m long and massed 80 tonnes; but other published estimates say 58 m and 122 tonnes. We really can’t say from the very poor remains.

So if you get asked this question in a pub quiz, your best bet is to roll a dice, pick an answer, close your eyes and hope. Roll 1 for Giraffatitan, 2 for Brachiosaurus, 3 for Apatosaurus, 4 for Argentinosaurus, 5 for Dreadnoughtus and 6 for Amphicoelias fragillimus. Good luck!

 

Advertisements

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.

We’re starting the new year with a new feature, in which we answer questions that have come our way. We never had a policy about not answering questions, it’s just that previous ones have tended to arrive in the comments section and have been dealt with there. But suddenly in the last few days I’ve gotten two questions from extrabloggular sources, and rather than hide the replies I thought I’d make them available to all.

One of my cohort at Berkeley texted me the other day with the following questions:

OK, phylobuddy: can you suck the marrow from a chicken bone? If they have hollow bones, where’s the marrow?!? Google is getting me nowhere.

Short answer: yes, one can get marrow from chicken bones, from those bones that contain marrow rather than air. In most fully mature chickens, the pneumatic bones include the braincase, the cervical, dorsal, and most or all synsacral vertebrae, some of the dorsal ribs, the central portion of the sternum, the coracoids, and the humeri (if you’re not a regular and some of these terms are unfamiliar, check out these handy guides [1, 2] to the vertebrate skeleton). That leaves marrow in everything else, although the only bones with large marrow cavities–as opposed to tiny trabecular spaces, which also house marrow–are the radii, ulnae, femora, tibiotarsi, and tarsometatarsi. So if you want to actually see large amounts of chicken marrow, or suck the marrow out of chicken bones, you’re basically stuck with the big distal bones of the wing, the thigh, and the drumstick (tibiotarsus). If you are boiling chicken bones to get stock for soups or stews, might as well throw them all in; even the pneumatic bones will still have bits of adhering meat, cartilage, and ligaments that will give up molecules and flavor to the stock.

The long answer is that the expression “hollow bones” has caused no end of confusion, because there are at least two ways to interpret hollow: filled with air, or not filled with bone (the former is a subset of the latter). If you mean “not filled with bone”, then the bones of almost all amniotes* are hollow, and the spaces inside are occupied by marrow (most commonly) or air. If filled with air, the bones are referred to as pneumatic, and an accessible introduction to them is here.

* At least; I know less about amphibians and fish, although at least one osteoglossomorph (IIRC) pneumatizes its vertebrae from its swim bladder!

The reasons it gets confusing are twofold. First, sometimes authors describe bones as hollow and mean only that they have chambers inside, but later readers see ‘hollow’ and infer ‘pneumatic’. Not all hollow bones are pneumatic; in fact, the vast majority of them are not, including the long bones of your arms and legs. The criteria for inferring pneumaticity from dry bones are more strict, and are explored in this paper and this one. Anyway, this point is just confusion caused by an ambiguous term.

The second case is more interesting, because it involves real unknowns. In the fossil record we can almost always tell if a bone is hollow, sensu lato, but sometimes it is not possible to say for certain whether the hollow space(s) inside were filled with marrow or air. Particularly vexing and intriguing examples include the humerus of Eotyrannus and the iliac chambers of some sauropods, which are discussed in this paper. My guess is that the iliac chambers of sauropods are genuinely pneumatic, because they only occur in sauropods that already have sacral pneumaticity, and we know from broken ilia of more basal sauropods and sauropodomorphs that large marrow-filled chambers are not present in those taxa. Conversely, I suspect that the humerus of Eotyrannus was apneumatic (marrow-filled), given that humeral pneumaticity is otherwise unknown in non-avian theropods, although the pneumatic furcula of Buitreraptor at least shows that the necessary clavicular air sac was present in some.

Next question! This one came to me on Facebook, from ReBecca Hunt-Foster, whom you may know from her awesome Dinochick Blogs. You should also envy her and hubby John Foster for getting the most awesome wedding present of all time: a 1/12 scale skeleton of Apatosaurus sculpted by Phil Platt, which you can read about here. That’s cool enough that I am stealing it for this otherwise picture-challenged post.

ANYWAY, ReBecca wrote on my FB wall today to ask:

Random question: Have you seen many tooth marks on sauro cervical verts? I am debating on whether something I have is a dessication crack or really some tooth marks. Thanks :)

In all the 15 years that I have spent looking at sauropod remains in the bowels of many, many museums, I have never seen a single tooth mark on a sauropod vertebra.

[Update the next day: Er, except for the bitten Apatosaurus tail on display in the AMNH! Many thanks to reptilianmonster and steve cohen for reminding me about this in the comments. I’m going to go hide for a while now.]

Now, that doesn’t mean that they aren’t there. Truth be told, I’ve never looked for them, and my usual mental search pattern for pneumatic traces (large, irregular) would probably exclude tooth scratches (small, linear) as noise. But I’ve certainly never seen any vertebrae with easily recognizable signs of predation or scavenging or with obvious bites removed.

People also sometimes ask me what kinds of healed traumas I’ve seen in pneumatic sauropods bones. That’s easy: apart from vertebral fusions, most of which probably have nothing to do with trauma, I’ve seen zip. Nada. Null set. The wingspan of the average tadpole. I’ve seen some pretty cool pneumatic bones from extant birds that were broken and later healed, including a eagle femur in the UCMP comparative collection that is now shaped like the letter Z, but nothing in sauropods.

I can think of three possible reasons for this, which sort of flow into each other. The first is that apart from the very solid and blocky centra of apneumatic vertebrae, sauropod verts were pretty fragile, and prone to getting distorted and busted up even when they started out intact, and those verts that started out broken just had a tougher time with the taphonomic lottery.

The second is that pneumatic sauropod bones would been nothing to most predators other than a mouthful of relatively dry bone shards, so either carnivores left them alone, or if they were osteovores like T. rex, they ate the shards and whatever is left over is unrecognizable. I have seen, and mostly ignored, plenty of vert-shrapnel in quarries and in collections, and maybe sharper eyes than mine could have discerned evidence of predation from those bits. To me it mostly looked like trampling, hydraulic transport, erosion, and other mundane ways to explode a vertebra.

The third is that in addition to a preservation bias against half-destroyed verts, there is probably also a collection bias against them. I’m probably not the only one would pass up a few shards of excellence to dig out the complete fibula sitting next to them in the quarry, and I love this stuff. That said, we did get a LOT of blasted vert bits out of the Wolf Creek quarry in the Cloverly, so if you want to pore over sauropod shards looking for tooth marks, visit the OMNH.

And, if you do know of tooth marks on sauropod vertebrae, please let us know in the comments. And consider publishing them, given the apparent vacuum of such things.