Liem et al 2001 PPTs - intro slide

Functional Anatomy of the Vertebrates: An Evolutionary Perspective, by Liem et al. (2001), is by some distance my favorite comparative vertebrate anatomy text. When I was a n00b at Berkeley, Marvalee Wake assigned it to me as preparatory reading for my qualifying exams.

This scared me to death back then. Now I love it.

This scared me to death back then. Now I love it – sharkitecture!

The best textbooks, like Knut Schmidt-Nielsen’s Animal Physiology (which deserves a post or even series of its own sometime), have a clarity of writing and illustration that makes the fundamentals of life seem not only comprehensible, but almost inevitable – without losing sight of the fact that nature is complex and we don’t know everything yet. FAotV has both qualities, in spades.

Where vertebrae come from.

Where vertebrae come from. Liem et al. (2001: fig. 8.4).

I’m writing about this now because Willy Bemis, second author on FAotV, has just made ALL of the book’s illustrations available for free on his website, in a series of 22 PowerPoint files that correspond to the 22 chapters of the book. All told they add up to about 155 Mb, which is trivial – even the $5 jump drives in the checkout lanes at department stores have five to ten times as much space.

Aiiiieeee - a theropod! Aim for its head!

Aiiiieeee – a theropod! Aim for its head! Liem et al. (2001: fig. 8.17).

Of course, to get the full benefit you should also pick up a copy of the book. I see used copies going for under $40 in a lot of places online. Mine will have pride of place on my bookshelf until I enter the taphonomic lottery. And I’ll be raiding these PPTs for images from now until then, too.

Countercurrent gas exchange in fish gills - a very cool system.

Countercurrent gas exchange in fish gills – a very cool system. Liem et al. (2001: fig. 18.6).

So do the right thing, and go download this stuff, and use it. Be sure to credit Liem et al. (2001) for the images, and thank Willy Bemis for making them all available. It’s a huge gift to the field. Here’s that link again.

Liem et al 2001 PPTs - shark jaw and forelimb musculature

Dangit, if only there was a free online source for illustrations of shark anatomy… Liem et al (2001: fig. 10.12).

But wait – that’s not all! Starting on June 28, Dr. Bemis will be one of six faculty members from Cornell and the University of Queensland teaching a 4-week massively open online course (MOOC) on sharks. Freakin’ sharks, man!

“What did you do this summer? Hang out and play Nintendo?”

“Yep. Oh, and I also took a course on freakin’ sharks from some awesome shark experts. You?”

As the “massively open” part implies, the course is free, although you have the option of spending $49 to get a certificate of completion (assuming you finish satisfactorily). Go here to register or get more info.


  • Liem, K.F., Bemis, W.E., Walker, W.F., and Grande, L. 2001. Functional Anatomy of the Vertebrates. (3rd ed.). Thomson/Brooks Cole, Belmont, CA.

I’ve been a bit nonplussed recently to see some strange claims about Alexandra Elbakyan, the creator of Sci-Hub. For example, this from Angela Cochrane in an article at the Scholarly Kitchen:

She sincerely believes that she is above the law.

I don’t think that’s the case at all. Nothing Elbakyan has said seems to communicate the kind of arrogance or exceptionalism that this implies. It’s more that she sees what she’s doing as obeying a higher law (whether correctly or incorrectly is, for the moment, beside the point). In other words, it’s not that she thinks she is anything special, but that what Sci-Hub is doing is special.

And by “a higher law” she doesn’t just mean an abstract sense of what is morally right, but very concretely article 27 of the UN declaration on human rights. And by the way, I notice that the International Covenant on Economic, Social and Cultural Rights, article 15, is even more explicit:

1. The States Parties to the present Covenant recognize the right of everyone […] To enjoy the benefits of scientific progress and its applications;

2. The steps to be taken by the States Parties to the present Covenant to achieve the full realization of this right shall include those necessary for the conservation, the development and the diffusion of science and culture.

3. The States Parties to the present Covenant undertake to respect the freedom indispensable for scientific research and creative activity.

4. The States Parties to the present Covenant recognize the benefits to be derived from the encouragement and development of international contacts and co-operation in the scientific and cultural fields.

This treaty has been in force since 3rd January 1976, and almost every country in the world has both signed and ratified it (with the USA being the obvious big example of a signatory that has not ratified):

States Parties and signatories of the International Covenant on Economic, Social and Cultural Rights. Updated to July 2007. Dark green states are states parties. Light green states are signatories. [From the Wikipedia article linked above.]

States Parties and signatories of the International Covenant on Economic, Social and Cultural Rights. Updated to July 2007. Dark green states are states parties. Light green states are signatories. [From the Wikipedia article linked above.]

So there is at least, as Elbakyan has asserted, a case to be made that her actions are in accordance with the law, and those of legacy barrier-based publishers against it.

Now let me say again that I’m not really sure what to think about all this — for those who don’t want to read my whole article on this, the punchline was “Heck if I know”. But I do think we at least owe Elbakyan a proper reading of her motivation, and I don’t think “above the law” really captures it.

Then there’s this from David Smith in a comment on the same post:

It’s pretty clear that […] this is not some principled stance – it’s a VERY shady operation indeed.

I don’t think “this is not some principled stance” is at all a tenable position. Again, you only have to look at the nature of Elbakyan’s arguments (including the appeal to human rights) to see that a principled stance is exactly what it is. They may not be principles that everyone agrees with, but they are evidently ones that Elbakyan believes in very strongly.

I thought that much was self-evident. But in a followup comment, Sandy Thatcher asked:

And how do you know she’s really not just evoking those principles as a way to justify her unprincipled behavior? […] Why should we rake her words at face value?

How do I know Elbakyan is not lying about her motivation? I suppose I don’t know, any more than I know Sandy Thatcher isn’t lying in his comments, or David Crotty in his, or Tom Reller in his. My policy is to assume people are telling the truth unless it can be shown that they’re not. I’d like to think that’s a pretty universal strategy.

The other half of this equation is: what do people think Elbakyan has to gain from all this? She is putting herself in the firing line of a big, well-resourced and litigious corporation in return for … what? A couple of BitCoin donations? I can’t see any credible motive for her actions other than the ones she claims, namely to make scholarly research freely available to the world. Doesn’t Occam’s Razor suggest that the stated reason is the real reason?

Once more — let me be clear — none of this means that I wholeheartedly support what Sci-Hub is doingas previously noted, I’ve yet to make up my mind. But I think that we’ll all be able to give the issue clearer-headed consideration if we can stop with the personal attacks and second-guessing of motives.

All the evidence says that Elbakyan is exactly what she appears to be: someone who believes that all scholarship should be free to everyone, and (rightly or wrongly) that when copyright impedes this, it should be ignored.

Clash of the Titans from above

Here’s the “Clash of the Titans” exhibit at the Sam Noble Oklahoma Museum of Natural History, featuring the reconstructed skeletons of the giant Oklahoma Apatosaurus – which I guess should now be called the giant Oklahoma apatosaurine until someone sorts out its phylogenetic position – and the darn-near-T. rex-sized Saurophaganax maximus, which may be Allosaurus maximus depending on who you’re reading.

Now, I love this exhibit in both concept and execution. But one thing that is more obvious in this view from the upper level balcony is that despite its impressive weaponry, a lone 3-to-5 ton Saurophaganax had an Arctic ice cap’s chance in the Anthropocene of taking down a healthy 30-meter, 40-50 ton apatosaur (which is to say, none). I like to imagine that in the photo above, the apatosaur is laughing at the pathetically tiny theropod and its delusions of grandeur.

Clash of the Titans from behind

In this shot from behind, you get a better look at the baby apatosaur standing under the big one, and it hints at a far more likely target for Saurophaganax and other large Morrison theropods: sauropods that were not fully-grown, which was almost all of them. I am hip to the fact that golden eagles kill deer, and some lions will attack elephants – as Cookie Monster says, “Sometime food, not anytime food” – but not only were smaller sauropods easier prey, they were far more numerous given the inevitable population structure of animals that started reproducing at a young age and made more eggs the bigger they got (as essentially all egg-laying animals do).

In fact, as discussed in our recent paper on dinosaur ontogeny (Hone et al. 2016), there may have been times when the number of fully-grown sauropods in a given population was zero, and the species was maintained by reproducing juveniles. The giant Oklahoma apatosaurine is a unique specimen today – by far the largest apatosaurine we have fossils of – but it may also have been an anomaly in its own time, the rare individual that made it through the survivorship gauntlet to something approaching full size.

Amazingly enough, there is evidence that even it was not fully mature, but that’s a discussion for another day. Parting shot:

Oklahoma Apatosaurus neck and head


What’s in Mike’s freezer?

February 26, 2016

What’s that in Mike’s freezer? Let’s take it out and have a look.

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Onto the table out in the garden …

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Unwrap another layer …

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Hang on! That looks like … It can’t be, can it?

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It is! It’s a buzzard!

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A buzzard with extremely serious claws!

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And a serious beak as well!

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Further bulletins down the line, when I get a chance to play with it properly.

(Title stolen shamelessly from John Hutchinson’s blog.)

The Chronicle of Higher Education‘s piece on Sci-Hub contains a disturbing claim that I’ve not seen elsewhere. I’ll quote:

Edward Sanchez, head of library information technology at Marquette University, says his biggest concern about Sci-Hub is how it obtains access to library databases, through a phishing campaign.

He says that many colleges have been targeted by Sci-Hub. In one case at Marquette, a professor received an email stating that he or she needed to update his or her university user name and password by following a link. Once on the site, which was actually in New Zealand, the faculty member typed in new credentials, which were then captured by what the publisher later linked to Sci-Hub.

“Then you start seeing your downloads going to unusual locations or downloads that are occurring in huge quantities — thousands of downloads,” Mr. Sanchez says.

If this is true, then it certainly undermines the narrative of Sci-Hub as hero. I was sceptical in part because the image of Sci-Hub downloading thousands of articles from a single account didn’t match with my understanding of how it works. So I emailed both Edward Sanchez and Sci-Hub founder Alexandra Elbakyan, asking for clarification.

I reproduce the relevant parts of these correspondences, with permission from both correspondents. Their comments are in bold, my own questions in regular font.

Talking with Elbakyan

I asked:

My understanding was that the GREAT majority of Sci-Hub requests are satisfied directly from LibGen, and require no download from a University account. Is that right? If so, what would account for the usage patterns that Sanchez saw?

Also, could you please comment on the claim that credentials are obtained by phishing rather then by voluntary donation?

She replied:

Hi. That is true that more than 90% of requests now are satisfied from the collection of papers that were already downloaded before (and now available on LibGen).

That is untrue that we obtain any passwords by phishing though the Sci-Hub website.

I followed up:

Sanchez seems to say that he saw thousands of Sci-Hub downloads from a *single* researcher’s account. Would that be possible? Or are requests spread around across enough different accounts that that wouldn’t happen?

Sanchez’s claim is not that the phishing expedition was carried out at Sci-Hub itself, but that it was done by a site in New Zealand (he doesn’t say what site) and that the phished credentials subsequently turned up in use at Sci-Gen. Is that possible?

Her reply:

In that case it is possible, because Sci-Hub acquires passwords from many different sources. So it may well be possible that this professor’s password finally ended up being used on Sci-Hub website.

Me again:

“Sci-Hub acquires passwords from many different sources” — that is interestingly ambiguous! Are you able to say anything about what those sources are, or would that compromise other people?

And Elbakyan’s last word for now:

At this moment I prefer not to disclose the thorough details of Sci-Hub operation, but I expect this to become possible in future.

Which I think is understandable given the present circumstances.

Talking with Sanchez

In parallel with this, I was corresponding with Edward Sanchez. I asked:

Does this correctly represent what you told the reporter? I ask because my understanding was that the great majority of Sci-Hub requests are satisfied directly from LibGen, and require no download from a University account. LibGen in effect serves as a cache for Sci-Hub. If that understanding is right, then it would be very odd for a single account to be used heavily as suggested.

His response:

I understand your confusion. There are millions of articles already in the Libgen database so one would naturally think that Sci Hub is only obtaining current articles, but in order to obtain a favorable ruling on the preliminary injunction Elsevier was able to prove that Sci-Hub was downloading between 2,000 and 8,500 articles a day.

I asked further:

I can easily imagine, given the total size of the research corpus, that SciHub would still be downloading 2000-8500 articles per day in total.

But I understood your quote “you start seeing your downloads going to unusual locations or downloads that are occurring in huge quantities — thousands of downloads” to mean that you say thousands of downloads from the account of just that one Marquette scholar. Did I misunderstand?

And Sanchez’s reply:

The reference I made was to the same login connecting from New Zealand and Florida at the same time. Also, looking at the logs I would say hundreds is more accurate per login. The total would be in the thousands.

The vendor would be able to confirm exact numbers.

Just so you know the request and interview were within a couple of hours and the article was published the next day. Very little time to get this out and the interviewee does not get a review option. The way this was put struck me as a bit unclear too. My apologies.

(No apologies necessary, of course!)

I went on to ask:

I contacted Alexandra Elbakyan and asked about the claim that Sci-Hub was obtaining credentials by phishing. She denies this, so I wanted to ask you whether you’re able to give more detail than you did in the interview. What led you to think that the New Zealand-based site that phished your colleague’s credentials is linked to Sci-Hub? When you say “… what the publisher later linked to Sci-Hub”, do you mean that you yourself didn’t make such a connection, but that a publisher asserted it? If so, are you able to disclose which publisher?

And Sanchez replied:

The credentials from the faculty member who fell prey to the phishing attack (New Zealand site) were used for the downloads.

That is where things stand now.

What does it all mean?

How did the Marquette professor’s credentials make it into Sci-Hub?

We have an observation — that the credentials were phished in New Zealand, and turned up in Sci-Hub. We have a hypothesis that would explain it (Sci-Hub runs the New Zealand site), but Elbakyan robustly denies this, both here and elsewhere.

We also have a second hypothesis: that the New Zealand site is independent from Sci-Hub, but that Sci-Hub somehow obtained the credentials that it phished. There is some evidence for this — the fact that those credentials turned up on Sci-Hub — but nothing conclusive.

Crucially, there seems to be no evidence either for or against that hypothesis. And I can’t think of any way to test it, short of tracking down the New Zealand site (whose identity we don’t know), deliberately feeding it scholarly credentials, and waiting to see whether they are used by Sci-Hub. Even that may well not work, since I doubt most Sci-Hub accesses can be traced back to an individual set of credentials.

Of course one possibility is that the Marquette professor voluntarily donated his credentials to Sci-Hub, but made up a cover story when a download was traced back to him. But again, there is no way to test that possibility — especially as we (quite properly) do not know the identity of that professor.

Comments are open. Fire away!

So, Sci-Hub is the talk of the town. Everyone’s talking about it. I spent Friday afternoon at Manchester University library, giving a couple of taks about open access, and hearing several others about copyright. It was fascinating being a room full of librarians, all of them aware that Sci-Hub is out there, all of them torn between disapproval and excitement. As Martin Eve said on Twitter:

SciHub. I can’t condone and don’t think it’s the answer. But it is a symptom of the problem.

Me, I’m not so sure whether I can condone it or not.


All About Alexandra

I like that its creator, Alexandra Elbakyan, isn’t at all shifty or covert about what she’s done. She’s loud and proud, and when Elsevier sued her in a New York court, her letter to the judge was defiant and well argued. When confronted with the illegality of Sci-Hub, she has argued that the business model of Elsevier and the other barrier-based legacy publishers is itself illegal, citing article 27 of the UN declaration on human rights:

Everyone has the right freely to participate in the cultural life of the community, to enjoy the arts and to share in scientific advancement and its benefits.

Other have chipped in: the extraordinary open letter In solidarity with Library Genesis and Sci-Hub has been publicly signed by fourteen people who are prepared to be known as supporters.

And yet there is also a very widespread uneasiness about what is self-evidently a pirate site that systematically violates copyright law.

What should we think about it?

Previously on Scholarly Piracy

The first thing to say is that there is precedent, and plenty of it. Aaron Swartz, before the FBI hounded him to his death for downloading scholarly articles, wrote the Guerilla Open Access Manifesto, which unashamedly advocates violating copyright in the name of fairness and progress:

Many say, “but what can we do? The companies hold the copyrights, they make enormous amounts of money by charging for access, and it’s perfectly legal — there’s nothing we can do to stop them.” But there is something we can, something that’s already being done: we can fight back.

Those with access to these resources — students, librarians, scientists — you have been given a privilege. You get to feed at this banquet of knowledge while the rest of the world is locked out. But you need not — indeed, morally, you cannot — keep this privilege for yourselves. You have a duty to share it with the world. And you have: trading passwords with colleagues, filling download requests for friends.

Sci-Hub is essentially the implementation in software of Swartz’s vision. And honestly, I do find it hard to be outraged by Karin Hildebrand’s copyright violation:

So happy when I discovered SciHub last week! FINALLY can learn more about my daughter’s rare birth defect w/o paying $30 a pop.

It’s worth bearing in mind, when Elsevier brings its legal machinery to bear on Sci-Hub, that people like Karin are among the ones who will suffer — along with disability-rights campaigner Stef Benstead, M-CM patient advocate Christy Collins, and many others.

Illegal ≠ Immoral

Nor do I find it a slam-dunk argument to be told that what Sci-Hub is doing is illegal. Even assuming that the human-rights argument won’t wash and the courts do definitively decide that Sci-Hub is in violation of the law, that won’t in itself make it wrong. Rosa Parks was in violation of the law when she declined to give up her seat for a white man. Dietrich Bonhoeffer was in violation of the law when he preached pacifism in Nazi Germany.

[Note for the hard of thinking: no I am not saying that scholarly paywalls are the moral equivalent of state-sanctioned racism or that Elsevier are as bad as Hitler. I am using extreme examples to demonstrate the principle that an illegal action is not always or necessarily an immoral one.]

None of this means that Sci-Hub is necessarily in the right. What it does mean is that it’s not immediately clear that it’s in the wrong, either. There are subtleties and complexities here. Not to mention a certain poetry in the idea that single Russian researcher, acting alone, has gone right ahead and made the anyone-can-access-any-paper system we’ve all been dreaming about for years.

What are the publishers doing?

Elsevier’s lawsuit is an oddity. Although they’re the ones suing, as the Chronicle of Higher Education found they are not really standing behind it:

An Elsevier representative, Thomas Reller, vice president for global corporate relations, refused to answer questions for this article, saying only that “Elsevier is simply the named plaintiff in the lawsuit that is filed on behalf of the industry.” He urged The Chronicle to speak with officials at the Association of American Publishers.

The AAP has spoken, but its statement is rather bizarre in places:

These activities also have a detrimental effect on public health and safety [because] Sci-hub and LibGen also provide indiscriminate access to content. Certain information, regulated for distribution by publishers, may be available to parties not intended to have this technical knowhow.

They may or may not have a strong moral case against Sci-Hub; but if they do, this ain’t it. Anyone who knows anything at all about scholarly publishing will see through this flimy argument in a second — state secrets can’t be protected by a $30 paywall — so why even make such an argument?

Also relevant here is the question of what publishers can do. As the Library Loon has noted, in her excellent though irritatingly mannered pseudonymous blog, their choices are few and unappealing. When Elsevier won the New York court case, an injunction resulted in the old domain being shut down, but it took no time for the site to pop up again as The site’s not going to be possible to block, any more than The Pirate Bay has been vulnerable to the many, many attempts to shut it down. What does that leaves the publishers? Going after individuals? Even by their standards, that would surely be a PR nightmare.

So what should we think?

Heck if I know.

In the world of novel-writing, people spend their own time creating art — writing. Creative works come into being, and their copyright is (at least initially) owned by the creators. This gives them a legal monopoly on copies of their own work, which they can exploit either directly (by selling copies) or indirectly (by selling the copyright itself to a body that will make that money back over time by selling copies). Either way, the creators get paid, which recompenses them for the time they spent creating, and gives them both the incentive and opportunity to create more.

That may be an idealised version of how things work, but it’s basically right.

In the world of scholarship, things work very differently. Researchers write papers, and their copyright is (at least initially) owned by the creators. The creators then give the copyright to publishers, often even paying the publishers for the privilege. The publishers — whose job, remember, is to “make public”, which is what “publish” means — then do the exact opposite of their job, and lock the research behind a paywall. Copyright is then hidously perverted, and becomes a means of preventing people from accessing that research. Progress is retarded; diseases flourish; lives are lost.

In this scenario, none of the intended goals of copyright are achieved. The researcher is not financially compensated for her work, because she doesn’t own the copyright. She receives no incentive to do more work, because her income has always been grants from the public purse and from charities.

In this model, the sole purpose of copyright is to prevent access to the research. The only thing it achieves is to stop people from reading, using and re-using the work.


[Image from here.]

On Friday, I had the privilege of speaking about open access at a PG Cert course at Manchester University, Open Knowledge in Higher Education. Since I was there I took the opportunity to stay and listen to the other speakers. I heard two intelligent, committed library professionals talk about their jobs in guiding scholars through the maze of twisty little copyright passages that is imposed on them: helping researchers to find free-to-reuse content, to stick within the limit of what’s considered “safe” fair dealing (i.e. nearly none), to avoid arousing the ire of the Copyright Licensing Agency. It fair broke my heart. What a ridiculous waste of everyone’s time and effort.

Just like the time and effort I’ve wasted seeking permission from publishers to reproduce and modify illustrations from others’ papers — in some cases, illustrations that are over century old. A waste of my time, and a waste of the publishers’ time. (And I’m one of the lucky ones: the publishers have at least graciously allowed me to do this every time I’ve asked so far. I’ve heard stories of scholars being charged £1000 for permission to re-use their own illustrations.)

Scholarly copyright is not merely a net negative. Every single aspect of what it does is a negative. Its value is not the sum of plusses and minuses that come out on the minus side of the balance sheet. It’s a sum of minuses. In the scholarly arena, copyright is pure damage.

This, of course, is why the original Budapest Open Access Initiative, back in 2003, declared:

The only role for copyright in this domain should be to give authors control over the integrity of their work and the right to be properly acknowledged and cited.

And it’s why the ten-year anniversary document reasserted the same thing in exactly the same words.

As a long-standing proponent of preprints, it bothers me that of all PeerJ’s preprints, by far the one that has had the most attention is Terrell et al. (2016)’s Gender bias in open source: Pull request acceptance of women versus men. Not helped by a misleading abstract, we’ve been getting headlines like these:

But in fact, as Kate Jeffrey points out in a comment on the preprint (emphasis added):

The study is nice but the data presentation, interpretation and discussion are very misleading. The introduction primes a clear expectation that women will be discriminated against while the data of course show the opposite. After a very large amount of data trawling, guided by a clear bias, you found a very small effect when the subjects were divided in two (insiders vs outsiders) and then in two again (gendered vs non-gendered). These manipulations (which some might call “p-hacking”) were not statistically compensated for. Furthermore, you present the fall in acceptance for women who are identified by gender, but don’t note that men who were identified also had a lower acceptance rate. In fact, the difference between men and women, which you have visually amplified by starting your y-axis at 60% (an egregious practice) is minuscule. The prominence given to this non-effect in the abstract, and the way this imposes an interpretation on the “gender bias” in your title, is therefore unwarranted.

And James Best, in another comment, explains:

Your most statistically significant results seem to be that […] reporting gender has a large negative effect on acceptance for all outsiders, male and female. These two main results should be in the abstract. In your abstract you really should not be making strong claims about this paper showing bias against women because it doesn’t. For the inside group it looks like the bias moderately favours women. For the outside group the biggest effect is the drop for both genders. You should hence be stating that it is difficult to understand the implications for bias in the outside group because it appears the main bias is against people with any gender vs people who are gender neutral.

Here is the key graph from the paper:

TerrellEtAl2016-fig5(The legends within the figure are tiny: on the Y-axes, they both read “acceptance rate”; and along the X-axis, from left to right, they read “Gender-Neutral”, “Gendered” and then again “Gender-Neutral”, “Gendered”.)

So James Best’s analysis is correct: the real finding of the study is a truly bizarre one, that disclosing your gender whatever that gender is reduces the chance of code being accepted. For “insiders” (members of the project team), the effect is slightly stronger for men; for “outsiders” it is rather stronger for women. (Note by the way that all the differences are much less than they appear, because the Y-axis runs from 60% to 90%, not 0% to 100%.)

Why didn’t the authors report this truly fascinating finding in their abstract? It’s difficult to know, but it’s hard not to at least wonder whether they felt that the story they told would get more attention than their actual findings — a feeling that has certainly been confirmed by sensationalist stories like Sexism is rampant among programmers on GitHub, researchers find (Yahoo Finance).

I can’t help but think of Alan Sokal’s conclusion on why his obviously fake paper in the physics of gender studies was accepted by Social Text:it flattered the editors’ ideological preconceptions“. It saddens me to think that there are people out there who actively want to believe that women are discriminated against, even in areas where the data says they are not. Folks, let’s not invent bad news.

Would this study have been published in its present form?

This is the big question. As noted, I am a big fan of preprints. But I think that the misleading reporting in the gender-bias paper would not make it through peer-review — as the many critical comments on the preprint certainly suggest. Had this paper taken a conventional route to publication, with pre-publication review, then I doubt we would now be seeing the present sequence of misleading headlines in respected venues, and the flood of gleeful “see-I-told-you” tweets.

(And what do those headlines and tweets achieve? One thing I am quite sure they will not do is encourage more women to start coding and contributing to open-source projects. Quite the opposite: any women taking these headlines at face value will surely be discouraged.)

So in this case, I think the fact that the study in its present form appeared on such an official-looking venue as PeerJ Preprints has contributed to the avalanche of unfortunate reporting. I don’t quite know what to do with that observation.

What’s for sure is that no-one comes out of this as winners: not GitHub, whose reputation has been wrongly slandered; not the authors, whose reporting has been shown to be misleading; not the media outlets who have leapt uncritically on a sensational story; not the tweeters who have spread alarm and despondancy; not PeerJ Preprints, which has unwittingly lent a veneer of authority to this car-crash. And most of all, not the women who will now be discouraged from contributing to open-source projects.


Zuniceratops ontogeny - Hone et al 2016 fig 2

Various methods that may be used to determine the age/ontogenetic status of a given dinosaur specimen. Central image is a reconstruction of the skeleton of an adult ceratopsian Zuniceratops, with surrounding indications of maturity (taken from multiple sources and do not necessarily relate to this taxon). (a) Development of sociosexual signals (adult left, juvenile right—modified from [9]), (b) surface bone texture (traced from [17]), (c) large size, represented here by an ilium of the same taxon that is considerably larger than that of a known adult specimen, (d) reproductive maturity, here based on the presence of medullary bone here shown below the black arrow (traced from [18]), (e) fusion of the neurocentral arch—location of the obliterated synchondrosis indicated by black arrow (traced from [19]), (f) asymptote of growth based on multiple species indicated by black arrow (based on [20]). Central image by Julius Csotonyi, used with permission. Hone et al. (2016: fig. 2).

New paper out in Biology Letters:

Hone, D.W.E., Farke, A.A., and Wedel, M.J. 2016. Ontogeny and the fossil record: what, if anything, is an adult dinosaur? Biology Letters 2016 12 20150947; DOI: 10.1098/rsbl.2015.0947.

The idea that dinosaurs had unusual life histories is not new. The short, short version is that it is usually pretty straightforward to tell which mammals and birds are adults, because the major developmental milestones that mark adulthood – reproductive maturity, cessation of growth, macro-level skeletal fusions, histological markers of maturity – typically occur fairly close together in time. This is radically untrue for most dinosaurs, which started reproducing early, often well before they were fully grown, and for which the other signals of adulthood can be wildly inconsistent.

Puny ‘pod

We don’t talk about this much in the paper, but one aspect of dinosaur life history should be of particular interest to sauropodophiles: most of the mounted sauropod skeletons in the world’s great museums belong to animals that are demonstrably not mature. They’re not the biggest individuals – witness the XV2 specimen of Giraffatitan, the giant Oklahoma Apatosaurus, and Diplodocus hallorum (formerly “Seismosaurus”).* They’re not skeletally mature – see the unfused scapulocoracoids of FMNH P25107, the holotype of Brachiosaurus mounted in Chicago, and MB.R.2181, the lectotype of Giraffatitan mounted in Berlin. And histological sampling suggests that most recovered sauropods were still growing (Klein and Sander 2008).

* The Oklahoma Museum of Natural History does have a mounted (reconstructed) skeleton of the giant Apatosaurus, and the New Mexico Museum of Natural History has a mounted reconstructed skeleton of Diplodocus hallorum. But as nice as those museums are, in historical terms those mounts are brand new, and they have not shaped the public – and professional – conception of Apatosaurus and Diplodocus to anywhere near the same degree as the much smaller specimens mounted at Yale, AMNH, the Field Museum, and so on.

OMNH baby Apatosaurus

Apatosaurs large and small at the Sam Noble Oklahoma Museum of Natural History

Basically, very little of what we think we know about sauropods is based on animals that were fully grown – and the same problem extends to many other groups of dinosaurs.

This is kind of a methodological nightmare – a colleague on Facebook commented that he had pulled his hair out over this problem – and in the paper we suggest some ways to hopefully alleviate it. I mean, the biology is what it is, but we can minimize confusion by being really explicit about which criteria we’re using when we assign a specimen to a bin like “juvenile”, “subadult”, and so on.

Supposed Former Evolution Junkie

Personally, I’m more excited about the possibilities that dinosaur life history weirdness open up for dinosaur population dynamics and ecology.

Confession time: I am a recovering and relatively high-functioning evolutionary theory junkie. In grad school I was on the heavy stuff – I read tons of Gould and Dawkins and admired them both without being smitten by either. I took seminars on Darwin and evolutionary morphology, and lots of courses in ecology – ever mindful of Leigh Van Valen’s definition of evolution as “the control of development by ecology”. I read a fair amount of Van Valen, too, until “Energy and evolution” (Van Valen 1976) burned out most of my higher cognitive centers.

I say “recovering” evolutionary theory junkie because after grad school I mostly went clean. The problem is that dinosaurs are good for a lot of things, but exploring the inner workings of evolution is usually not one of those things. As products of evolution, and demonstrations of what is biomechanically possible, dinosaurs are awesome, and we can look at macroevolutionary patterns in, say, body size evolution or morphospace occupation, but we almost never find dinos in sufficient numbers to be able to test hypotheses about the tempo and mode of their evolution on the fine scale. I suppose I could have switched systems and worked on critters in which the machinations of selection are more visible, but for me even the charms of evolutionary theory pale next to the virulent allure of sauropods and pneumaticity.

Anyway, keeping in mind that Van Valenian dictum that evolution stands with one foot in the organism-internal realm of genes, cells, tissue interactions, and other developmental phenomena, and the other in the organism-external world of competition, predation, resource partitioning, demographics, and other ecological interactions, then it stands to reason that if dinosaurs had weird ontogenies – and they did – then they might have had weird ecologies, and weird evolution full stop. (Where by ‘weird’ I mean ‘not what we’d expect based on modern ecosystems and our own profoundly mammal-centric point of view’.)

LACM Tyrannosaurus trio - Hone et al 2016 fig 1

Three growth stages of Tyrannosaurus on display at the Natural History Museum of Los Angeles County. Hone et al. (2016: fig. 1).

Actually, we can be pretty sure that the weird ontogenies and weird ecologies of dinosaurs were intimately linked (see, for example, Varricchio 2010). Like the tyrannosaurs shown here – they didn’t all fill the same ecological niche. This casts some old arguments in a new light. Was T. rex adapted for fast running? Prrrrobably – just not as a full-size adult. The skeleton of an adult tyrannosaur is that of a 500 kg cursor pressed into service hauling around 10 tons of murder. And all of this has some pretty exciting implications for thinking about dinosaurian ecosystems. Whereas mammals tend to fill up ecospace with species, dinosaurs filled up their world with ecologically distinct growth stages.

Does all of this add up to weird evolutionary dynamics for dinosaurs? Possibly. As we say in the paper,

Correct identification of life stage also is relevant to fundamentals of evolution—if the onset of sexual reproduction substantially preceded cessation of growth in dinosaurs then the ‘adult’ phenotype may not have been the primary target of selection. In fact, once juveniles or subadults are capable of reproducing, it is conceivable a population could exist with potentially no individuals making it through the survivorship gauntlet into ‘adulthood’ and close to maximum body size. The occasional hints from the fossil record of anomalously large sauropods like Bruhathkayosaurus [51], and the Broome trackmaker [52] might be explained if many sauropods were primarily ‘subadult’ reproducers, and thus extremely large adults were actually vanishingly rare.

Did that actually happen? Beats me. But it’s consistent with what we know about sauropod life history, and with the observed scarcity of skeletally mature sauropods. And it might explain some other oddities as well, such as the high diversity of sauropods in seasonally arid environments like the Morrison Formation (see Engelmann et al. 2004), and the fact that sauropods – and large dinosaurs generally – are much larger than predicted based on the land areas available to them (see Burness et al. 2001). Because the age structure of sauropod populations was so skewed toward juveniles, the average body size of most sauropod populations was probably fairly modest, even though the maximum size was immense. So maybe a continuously reproducing population didn’t require as much food or space as we’ve previously assumed.

If we can falsify that, cool, we’ll have learned something. And if we can falsify the alternatives, that will be even cooler.

I’ll stop waving my arms now, lest I achieve powered flight and really inspire controversy. Many thanks to Dave and Andy for bringing me on board for this. It was a fun project, and we hope the paper is useful. You can read Dave’s thoughts on all of this here.


Thirteen years ago, Kenneth Adelman photographed part of the California coastline from the air. His images were published as part of a set of 12,000 in the California Coastal Records Project. One of those photos showed the Malibu home of the singer Barbra Streisand.

In one of the most ill-considered moves in history, Streisand sued Adelman for violation of privacy. As a direct result, the photo — which had at that point been downloaded four times — was downloaded a further 420,000 times from the CCRP web-site alone. Meanwhile, the photo was republished all over the Web and elsewhere, and has almost certainly now been seen by tens of millions of people.

Oh, look! There it is again!

Oh, look! There it is again!

Last year, the tiny special-interest academic-paper search-engine Sci-Hub was trundling along in the shadows, unnoticed by almost everyone.

In one of the most ill-considered moves in history, Elsevier sued Sci-Hub for lost revenue. As a direct result, Sci-Hub is now getting publicity in venues like the International Business Times, Russia Today, The Atlantic, Science Alert and more. It’s hard to imagine any other way Sci-Hub could have reached this many people this quickly.


I’m not discussing at the moment whether what Sci-Hub is doing is right or wrong. What’s certainly true is (A) it’s doing it, and (B) many, many people now know about it.

It’s going to be hard to Elsevier to get this genie back into the bottle. They’ve already shut down the original domain, only to find it immediately popping up again as That’s going to be a much harder domain for them to shut down, and even if they manage it, the Sci-Hub operators will not find it difficult to get another one. (They may already have several more lined up and ready to deploy, for all I know.)

So you’d think the last thing they’d want to do is tell the world all about it.