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.

 

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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.

References

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.

5WaysToStopSabotagingYourSuccessArticle

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 sci-hub.com domain, only to find it immediately popping up again as sci-hub.io. 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.