I just read this on Zen Faulkes’ NeuroDojo blog:

How should scientists, and reporters, discuss work that has failed to replicate? The original Barr and colleagues article remains in the scientific literature; failed replication alone is not grounds for retraction.

He’s right, of course: we certainly don’t want to retract every paper whose conclusions can’t be replicated, for all sorts of reasons: they may subsequently be replicated after all; the paper may contain other useful information even if the experiment in question was flawed; the replication studies themselves probably rely on the original’s Methods section; authors should not be punished for unfortunate outcomes unless they were fraudulently obtained.

What we want is for that Barr et al paper, whenever anyone looks at it, to be displayed with a prominent header that says “The following studies attempted to replicate this finding but failed:”, and a list of references/links. And, for that matter, another header saying that the following other studies did replicate it.

For web-sites to automatically produce that kind of annotation, they need articles that cite the original to include an additional piece of metadata, along with the author/year/title/journal/etc. metadata that identifies the cited paper. That additional ingredient is the citation’s type, which should be one of a small set of defined values.

What values are relevant? I won’t try to come up with an exhaustive list at this point, but obvious ones include:

  • Replicates — the current paper replicates work done in the cited paper (and so provides evidence, though not proof, that the cited paper’s conclusion is correct).
  • FailsToReplicate — the current paper attempts to replicate work done in the cited paper, but fails (and so provides evidence that the cited paper is mistaken).
  • Falsifies — the current paper shows definitely that the cited paper is wrong. This is a stronger statement than FailsToReplicate, and would be used for example when the new work shows conclusively that the experimental protocol of the original was critically flawed.
  • DependsOn — the current paper depends on information from the cited paper, such as the phylogeny that it proposes or the vertebral formula that it gives. For these purposes, the cited paper is treated as an authoritative source.
  • Acknowledges — the current paper uses ideas proposed in the cited paper, and gives credit to the original.

(We discussed the distinction between those last two previously.)

There are all sorts of practical issues that will impede the adoption of this idea (not least the idiot fact that the citation graph is a trade secret rather than a freely available database), but let’s ignore those for now, and figure out what taxonomy of citation-types we want.

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AMNH T. rex mount, photo by Mike Taylor.

In a recent comment, Doug wrote:

If I want to be a truly educated observer of Tyrannosaurus rex mounts, what 5 things should I look for in a reconstruction to assess if it is true to our current scientific understanding? I’m not talking tail dragging/upright at this point…we are well past that I hope.

If he had asked about Apatosaurus, I could have written him a novel. But it is a point of pride with me not to contribute to the over-application of human attention to T. rex; not only would it be vulgar, it would also be a waste of resources, considering how many people already have that covered. So, you theropod workers and avocational “rexperts”, we’re finally inviting you to the high table. Please, tell us–and Doug–what separates the good T. rex mounts from the crappy ones. Big piles of SV-POW! bucks will be showered on whoever brings the most enlightenment, especially if you adhere to the requested List of 5 Things format.

The comment lines are open–go!

The LSE Impact blog has a new post, Berlin 11 satellite conference encourages students and early stage researchers to influence shift towards Open Access. Thinking about this,  Jon Tennant (@Protohedgehog) just tweeted this important idea:

Would be nice to see a breakdown of OA vs non-OA publications based on career-stage of first author. Might be a wake-up call.

It would be very useful. It makes me think of Zen Faulkes’s important 2011 blog-post, What have you done lately that needed tenure?. We should be seeing the big push towards open access coming from senior academics who are established in their roles don’t need to scrabble around for jobs like early-career researchers. Yet my impression is that in fact early-career researchers are doing a lot of the pro-open heavy lifting.

Is that impression true?

We should find out.

Here’s one possible experimental design: take a random sample of 100 Ph.D students, 100 post-docs, 100 early-career researchers in tenure-track jobs and 100 tenured researchers. For each of them, analyse their last ten years of publications and determine what proportion are paywalled, what proportion are free to read (e,g, on arXiv or in an all-rights-reserved IR), and what proportion are true (BOAI-compliant) open access.

An alternative approach would be to randomly sample 1000 open-access papers (from PLOS and BMC journals, for example), and 1000 paywalled papers (from Elsevier and Springer, say) and find the career-stage of their authors. I’m not sure which approach would be better?

Who is going to do this?

I think it would be a nice, tractable first project for someone who wants to get into academic research but hasn’t previously published. It would be hugely useful, and I’m guessing widely cited. Does anyone fancy it?

Update

Georg Walther has started a hackpad about this nascent project. Since Jon “Protohedgehog” Tennant has now tweeted about it, I assume it’s OK to publicise. If you’re interested, feel free to leap in!

I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!

Figure6-vertebra-q-composite

Taylor and Wedel (2013b: figure 6). Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view.

I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:

Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.

Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.

If the PrePrint successfully passes these checks, it will be made public.

You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.

Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).

Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.

And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.

xx

Taylor and Wedel (2013b: Figure 9). Partial reconstruction of the Barosaurus lentus holotype YPM 429, cervical vertebra R, approximating its undamaged state by allowing for dorsoventral crushing, shearing and loss of some extremities. Anterior and posterior views scaled to 125% of uncorrected width and 80% of uncorrected height. Dorsal view scaled to 80% of uncorrected height; condyle moved forward and cotyle scaled to 50% of uncorrected width to allow for shearing. Lateral view scaled to 125% of uncorrected height, and sheared backwards 15 degrees. Metapophyses and postzygapophyses drawn in multiple views based on vertebrae Q and S and AMNH 6341 material.

I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.

Now here’s what we’d like:

We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.

So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.

Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
  • Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1

Let’s take another look at that Giraffatitan cervical. MB.R.2180:C5, from a few days ago:

FigureA-Giraffatitan-SI-C5

That’s a pretty elongate vertebra, right? But how elongate, exactly? How can we quantify whether it’s more or less elongate than some other vertebra?

The traditional answer is that we quantify elongation using the elongation index, or EI. This was originally defined by Upchurch (1998:47) as “the length of a vertebral centrum divided by the width across its caudal face”. Measuring from the full-resolution version of the image above, I make that 1779/529 pixels, or 3.36.

But then those doofuses Wedel et al. (2000:346) came along and said:

When discussing vertebral proportions Upchurch (1998) used the term elongation index (EI), defined as the length of the centrum divided by the width of the cotyle. Although they did not suggest a term for the proportion, Wilson & Sereno (1998) used centrum length divided by the height of the cotyle as a character in their analysis. We prefer the latter definition of this proportion, as the height of the cotyle is directly related to the range of motion of the intervertebral joint in the dorsoventral plane. For the purposes of the following discussion, we therefore redefine the EI of Upchurch (1998) as the anteroposterior length of the centrum divided by the midline height of the cotyle.

Since then, the term EI has mostly been used in this redefined sense — but I think we all agree now that it would have been better for Wedel et al to have given a new name to Wilson and Sereno’s ratio rather than apply Upchurch’s name to it.

Aaaanyway, measuring from the image again, I give that vertebra an EI (sensu Wedel et al. 2000) of 1779/334 = 5.33. Which is 58% more elongate than when using the Upchurch definition! This of course follows directly from the cotyle being 58% wider than tall (529/334 pixels).

So one of principal factors determining how elongate a vertebra seems to be is the shape of its cotyle. And that’s troublesome, because the cotyle is particularly subject to crushing — and it’s not unusual for even consecutive vertebrae from the same column to be crushed in opposite directions, giving them (apparently) wildly different EIs.

Here’s an example (though not at all an extreme one): cervicals 4 and 6 of the same specimen, MB.R.2180 (formerly HM SI), as the multi-view photo above:

DSCN5527-5535-SI-c4-and-c6-posterior

Measuring from the photos as before, I make the width:height ratio of C4 683/722 pixels = 0.95, and that of C6  1190/820 pixels = 1.45. So these two vertebrae — from the same neck, and with only one other vertebrae coming in between them — differ in preserved cotyle shape by a factor of 1.53.

And by the way, this is one of the best preserved of all sauropod neck series.

Let’s take a look at the canonical well-preserved sauropod neck: the Carnegie Diplodocus, CM 84. Here are the adjacent cervicals 13 and 14, in posterior view, from Hatcher (1901: plate VI):

Hatcher1901-plate-VI-C13-C14-posterior

For C14 (on the left), I get a width:height ratio of 342/245 pixels = 1.40. For C13 (on the right), I get 264/256 pixels = 1.03. So C14 is apparently 35% broader than its immediate predecessor. I absolutely don’t buy that this represents how the vertebrae were in life.

FOR EXTRA CREDIT: what does this tell us about the reliability of computer models that purport to tell us about neck posture and flexibility, based on the preserved shapes of their constituent vertebrae?

So what’s to be done?

The first thing, as always in science, is to be explicit about what statements we’re making. Whenever we report an elongation index, we need to clearly state whether it’s EI sensu Upchurch 1998 or EI sensu Wedel et al. 2000. Since that’s so cumbersome, I’m going propose that we introduce two new abbreviations: EIH (Elongation Index Horizonal), which is Upchurch’s original measure (length over horizontal width of cotyle) and EIV (Elongation Index Vertical), which is Wilson and Sereno’s measure (length over vertical height of cotyle). If we’re careful to report EIH and EIV (or better still both) rather than an unspecified EI, then at least we can avoid comparing apples with oranges.

But I think we can do better, by combining the horizontal and vertical cotyle measurements in some way, and dividing the length by the that composite. This would give us an EIA (Elongation Index Average), which we could reasonably expect to preserve the original cotyle size, and so to give a more reliable indication of “true” elongation.

The question is, how to combine the cotyle width and height? There are two obvious candidates: either take the arithmetic mean (half the sum) or the geometric mean (the square root of the product). Note that for round cotyles, both these methods will give the same result as each other and as EIH and EIV — which is what we want.

Which mean should we use for EIA? to my mind, it depends which is best preserved when a vertebra is crushed. If a 20 cm circular cotyle is crushed vertically to 10cm, does it tend to smoosh outwards to 30 cm (so that 10+30 = the original 20+20) or to 40 cm (so that 10 x 40 = the original 20 x 20)? If the former, then we should use arithmetic mean; if the latter, then geometric mean.

Does anyone know how crushing works in practice? Which of these models most closely approximates reality? Or can we do better than either?

Update (8:48am): thanks for Emanuel Tschopp for pointing out (below) what I should have remembered: that Chure et al.’s (2010) description of Abydosaurus introduces “aEI”, which is the same as one of my proposed definitons of EIA. So we should ignore the last four paragraphs of this post and just use aEI. (Their abbreviation is better, too.)

 

References

  • Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.
  • Upchurch, Paul. 1998. The phylogenetic relationships of sauropod dinosaurs. Zoological Journal of the Linnean Society 124:43-103.
  • Wedel, Mathew J., Richard L. Cifelli and R. Kent Sanders. 2000b. Osteology, paleobiology, and relationships of the sauropod dinosaur Sauroposeidon. Acta Palaeontologica Polonica 45(4):343-388.
  • Wilson, J. A. and Paul C. Sereno. 1998. Early evolution and higher-level phylogeny of sauropod dinosaurs. Society of Vertebrate Paleontology, Memoir 5:1-68.

Every year I invest many days’ effort into preparing a 20-minute talk for SVPCA. Then I deliver it to maybe 80 people, and that’s the end — it’s over. It seems like a terrible waste of effort, and it occurred to me that I should make a video of this year’s talk, Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens (which at the last minute I retitled Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens).

But I don’t know how to do that. What I want is a simple program, for either Ubuntu GNU/Linux or MacOS, which will record both the video of my screen (as I step through PowerPoint slides) and the audio of the microphone (as I give the talk), resulting in a single video file that I can upload to YouTube.

Can anyone recommend such a program?

Update 1

I got an almost immediate suggestion from @Stephen_Curry that I use ProfCast. I downloaded the trial version, but it insists on running official Microsoft PowerPoint, which I don’t have. (I prepare my talks using OpenOffice’s low-rent PowerPoint-alike.) Rats.

Update 2

@emckiernan13 cleverly suggested that I do a Google hangout (on air, recording to YouTube) with me as the only participant. So far I’ve not been able to get this to work. It won’t start a video hangout unless I have at least one other live person on the call; and although I can make it go in and out of capture mode, I can’t find a way to get hold of the captured stream.

Has anyone done this successfully?

 

In his classic monograph, Hatcher (1901) illustrated the cervical vertebrae of the Diplodocus carnegii holotype CM 84 with beautiful drawings:

Wedel and Taylor 2013 bifurcation Figure 13 - Diplodocus cervicals from Hatcher

But only in lateral view.

Other plates show photos in lateral, anterior and posterior views, and these are useful even though they’re much less clear than the drawings.

But he didn’t illustrate the vertebrae at all in dorsal or ventral view — and as far as I know, no-one else has done so either. I would find these views really useful for something I’m working on. Does anyone have photos?

Help!

Reference

Hatcher, Jonathan B. 1901. Diplodocus (Marsh): its osteology, taxonomy and probable habits, with a restoration of the skeleton. Memoirs of the Carnegie Museum 1:1-63 and plates I-XIII.