DEmic 2012 figure 5 titanosauriform phylogeny

D’Emic (2012: figure 5)

Now this is super-freakin’ cool, and I’ve been meaning to blog about it for a while. In Mike D’Emic’s recent titanosauriform phylogeny (D’Emic 2012), he (correctly) included Brachiosaurus and Giraffatitan as separate OTUs, and, hey, whaddayaknow, they’re not sister taxa anymore: Brachiosaurus is more closely related to a trio of Early Cretaceous North American brachiosaurids than it is to Giraffatitan.

The potential for someone to find this result was there ever since Mike broke Brachiosaurus and Giraffatitan apart, as a previously composite OTU, in his 2009 paper. It just hadn’t materialized. In fact, some authors have gone out of their way to not find this out, by keeping the old composite coding. That seems…unwise, in retrospect. Whether one agreed with Mike on the nomenclatural point of generic separation or not, not coding the two taxa as separate OTUs (especially after Mike had done that work for them) was a poor phylogenetic decision–in essence, it constrained Brachiosaurus and Giraffatitan to be sister taxa in the analysis, and outlawed any more interesting results–like the one obtained by D’Emic (2012)–before the software even started crunching trees.

So anyway, back to the coolness inherent in D’Emic’s tree. Of course, like all phylogenetic results this is just a hypothesis and it is subject to revision based on new information blah blah blah…but it is really interesting that there is now some phylogenetic support for an endemic radiation of brachiosaurids in North America (bonus goofy observation–you can’t spell ‘endemic’ without D’Emic). Or perhaps Lauriasia–I would kill to know where the British brachiosaurids (or basal titanosauriforms) fit into this story, and Lusotitan, and the apparently tiny Croatian carbonate platform brachiosaurs.

Also super-interesting that, if this tree is accurate, these endemic Early Cretaceous brachiosaurids were living alongside a giant basal somphospondyl in the form of Sauroposeidon, which came from heaven knows where. Look who it’s surrounded by–Ligabuesaurus is from Argentina, Tastavinsaurus is from Spain, and the euhelopodids are from eastern Asia. Evidently there was also a global radiation of basal somphospondyls. And why are all the Early Cretaceous North American brachiosaurids small–smaller than Brachiosaurus and Giraffatitan, anyway (at least until we find bigger individuals of the former)–while Sauroposeidon is so big? Or is that just an effect of tiny sample sizes, and one lucky strike in the form of the Sauroposeidon holotype?

So much cool stuff to think about. I don’t usually get this much enjoyment out of a tree unless it has lights and ornaments.

References

Plateosaurus is pathetic

January 16, 2013

DSCN5593-giraffatitan-vs-plateosaurus

This photograph is of what I consider the closest thing to the Platonic Ideal sauropod vertebra: it’s the eighth cervical of our old friend the Giraffatitan brancai paralectotype MB.R.2181. (previously known as “Brachiosaurusbrancai HM S II — yes, it’s changed genus and specimen number, both recently, but independently.)

And if you look very carefully, down at the bottom, you can see the same vertebra, C8, of the prosauropod Plateosaurus. Pfft.

This photo was taken down in the basement of the Museum für Naturkunde Berlin, on the same 2008 trip where Matt took the “Mike in Love” photo from two days ago. For anyone who didn’t recognise the specific vertebra I was in love with in that picture, shame on you! It is of course our old friend the ?8th dorsal vertebra of the same specimen, which we’ve discussed in detail here on account of its unique spinoparapophyseal laminae, its unexpectedly missing infradiapophyseal lamina and its bizarre perforate anterior centroparapophyseal laminae.

I don’t have time to write about this properly, but a few people have asked me about the new Sellers et al. (2012) paper on measuring the masses of extinct animals — in particular, the Berlin Giraffatitan — by having a CAD program generate minimal complex hulls around various body regions. Rather than write something new about it, I’m going to publish the comments that I sent Ed Yong for his Discover piece on the new technique:

Hi, Ed, good to hear from you. Yes, it’s a good paper: a useful new technique that has some useful properties, most importantly that it requires no irreproducible judgements on the part of the person using it, and that it’s ground-truthed on solid data from extant animals.

It’s a reassuring sanity-check to find that my (2009) mass estimate falls well within their method’s 95% confidence interval, and is in fact within 0.6% of their best estimate.

There are a couple of problems with this study, which I hope will be addressed in followups. The authors are honest enough to touch on all of these problems themselves, though! They are:

1. All the extant animals used to determine the fudge factor are mammals, which means they are not necessarily completely relevant to dinosaurs. In particular I would very much like to have seen regression lines and correlation coefficients for this method for birds and crocodilians, both of which are much more closely related to Giraffatitan.

2. Much depends on the reconstruction of the torso, particular the position of the ribs, which is very difficult to do well and confidently with dinosaurs. In my volumetric analysis (Taylor 2009:803) I found that the torso accounts for 70% of total body volume in Giraffatitan, so rib orientation will make a big difference to overall mass. Sauropod ribs that are well preserved and undistorted along their whole length are extremely rare.

3. Use of a single density value for the whole animal, while appropriate for mammals, really isn’t for brachiosaurs, in which the very long neck likely had a density no more than half that of the legs. I’m not sure what can be done about this, though, since any attempt to correct for density variation involves subjective guesswork. Then again, so do all guesses at overall body density in dinosaurs.

Issue 1 bothers me most, because the convex hulls of limb segments in mammals will be proportionally much larger than in sauropods, due to the complex shapes of mammalian long-bone ends. I worry that using mammals as a baseline will underestimate sauropod leg mass.

Still, even with these caveats, it’s a good exposition of an important new method which I expect to see widely adopted.

Hope that’s helpful.

In short: good work, widely applicable, and probably the best mass-estimation technique we now have available for complete and near-complete skeletons. It would be good to see it applied to (say) the Yale, AMNH and CM apatosaurs.

Composite illustration from Sellers et al.’s press release. Top left: bear skeleton from the Oxford University Natural History Museum, presumably Ursus maritimus: original skeleton, derived point cloud and convex hulls (also used as Sellers et al. 2012:fig. 1). Top right: shedloads of awesome. Bottom: complex hulls around body segments of Giraffatitan.

References

Sellers, W. I., J. Hepworth-Bell, P. L. Falkingham, K. T. Bates, C. A. Brassey, V. M. Egerton and P. L. Manning. 2012. Minimum convex hull mass estimations of complete mounted skeletons. Biology Letters, online ahead of print. doi:10.1098/rsbl.2012.0263

Taylor, Michael P. 2009a. A re-evaluation of Brachiosaurus altithorax Riggs 1903 (Dinosauria, Sauropoda) and its generic separation from Giraffatitan brancai (Janensch 1914). Journal of Vertebrate Paleontology 29(3):787-806.

I only became aware of the term Academic Spring the other day but I instantly loved it. The OA wars have heated up significantly in the past few weeks, and Academic Spring crystallizes a lot of what is going on.

Although we always welcome new readers, and no-one who cares about science can afford to be ignorant about access to scholarly publications, we do sometimes feel that at SV-POW! we are mostly preaching to the converted. But access is not just a problem for scientists and academics, it’s a problem for everyone, including physicians, patient groups, engineers, small business owners, students, and, frankly, anydamnbody who wants to inspect the fruits of the research their taxes paid for. So it’s important to get the message out, broadly, to the most people possible, in as many venues as possible, until Joe and Jane Citizen get mad enough about the situation to demand better behavior by their elected representatives and better service from the corporations that allegedly have their interests at heart.

To that end, Mike has a new piece up at The Independent today. Because he couldn’t assume that his readers would be familiar with the OA wars or Academic Spring, he had to lay out the whole case in a limited number of words. I think he did a bang-up job. Because the piece is so self-contained (although it has some choice links that are worth following up), it serves as a front-line report for those of us familiar with the OA wars, and a solid overview for everyone else. Go check it out.

Finally, since you haven’t gotten a lot of sauropod action lately, here are some small Giraffatitan humeri in the basement of the  Museum für Naturkunde with Vanessa Graff for scale. You can tell these are small ones because they’re Vanessa-sized or smaller; the big ones are taller than I am…and they’re still from subadults. Must blog sometime about the awesomeness of the basement full o’ sauropods at the MfN, but not today. Excelsior!

I’m very aware that I’ve been whining incessantly on this blog recently: RWA this, Elsevier that, moan whine complain.  So I’m delighted to be able to bring some good news.  Mike Keesey’s site PhyloPic.org is back up, in new and improved form, and providing free silhouettes of organisms extincts and extant.  To quote the site’s FAQ:

PhyloPic‘s database stores reusable silhouette images of organisms. Each image is associated with one or more taxonomic names and indicates roughly what the ancestral member(s) of each taxon looked like.

PhyloPic also stores a phylogenetic taxonomy of all organisms. This means that you can perform phylogenetic searches. For example, if you need an image for a certain taxon, but there is no exact match in the database, you can easily search that taxon’s supertaxa, subtaxa, and related taxa for an image that may work as well.

For example, there is a page about Giraffatitan brancai, which includes a link to a silhouette by Scott Hartman; and a page about Brachiosaurus altithorax, which has two silhouettes — one by Scott and one by me.

More interestingly, for each taxon, you can ask for an illustrated lineage.  For example, the illustrated lineage of Giraffatitan brancai starts with that animal, then works its way up via images for Brachiosauridae, Titanosauriformes, Camarasauromorpha, and continues up through a total of 36 images, finishing up with Holozoa, Cytota and Panbiota.

Better still, because all the images are available to re-use (subject to some restrictions which I’ll discuss below), you’re free to use them to make collages like this one, which Mike Keesey did for our friend Giraffatitan brancai:

One of the great things about this site is that it’s a community effort: Mike built the site and has prepared a good chunk of the artwork so far, but PhyloPic is open to submissions from anyone who cares to register (or to login via Google, Twitter, etc.)

Mike has allowed some latitude in the licences that can be used when images are added.  You can currently choose from any of:

  • Public Domain Mark 1.0 [for declaring that an image is already PD]
  • Public Domain Dedication 1.0 [for putting an image into the PD]
  • Creative Commons Attribution 3.0 Unported
  • Creative Commons Attribution-Noncommercial 3.0 Unported
  • Creative Commons Attribution-ShareAlike 3.0 Unported
  • Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported

That choice is nice for contributing artists, but makes life a bit more awkward for users because any composite artwork has to be licenced under the most restrictive combination of the licences of its parts.  In the case of the collage above, because Scott’s Giraffatitan brancai was uploaded as CC-BY-NC-SA, that’s how the whole image ends up, too.  This means that if, say, you want to make T-shirts on Cafe Press with this image on them, you’ll have a bit of nightmare figuring out exactly who you need to get permission from.

Mike has to walk a fine line with this.  The images would be most useful to the world if they were all public domain and could be remixed, reused and reproduced with no restrictions whatsoever; but you can’t blame artists for wanting to put some limits on this.  Yet even when the most permissive non-public domain licence is used (CC-BY), the light requirement that the image must be credited ends up as a heavy requirement when, as with the collage above, you use thirty images that all need to be acknowledged.

Anyway, these are wrinkles.  The point is: free, re-usable art!  Go and use it; and add to it!

Best. Exhibit. Ever.

December 13, 2011

Wedel lab group photo, December 12, 2011. Vanessa Graff and Mathew Wedel, with Diplodocus carnegii, Giraffatitan brancai, Dicraeosaurus hansemanni and assorted stinkin’ theropods and ornithischians for scale.

Hello again, old friend

December 5, 2011

This week the SV-POW!sketeers are off to Bonn, Germany, for the Second International Workshop on Sauropod Biology and Gigantism. All three of us will be there, plus SV-POW! guest blogger Heinrich Mallison, plus Wedel Lab grad student Vanessa Graff, plus about 50 other awesome scientists from around the world. So we’ll have a ton of fun, but we probably won’t get much posted.

In the meantime, enjoy this cool encounter from the bone cellar at the Humboldt Museum in Berlin, where Mike and I fetched up at the end of the last IWSBG back in 2008. It’s a transversely-sectioned dorsal centrum of Giraffatitan, one that Janensch illustrated in his 1950 monograph on the vertebrae of Giraffatitan. Mike and I were very familiar with the cross-section image from the paper, so it was cool and a bit unreal to find the actual item.

Reference

Janensch, Werner. 1950. Die Wirbelsaule von Brachiosaurus brancai. Palaeontographica (Suppl. 7) 3:27-93.

Preparing a talk is a time-consuming process, and there’s no question that getting the slides ready is where the bulk of that time goes.  But unless you understand exactly what it is that you’re going to talk about, even the best slides won’t rescue your talk from mediocrity, so before you fire up PowerPoint, go and read part 1 of this tutorial, on finding the narrative.  Seriously.  The slides are how you convey your message, and they’re important.  But not as important as what your message is.

Assuming you know what story you’re trying to tell, here is the overriding principle of slide design: make yourself understood.  Remember again that you have something less than twenty minutes in which to make your rich, complex research project understood to a hall full of strangers who have just sat through five or ten or fifteen other presentations.  They will be mentally tired.  Help them out.  Make every slide tell a clear story.

The slides for a conference talk are science, not art.  That doesn’t mean they have to be ugly — of course it doesn’t.  But it does mean that whenever you find yourself facing a choice between clarity and beauty, go with clarity.

That means you do not want your slides to look like this:

OK, that is not even beautiful.  But it does illustrate some horrible mistakes, and we’ll touch on all of them  in what follows.  For now, just remember that the purpose of a Results slide is to help the audience know what your results were.

So how do you make yourself understood?

1. Use the full size of the screen

Most importantly, don’t “frame” your content.  You have a specific amount of space in which to present your work.  Don’t throw any of it away.  Although the super-bad slide above may look extreme, I have seen plenty to slides that present, say, specimen photos in about the same amount of space as the graph above occupies.  So, then:

  • No picturesque borders.
  • We don’t need the talk title, or your name or address on every slide.  You can tell us once at the start of the talk and then, if you like, once more at the end.  If we truly forget who you are in the middle, we can always look at the programme.  If we forget what you’re talking about, then your talk has more profound problems.
  • That goes double for logos.  We do not need to see the following more than once (or indeed once):
    • Your institution’s crest
    • The conference logo
    • Logos of funding bodies

We don’t need any of that stuff, and all of it wastes precious real-estate.  Space that you could be using to tell your story.

Most important of all: use as much space as you can for your images.  Specimen photographs, interpretive drawings, reproduced figures from the literature, graphs, cladograms, strat sections — whatever you’re showing us, let us see it.

In my own talks, I like to make the picture fill the whole slide.  You can usually find a light area to put a dark text on, or vice versa.  I often find it’s useful to give the text a drop-shadow, so that it stands out against both light and dark background.  (You can find that option in Format -> Character… -> Font Effects if you use OpenOffice, and no doubt somewhere similar in PowerPoint.)

If the aspect ratio of an image that I want to use is not the 4:3 that projectors give you, then I will often crop it down to that aspect ratio, if some of the edges of the image are dispensable, so that the cropped version is properly shaped to fill the screen.

(On image resolution: most projectors seem to be 1024 x 768, maybe some these days are 1280 x 960.  There’s no point using images at a higher resolution than that: your audience won’t see the additional information.)

2. Legibility

Hopefully you won’t need too many words on your slides, since you’ll be talking to us about what we can see.  But what words you use, we need to see.  Specifically, this means:

  • Use big fonts.  There is absolutely no point in showing us an eighty-taxon phylogenetic tree: we just won’t be able to read the taxon names.  I tend to make my fonts really big — 32-point and up, which actually is probably bigger than you really need.  But you don’t want to be smaller than 20-point at the absolute minimum.
  • Use high contrast between the text and background.  That usually means black on white, or (if you must) white on black.  Well, OK — it doesn’t literally have to be black, but it needs to be a very dark colour (I often use very dark blue).  And it doesn’t literally have to be white, but it needs to be a very light colour.  (I occasionally use a very pale yellow “parchment”-type colour, but less often.)  Do not use grey text or a grey background.  Especially do not use grey text on a grey background, even if they are fairly different greys and the muted effect looks classy.  You’re not shooting for “classy”, you’re shooting for “legible”.  Because you remember the prime directive that you’re trying to make yourself understood.
  • If for some reason you must use a non-black, non-white text or background, don’t make it a highly saturated colour.  Some combinations, such as a red on blue, and virtually impossible to read.
  • No vertical writing (with the possible exception of short y-axis labels on graphs).  If your cladogram’s taxon names are vertical, turn your cladogram around.  Redraw it if necessary.  If the audience have their heads on one site, you’re doing it wrong.

3. Font Choice

Apart from size, what else matters about fonts?

  • Avoid elaborate fonts, such as the URW Chancery L Medium Italic that I used for my name and affiliation in the Bad Slide at the top.  They’re hard to read, and at best they draw attention away from the message to the medium.
  • Pick a single font and stick with it for consistency.  Or if you wish, one serifed font (for body text) and one sans-serif (for headings).  But you should have little enough text on your slides that it’s practically all headings.
  • Stick to standard fonts which you know will be on the computer that will be displaying your presentation.  In practice, the safest approach is it stick to Microsoft’s “core fonts for the web” — which is plenty enough choice.
  • You might want to avoid Ariel, which is widely considered particularly ugly.  Other ubiquitous sans-serif fonts include Trebuchet and Verdana, which are both rather nicer than Ariel (though Verdana’s glyphs are too widely spaced to my eye).
  • Do not use MS Comic Sans Serif, or no-one will take anything you say seriously.  I don’t just mean your talk, I mean ever, for the rest of your life.

Why is it important to stick to standard fonts?  Because of size, spacing and positioning.  Your computer may have the super-beautiful Font Of Awesomeness and it might make your slides looks beautiful; but when you run your PowerPoint file on the conference computer, it won’t have Font Of Awesomeness, so it will substitute whatever it thinks is closest — Arial or Times or something.  Not only will you not get the visual effect you wanted, but the glyphs will be different sizes, so that your text will run off the edge of the page, or fall right off the bottom.

(Handy household hint for users of Debian GNU/Linux and variants such as Ubuntu.  Make sure that you have the MS core fonts installed on your computer, so that OpenOffice can properly display your slides as you’re designing them, rather than substituting.  sudo apt-get install ttf-mscorefonts-installer, restart OpenOffice, and you’re good to go.)

4. How many slides?

I need to mention this issue, if only to say that there’s no right answer.  I don’t say that lightly: for most slide-design issues, there is a right answer.  (Example: should you use MS Comic Sans Serif?  Answer: no.)  But number of slides has to vary between people to fit in with presentation styles.

I tend to use a large number of slides and whiz through them very quickly — my SVPCA 2011 talk had 80 slides, and in 2010 I had 92 slides.  Lots of them are parenthetical, sometimes just a silly joke to make in passing a point that I am already making.  If you miss such a slide, it doesn’t really matter: it’s just light relief and reinforcement, not an integral part of the narrative.

.

But that many-slides-slipping-quickly-past style doesn’t suit everybody. In the eighteen minutes or so that you get to give a talk (allowing a minute for messing about getting set up and a minute for questions), getting through 80 slides in those 1080 seconds gives you an average of 13.5 seconds per slide.

Lots of people prefer to use fewer slides and talk about them for longer. You can give an excellent talk with very few slides if that approach comes naturally to you: step slowly through nine slides, talk about each one for two minutes.

Once you’ve given a few talks you’ll know which approach works best for you, and you can design accordingly. For your first talk, you’re probably best off aiming initially somewhere in the middle — thirty or so slides — and then seeing what happens when you dry-run the talk. (We’ll discuss that next time around.)

5. Miscellaneous

I’ve touched on this one already, but it’s best to use as little text as possible. That’s because you want your audience listening to your story, not reading your slides. I used to put a lot of text in my slides, because I wanted the PowerPoint file to stand alone as a sort of a record of the talk. But I don’t do that now, because a talk involves talking (clue’s in the question). I include enough text to remind myself what I want to say about each slide (sometimes just one or two words; often none at all). And I try to make sure there’s enough to let the audience know what they’re looking at if I zoom straight past it. For example:

.

I used this slide to briefly tell a typical taphonomic story of a sauropod neck.  But I didn’t need to say that I was using diagrams of the neck of Sauroposeidon taken from Wedel et al. 2000, so I just shoved that information on the slide for anyone who was interested.  That way I didn’t have to break the flow of my narrative to impart this information.

Use a consistent colour palette.  If you’ve used dark blue text on white for half of your slides, don’t switch to black on pale yellow for the other half.  It’s not a hugely important point, but it all contributes to helping the talk go down smoothly.  You’re getting rid of mental speed-bumps that could stop your audience from giving their full attention to the story you’re telling.

Where possible, avoid putting important information at the bottom — in, say, the lower 10-15% of the slide.  That’s because the lower part of the screen can sometimes be obscured by the heads of the people in the front rows.

Avoid hatching, which can look terrible on a screen, in a way that’s very hard to predict.  In the Sauroposeidon taphonomy slide above, for example, the lost bones are “greyed out” using a flat grey colour rather the close diagonal lines of the original.  I knew it would look right on the screen.

Skip the fancy slide transitions, animated flying arrows, and suchlike. It’s just distracting nonsense that no one in the audience (or anywhere else, for that matter) needs to be exposed to. It’s just gross. Also, as with fonts, you may end up giving your talk from a machine with an older version of PowerPoint that doesn’t support the turning of animated pages and the bouncing arrival of arrows and clipart, and then your presentation will either look stupid or fail to run entirely.

You might want to draw highlighting marks on your slides, e.g. circles around the relevant parts of a specimen photos.  That will save you having to mess about with the laser pointer later.  (I will have much to say about the laser pointer in part 4).  I like to show two consecutive slides: one of the unadorned photo, then one that’s identical apart from the addition of the highlight, like this:

Then as I am talking about the first slide, “in order to mount the vertebrae in something approaching a straight line, they had to leave a huge gap between consecutive centra”, I’ll step on to the next one, which highlights what I’m saying.  Slick, no?  (This is part of why I end up with such high slide counts.)

A pet hate: don’t write “monophyletic clade”.  If it’s a clade, it’s monophyletic by definition.  “Monophyletic clade” is like “round circle”, “square square” or “boring ornithopod”.

And finally …

Show us specimens.  We are vertebrate palaeontologists, and we love vertebrate fossils.  No-one goes into the field because of a deep and abiding passion for graphs or for tables of numbers.  We understand that from time to time you’ll need to show us those things in order to tell the story, but nothing makes an audience happier than big, clean photos of beautiful specimens.

Well, that’s it — how to make good slides.  Next time we’ll look at rehearsing the talk.  (It’ll be a much shorter post than this one.)

Last month, over at Love in the Time of Chasmosaurs, David Orr wrote about the dinosaur conflicts he’d like to see, in place of the ubiquitous T. rex-vs.-Triceratops.  Among the fights he wanted to see was:

2. Four strategically placed Incisivosaurus vs. Giraffatitan: Two words: beaver style.

I commented on that article, saying:

I hate to spoil your fun, but a single Giraffatitan individual could effortlessly destroy countless Incisivosaurus by sheer awesomeness alone.

To which David replied, saying:

Though when I think about it, Giraffatitan just being awesome while wave after wave of Incisivosaurus perish in its glorious presence is a totally acceptable outcome.

So true.

Now comes a follow-up post, in which professional illustrator Niroot Puttapipat has beautifully drawn both scenarios (and a bunch of other, less awesome, suggestions).  So without futher ado, here is his interpretation of the first scenario:

And the much more credible second scenario:

Update (two days later)

The originals of the first picture and the second picture are both at DeviantArt, in higher resolution and with (very positive) comments.  Thanks to Niroot for the links.

Also at DeviantArt: patriatyrannus’s version of the first scenario, which I’d not seen before:

 

Every now and then, you come across a sauropod skull so beautiful, it’s almost enough to distract you from the vertebrae that it was attached to.  One such is the Giraffatitan brancai skull HMN T1, which you’ve seen here before if you’ve been around for a while.

(I am not kissing the real thing, but a slightly scaled 3d print of a scan made from the original.)

This is one of the many photos from the Berlin visit that was part of the German sauropod working group‘s 2008 conference.  That conference, the first they held that was open to people outside of their group, was the best one I have ever been to.  This year, they are holding a second conference, and Matt and I plan to be there again.  It’ll be in early December; no doubt we’ll report back when we return.

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