Monthly Archives: June 2009

Sauropods were corn-on-the-cob, not shish kebabs

This is corn on the cob:

Corn on the cob, in cross section, stolen from http://www.istockphoto.com/file_thumbview_approve/214165/2/istockphoto_214165-co rn-cob-cross-section.jpg

Corn on the cob, in cross section. Stolen from http://www.istockphoto.com/file_thumbview_approve/214165/2/istockphoto_214165-co rn-cob-cross-section.jpg

This is a shish kebab:

Most tetrapods are like shish kebabs: a whole lot of meat stuck on a proportionally tiny skeleton.  If you don’t believe me, you can look at the human and cow neck torso cross-sections in Matt’s last post, or check out this ostrich-neck cross-section from his 2003 Paleobiology paper:

Ostrich neck in cross section, CT scan. From Wedel (2003a: fig. 2)

Ostrich neck in cross section, CT scan. From Wedel (2003a: fig. 2)

Remember that this is a freakin’ ostrich — of all extant animals, one of the ones with a most extreme long, skinny neck.  And yet, if sauropods were muscled like ostriches, then their necks would have looked like this in cross section:

Putative shish kebab-style sauropod neck in cross section. Ostrich soft-tissue from Wedel (2003a: fig. 2), Diplodocus vertebra cross-section from Paul (1997: fig. 4) scaled to match size of ostrich vertebra

Putative shish kebab-style sauropod neck in cross section. Ostrich soft-tissue from Wedel (2003a: fig. 2), Diplodocus vertebra cross-section from Paul (1997: fig. 4) scaled to match size of ostrich vertebra

And soft-tissue reconstructions would have to look like this:

Diplodocus with its neck as fat as an ostrich's. Modified from Paul (1998: fig. 1F)

Diplodocus with its neck as fat as an ostrich's. Modified from Paul (1998: fig. 1F)

Which, happily, no-one is suggesting.  Instead, published reconstructions of sauropod neck soft-tissue are startlingly emaciated.  As exhibit A, I call this pair of Greg Paul cross-sections:

Diplodocus and Brachiosaurus neck cross-sections, showing very light musculature. From Paul (1997: fig. 4)

Diplodocus and Brachiosaurus neck cross-sections, showing very light musculature. From Paul (1997: fig. 4)

(Yes, the Diplodocus on the left is the one I used in the photoshopped ostrich cross-section above.  It’s instructive to compare Paul’s original with the What If It Was Like A Big Ostrich version.)

Paul’s reconstructions seem to be widely considered too lightly muscled.  But even the very careful and rigorous more recent reconstructions of Daniela Schwarz and her colleague show a neck much, much thinner than that of the ostrich:

Diplodocus neck cross-sections. From Schwarz et al. (2007: fig. 7a)

Diplodocus neck cross-sections. From Schwarz et al. (2007: fig. 7a)

Although Schwarz has put a lot more soft tissue onto the neck vertebrae than Paul did, it is still a tiny proportion of what we see in extant animals — even the ostrich, remember, which has a super-thin neck compared with pretty much anything else alive today.  If sauropod necks were muscled as heavily as those of, say, cows, then the soft tissue would pretty much reach down to the ground.  But they weren’t: they were more like corn on the cob, with a broad core of skeleton and relatively little in the way of delicious edibles festooned about it.

So why is this?  Why does everyone agree that sauropod necks were much less heavily muscled than those of any extant animal?

It’s a simple matter of scaling.  A really big ostrich might have a neck 1 m long.  (Actually, ostriches don’t get that big, but let’s pretend they do because it makes the maths easier).  If the x meter-long neck of a sauropod was just a scaled-up ostrich neck, then it would be x times longer, x times taller and x times wider, for a total of x^3 times as voluminous and therefore x^3 times as heavy.  But the cross-sectional area of the tension members that support it is only x times taller and x times wider, for a total of x^2 times the strength.  In total, then, the neck’s mass/strength is x^3/x^2 = x times as great as in the ostrich.  (The sauropod neck’s mass also acts further out from the fulcrum by an additional factor of x, but that is cancelled by the fact that the tension in the neck also acts x times higher above the fulcrum.)

It seems intuitively obvious (which is is code for “I have no way to prove”) that you can’t reasonably expect the neck muscles of a giant ostrich to work ten times as hard as they do in their lesser cousins, which is what you’d need to do for the 10 m neck of, say, Sauroposeidon.  So simple isometric scaling won’t get the job done, and you need to restructure the neck.

But how?  Surely just reducing all the muscle around the vertebrae can’t help?  No indeed — but that is not really what sauropods were doing.  If you look at the typical sauropod-neck life restoration, you’ll see that the proportional thickness of the neck is actually not too dissimilar to that of an ostrich — rather thicker, in fact.  If you scaled an ostrich neck up to sauropod size and compared it with a real sauropod neck, you would find not that the soft tissue was too fat, but that the vertebrae were too thin.

And so we come to it at last: rather than thinking of sauropods as having reduced the amount of soft-tissue hanging on the cervical vertebrae, we do better to think of them as having kept a roughly similar soft-tissue profile to that of an an ostrich, but enlarging the vertebrae within the soft-tissue envelope.  Of course if you just blindly made the vertebrae taller and wider, they would become heavier in proportion, which would defeat the whole purpose of the exercise — but as everyone who reads this blog surely knows by now, sauropod cervicals were extensively lightened by pneumaticity.  By bringing air into the center of the neck, they were effectively able to displace bone, muscle and ligament away from the centre, so that they acted with greater mechanical advantage: higher epaxial tension members, lower hypaxial compression members, and more laterally positioned paraxials.

It’s a rather brilliant system — using the same volume of bone to achieve greater strength by displacing it outwards and filling the center with air (and, in doing so, also displacing soft tissue outwards).  And it will be hauntingly familiar to anyone who loves birds, because it is of course exactly what birds (and pterosaurus) have done in their long bones: the hollow humeri of flying vertebrates famously allow them to attain greater strength — specifically, resistance to bending — for the same volume and mass of bone.  It’s a neat trick when done with long bones, but it takes a truly awesome taxon to do it with the neck.

So maybe sauropods were not corn on the cob after all.  Maybe they were Hostess Twinkies.

Hostess Twinkie. Not truly pneumatic, as the internal cavity is filled with adipose tissue rather than air, but do you have any idea how difficult it is to find good images of hollow junk food?

Hostess Twinkie. Not truly pneumatic, as the internal cavity is filled with adipose tissue rather than air, but do you have any idea how difficult it is to find good images of hollow junk food? Stolen from http://dixiedining.files.wordpress.com/2008/07/twinkie_070918_ms1.jpg

And now for something completely different

Now that I’ve finished my Ph.D at the University of Portsmouth, what am I going to do with the rest of my scientific life?  I’ve always said that I have no intention of going into palaeo full time: my knowledge is far too narrow for that, so that even if paid jobs were not in insanely short supply, I wouldn’t stand much chance of getting one.  And in any case, I’d hate to get into the all-too-common situation of being up against a friend for a position we both wanted. Throw in the fact that I really enjoy my computer-programming day-job and it seems pretty clear that what I need is an unpaid affiliation that lets me get on with lovely research.

Well: I am absolutely delighted to announce that, as of last month, I am an Honorary Research Associate in the Department of Earth Sciences at UCL.  It’s not just that UCL is such a well-respected institution — see that Wikipedia article for some details — more importantly, it’s where Paul Upchurch hangs out, as Senior Lecturer in Palaeobiology.  Sauropod fans will be familiar with Paul’s characteristically detailed and careful work, from his pioneering work on sauropod phylogeny (Upchurch 1995, 1998), through his and John Martin’s indispensible Cetiosaurus makeovers (Upchurch and Martin 2002, 2003) to the state-of-the art review that he lead-authored for Dinosauria II (Upchurch et al. 2004) and the Tokyo Apatosaurus monograph (Upchurch et al. 2005).  What many of you won’t know is what an excellent collaborator he is — quick, conscientious, insightful and diplomatic.  We’ve already collaborated on a few short papers (Upchurch et al. 2009 and a couple of Phylocode companion-volume chapters that are in press), and I hope there will be more in the future.

References

Sauropods were tacos, not corn dogs

Taco

This is a taco.

Corndog

This is a corn dog.

Vertebra outlined in green. Click for unmarked original.

Vertebra outlined in green. Click for unmarked original.

Here’s a cross-section of a human. In the terms of fast food, people are corndogs. Most of us even have an outer ring of yellow adipose ‘breading’.

Vertebra oulined in red. Click for unmarked original.

Vertebra oulined in red. Click for unmarked original.

Here’s a cross-section of a cow. In an example of function following form, cows are, and often become, corndogs.

Note that in both the human and the cow the spaces between the neural spine and transverse processes are completely filled with back muscles, which in fact bulge out beyond the tips of the neural spine, as we also saw here. This despite the common paleoart convention of presenting dinosaurs as thin layers of skin conforming perfectly to the underlying skeleton. Just Say No to shrink-wrapped sauropods!

Diplodocus torso xs

Here is Figure 17 from Holland (1910), one of the most badass scientific smackdowns ever published, in which Holland wiped the floor with Hay, Tornier, and the idea of sprawling sauropods. On the left are torso skeletons of three lizards and a croc; on the right is an anterior dorsal with articulated ribs from Diplodocus. As you can see, it’s a taco, and its taconic form would be perfected if it could roll supine.

The point of the post is not that sauropods had deep, slab-sided bodies. We’ve covered that before. The point is that sauropod torsos are seriously weird. In mammals, the dorsal ribs arch up and out, away from the vertebra, before sweeping around to define the anterior body wall.  In lizards, the proximal part of each rib sticks out sideways. In sauropods, the ribs point down. This is mainly because the vertebrae are FREAKIN’ HUGE compared to the size of the body. Whereas in the mammals and lizards the dorsal vertebrae are titchy little things that span a small fraction of the width of the torso, in Diplodocus and other sauropods the dorsal vertebrae account for about half. (The cow cross-section missed the transverse processes, so that vert looks narrower than it actually is.)

This is relevant when we think about the function of pneumaticity. When I write that pneumaticity lightened vertebrae, I usually mean relative to that same vertebra if it wasn’t pneumatized. But we could also ask if the pneumatic vertebra is lighter than a vertebra from a similar-sized animal that lacks pneumaticity–except that, for big sauropods, there are no similar-sized terrestrial animals without pneumaticity to compare.

Imagine that in a big sauropod the dorsal vertebrae are three times as wide and three times as tall as they would be in a similar-sized mammal. They should weigh nine times more. But let’s also assume that the vertebrae of the sauropod are 85% air by volume, which is in fact pretty typical for Early Cretaceous brachiosaurids. The mass of the dorsal column relative to that of the mammal is then 9 x 0.15 = 1.35, a little heavier, but not much (I’m assuming the length of the torso is the same in the two animals). Bigger bones mean better lever arms for the muscles and lower bending stresses on the ribs, which can function more like curtains and less like cantilevered beams.

I can’t think of much published discussion of this stuff as it relates to sauropods, but it seems like it might be important.

Reference

Holland, W.J. 1910. A review of some recent criticisms of the restorations of sauropod dinosaurs existing in the museums of the United States, with special reference to that of Diplodocus carnegiei [sic] in the Carnegie Museum. American Naturalist 44:259-283.

Yet more uninformed noodling on the future of scientific publishing and that kind of thing

Sorry to keep dumping all these off-topic thoughts on you all, but I got an email from Matt today in which he suggested that there should be some system of giving people credit for particularly insightful blog comments.  (This came up for the obvious reason that SV-POW! readers tend to leave unusually brilliant comments, as well as having excellent reading taste and being remarkably good looking.)  That led me into the following sequence of thoughts, which I thought were worth blogging — not least in the hope that we can learn something from the comments.

But first, here is that photo of another fused atlas-axis complex that you ordered (seriously, what’s up with these things?):

Camarasaurus grandis YPM 1905, fused atlas and axis in right lateral view

Camarasaurus grandis YPM 1905, fused atlas and axis in right lateral view

And now, on with the uninformed noodling:

As things stand at this point, we have a hierarchy of sciency documents. At the top (which we’ll call level 1) come papers. The reputation of papers is largely determined by formal pre-publication reviews (which we will therefore classify as level 2) — and, increasingly, also by blog posts about the paper, which are also level 2. Classic peer-reviews are only ever seen by the editor and the author of the original paper; once they have been absorbed into the paper they’re critiquing, they disappear forever, which is a crying shame. But the other kind of level-2 literature, the blog post, has a life of its own: and so it gets commented on by blog-comments (level 3). Each level gives validity to the level above.

More important, documents at each level also give validity to each other. The most important case is that when one paper favourably discusses another, or refers to its authority, it gives the latter a credibility boost (which is why it’s such a sod that no-one cites any of my papers); similarly, our SV-POW! posts also get a credibility boost when they’re discussed on Tetrapod Zoology or Blog Around the Clock (and I just repaid the compliment by linking back to them).

(At present, all of this is done in a messy qualitative way, with no numbers attached, except occasionally in the case of pre-publication reviews. That’s a shame: if, for example, blog commenters allocated the posts a score out of ten, then we could use some kind of average score as a quality filter: to ameliorate rigging, I’d suggest discarding the highest and lowest 10% of awarded scores, and averaging the remainder.)

Now the problem: blog comments are right at the bottom of the pile: who is going to rate them? I’m certainly not going to spend any time on that.

OK, so suppose we ignore the arbitrary allocation of levels: papers, reviews, blog posts and comments are all just considered as documents, and all can discuss each other. (Clearly reviews will necessarily discuss papers more often the papers discuss blog comments, but that is a convention added to the system I am about to describe, not a precondition for it.) Each document has a reputation, which we will quantify as a single real number. Documents start with some arbitrary small reputation — probably 0.0 or 1.0, and it probably doesn’t much matter what it is. When any document discusses, cites or links to another — whether it’s paper, a review, a blog post or a comment — that linkee’s reputation is boosted by some proportion: 10%, say, of the linker’s reputation. Now of course this change in linkee reputation causes a trickle-down change of 1% in the reputation of the documents that it links to; and 0.1% in the reputation of the documents they link to, and so on. Reputations will change frequently and irregularly, and will be near impossible to calculate accurately, but that’s fine — they should be easy to approximate, and that’s good enough.

In this way, we get a nice solid score that we can use to decide what’s worth reading and what isn’t — the cream will naturally rise to the top. Hiring committees can throw away impact factors, and instead just add up the reputation scores of their candidates’ publications (either in the strict sense of the word, or including blog posts, reviews and/or comments). By the way, one of the positive effects of this would be that people like Darren and Jerry Harris would get some reward from their sterling reviewing efforts.

Sounds awesome? Here’s something even more awesome: we already have that system, more or less. Yes indeed: the reputation propagation algorithm I described is, in general outline, the same thing that Google does in the algorithm that it calls PageRank(tm)(r)(lol)(ymmv).  We can — and already do — use Google’s notion of reputation as a guide to finding what’s worth reading, and we can tell that in works well in practice because SV-POW! posts rank so highly :-)

So that’s it! We can all stop worrying, just Google for stuff we’re interested in, and read whatever pops up at the top of the list!

Are you convinced? I hope not, because this idea has at least three huge problems.

1. What counts? (Yes, that again.) Google-ranking works well for blog posts, because they are web pages, and Google can spider web pages. But that leaves out reviews, because they are typically not published at all, let alone as web pages. And it leaves out comments, because they are appended to the end of blog posts rather than being pages in own right, with their own PageRank. And, worst of all, it pretty much leaves out the papers themselves — because there is, in general, no one single web-page which is The Place a particular paper lives. For non-open papers that aren’t hosted on the author’s page or elsewhere, there is no page.  In short, reviews are not published, comments are not whole pages and papers are not single pages, so none of them is properly page-rankable.

2. All links count as positive reputation — there are no negative citations. So a document that says “Taylor, Wedel and Naish 2009 was talking a lot of nonsense about sauropod neck posture” would still be a score in our favour, even though it meant the exact opposite. Of course, this is not a new problem: both PageRank and Impact Factors suffer from the same problem, but it doesn’t seem to be a killer for either of them. The only fix for this would be to invite authors (of papers, reviews, blogs and comments) to explicitly score some or all of the other documents they mention — and I doubt people are going to be keen to do that unless the mechanism can be made very non-intrusive.

3. And here’s the killer: we wouldn’t, or shouldn’t, want Google to do this, even if they could overcome problems #1 and #2.  Google is a private corporation, and we don’t want to hand over reputation management to any private commercial venture with an obligation to shareholders rather than scientists, and with a proprietary secret algorithm. If you doubt me, consider Thompson’s ownership of the Impact Factor and see where that’s got us. No doubt when Eugene Garfield came up with the idea of the Impact Factor, he was pretty excited about how — at last! — we would have an objective, reliable way to evaluate science. But IF is not run by scientists, it’s run by a corporation.  With hilarious results.

I have no idea what the conclusion to all this is. I didn’t have a clear idea where it was headed when I started writing it. But, much in the manner of Dirk Gently when employing his usual method of navigation, I may not have ended up where I intended to, but I’ve arrived somewhere interesting.

Your move: what have I failed to take into account?

Blogs, papers, etc.: some more random thoughts, from Mike this time

I have a much less realised view of the digital future than Matt does, so I won’t be making a lot of predictions here.  But I do have some questions to ask, and — predictably — some whining to do.

What counts, what doesn’t, and why?

Assuming you have made some science (e.g. a description of fossil, a palaeobiological hypothesis supported by evidence, a taxonomic revision), there are plenty of different ways you can present it to the world.  I may have missed some, but here are the ones I’ve thought of, in roughly descending order of respectability/citability/prestige:

  • Peer-reviewed paper/book chapter
  • Unreviewed paper/book chapter
  • Peer-reviewed electronic-only paper
  • Published abstract (e.g. for SVP)
  • Conference talk
  • Conference poster
  • Dissertation
  • Online supplementary information
  • Blog post
  • Blog comment
  • Email to the DML (which is archived on the web)
  • Personal email
  • Chat over a beer

How many of these are Science?  Where is the line?  Is the line hard or fuzzy?  Why is it OK to cite SVP abstracts but not so much SVPCA abstracts?  And other such questions. I think a very good case can be made that dissertations — provided they are made available — are better sources than conference talks, posters and abstracts; and a pretty good case can be made that blog posts are (especially when webcitation’ed — see below).  Both dissertations and (good) blog posts have the advantage over talks and posters that they have a permanent existence, and over abstracts the simple fact that they are substantial: a 200-word abtract cannot, by its very nature, say anything much.

Zoological nomenclature

Unfortunately, for nomenclatural purposes, the ICZN’s Article 8 currently says that only publications on paper count, period, which counts out dissertations.  I say unfortunately because were it not for this rule, then at least part of Aetogate would never have happened: the ramifications of Bill Parker’s case would not have been so awful if the perfectly good description of Heliocanthus in his (2003) dissertation had been allowed priority over Lucas et al.’s (2006) rush-job which attached the name Rioarribasuchus to the same specimen. Happily, the ICZN is as we write this considering an amendment to recognise nomenclatural acts in electronic-only publications.  There has already been some published discussion of the pros and cons of this amendment, and the Commission is actively soliciting further comments, so those of you with strong feelings should put them in writing and send them to the Executive Secretary.  (I will certainly be doing so.)

Self-scooping

We all know that blog entries are Not Sufficiently Published to be citable, at least in most journals; but are they Too Published to let you re-use the same material?  When you submit to most journals, they ask you to formally state “this material has not previously been published” — is that true if we’ve blogged it?  I am guessing different editors would answer that differently. For what it’s worth, we’ve been reasonably careful up till now not to blog anything that we’re planning to make into a paper — which is why we were so mysteriously silent on the obviously important topic of sauropod neck posture during the first 19 months of SV-POW!.  We’ve not been 100% pure on this: for example, I have a paper on Brachiosaurus in press that mentions in passing the spinoparapophyseal laminae, absence of an infradiapophyseal laminae and perforate anterior centroparapophyseal laminae of the 8th dorsal vertebra of the Brachiosaurus brancai specimen HMN SII — the features that I have blogged here in detail, with illustrations that would certainly never have been given journal-space.  Since the relevant passage in my paper accounted for half a manuscript page (of a total of 75 pages), I’m assuming no-one’s bothered about that.  In a case like this, I guess the SV-POW! posts are best thought of as pre-emptive and unofficial online supplementary information.

Counts for what purpose?

We’ve already mentioned that dissertations, blog entries and suchlike don’t count for nomenclatural purposes.  Whether they count in the sense of being citable in published works is up for debate right now (and again, see below on webcitation).  It seems pretty clear that these forms of “grey publication” do count in establishing people’s reputations among their peers — dissertations are obviously important in this regard, and Darren’s ridiculously broad knowledge of tetrapods extant and extinct is near-universally recognised largely because of his blogging efforts (although you could argue — and Matt and I often have argued — that he might have been able to enhance his reputation even more if he’d taken some of that blogging time and invested it in formal publications). Conversely, it’s clear that blogs, however rigorous and scientific, count for squat when it comes to committees.  The world of dinosaur palaeontology is probably just as aware of Matt’s series of Aerosteon response articles here on SV-POW! as it would be if he’d put those together into a paper that was published in PLoS ONE; but when his tenure committee comes to count up the impact factors of the journals he’s published in, those articles will count for nothing.  One day that might change, but not while impact factors still exert their baleful influence.

Deciding what to blog and what to write up as a “proper paper”

Matt posted his response to the Aerosteon paper as a sequence of three blog entries even though he knew that what he had to say was substantial enough to make a paper.  Why throw away a potential publication that would look good on the CV?  Because he wanted to get it out there ASAP, and didn’t want to wait until all the media dust had settled.  So he fought people off when they pestered him to publish it as a paper.  He doesn’t really need to do it now, and he doesn’t really have time (especially since I keep badgering him about all the papers we’re supposed to be collaborating on).  If we were starving for publications, we could turn a lot of SV-POW! posts into LPUs — but we’re not starving.

Let me explain this by taking a digression though the economics of file-sharing and the way labels persistently — maybe deliberately — misunderstand them.  Let’s imagine for the sake of an example that a while back, I sent Matt the MP3s that make up Blue Oyster Cult’s awesome Fire Of Unknown Origin album.  Now anyone with their brain switched on can see that the net effect of this on his music-buying pattern would be positive: if he really liked Fire, there is a fair chance that he would then have gone and bought a BOC album or two, or three — just as I’ve been buying Dar Williams albums like crazy since someone slipped me MP3s of Mortal City.  The labels’ perception, however, is that instead I would have denied them a sale: that if I’d not sent the Fire of Unknown Origin MP3s, Matt would of course have bought his own legitimate copy, and so I’ve stiffed them out of $6.99 less whatever tiny slice they pass on to the artist.  The misunderstanding here is that they think — or would like to think, who knows if they really believe this themselves? — that people’s music consumption is limited by the time we have available to listen to music, and that one way or another we will obtain enough music to fulfil that need: for free if possible, but by paying for it if necessary.  But the truth is completely different: there would be zero chance of Matt’s ever buying any BOC album, since he’d never even heard of them (beyond Don’t Fear The Reaper, I guess) whereas in the hypothetical universe where I sent him the Fire MP3s, there is a non-zero chance.  And the labels’ failure to understand that is because of a wholly incorrect model of what factor limits music listening.

Digression ends.  Its relevance is this: in the same way, we are used to thinking that our ability to get papers published is limited by the number of publication-worthy ideas we have — so that every paper idea we “waste” on a blog entry is a net loss.  In truth, ideas are cheap, and our ability to get papers published is actually limited by our throughput — our ability to find time to actually write those ideas up with sufficient rigour, prepare high-resolution figures, format the manuscripts for journals, wait through the review period, deal with the reviews, revise, resubmit, handle editorial requests, and so on and on.  (That is especially true when the journal takes six months to come up with a rejection.) This is why Matt and I, like everyone else I know in palaeo who I’ve discussed this with, have huge stacks of POOP that we’ve not yet found time to convert into papers.  So when we spend a paper-worthy idea on a blog entry, we’re not wasting it: we’re putting it out there (in an admittedly inferior format) when otherwise it would never have made it out there at all. The remaining issue is whether the time we spend on blogging an idea would have been better spent on moving a paper further towards publication.  Maybe, sometimes.  But you have to stop and smell the roses every now and again.  So the real cost of SV-POW! for us is not the “waste” of paperable ideas, but the time we spend on writing it.  I am guessing that in the time I’ve put into SV-POW! so far, I could have got two more papers out — certainly one.  Has it been worth it?  I think so, but it’s not a no-brainer.  On the other hand, SV-POW! probably acts as a reader-funnel, so that when I do get a paper out, more people read it than otherwise would.  How big that effect is, I don’t know, and I can’t think of a way to measure it.

How to cite blog entries: WebCite

One of the great things about writing for SV-POW! is that you can learn some really useful stuff from the comments; and the most useful comment I’ve seen so far is the one in which Cameron Neylon pointed us at WebCite (http://webcitation.org/).  This is a superbly straightforward site that makes permanent archive copies of web-pages, and mirrors them around the world.  In doing so, it deals with the problems of web pages being vulnerable to disappearance and prone to change.  (In off-list emails with Matt, I had suggested that I might build something like this myself, as I am software engineer in my day job; I am delighted that these guys have done it properly instead.) So if you ever want to cite Matt’s second Aerosteon post in a journal, use the archive URL http://webcitation.org/5hPYTmWpW — and if you want to cite any other SV-POW! article, just submit its URL to WebCite yourself, and get back an archive URL which you can use. And tell all your friends about WebCite!

Oh, and by the way …

Here’s that photo of a monitor lizard getting its arse kicked by an elephant that you ordered:

Monitor lizard postcranium, aerial. Photograph by Hira Punjabi, downloaded from National Geographic.

Monitor lizard postcranium, aerial, strongly inclined. Photograph by Hira Punjabi, downloaded from National Geographic

References

  • Lucas, S. G., Hunt, A. P. and Spielmann, J. A. 2006. Rioarribasuchus, a new name for an aetosaur from the Upper Triassic of north-central New Mexico. New Mexico Museum of Natural History and Science, Bulletin 37: 581-582.
  • Parker, W. G. 2003a. Description of a new specimen of Desmatosuchus haplocerus from the Late Triassic of Northern Arizona. Unpublished MS thesis. Northern Arizona University, Flagstaff. 315 pp.

Blogs, papers, and the brave new digital world: Matt’s thoughts

First off, thanks to everyone for reading, commenting on, and discussing the previous post. Seeing the diversity of opinions expressed has been interesting and gratifying for us, and we’ve learned a lot from you about how the blogosphere is changing science already. My own thoughts follow, Mike chimes in at the end, and Darren will probably have something to add soon, too.

The Intolerable Problem

Sometimes people push back on posts of mine they don’t like by telling me I’m out of bounds. Somehow, they say, I’ve crossed the boundary of what I’m allowed to write about. They are angry that I’m now writing about something outside my defined area.

I’m usually taken aback by this, because I didn’t realize I’d actually agreed to any boundaries.

Seth Godin, 2009, “Out of Bounds”

Several commenters have brought up what I call the Intolerable Problem, which is that people online can critique papers and present new evidence and arguments in a format that is impermanent and not peer-reviewed. It’s intolerable because on one hand such material is not currently (operative word) citable in most outlets, and on the other hand repeating it sans citation in peer-reviewed literature smacks of plagiarism (to some, but not to all). Although this material is potentially valuable it “doesn’t count” professionally (see exceptions below), which some professionals (not necessarily those who have commented here) regard as a fatal argument against posting it in the first place. But–and this is crucial–it’s only a problem for the tiny fraction of the audience who might want to cite the freely exchanged material. If you’re in that fraction, we value your attention and comments, but don’t assume we’re writing only for you, or to further our professional standing. We blog because we love this stuff, and even at a technical niche blog like SV-POW! the majority of readers probably don’t care at all whether the information is peer-reviewed or “counts” for professionals; they mostly care whether it’s right or not.

One obvious solution to the Intolerable Problem is to simply let people cite anything they want, including blog posts and DML posts. This is already starting to be implemented–see examples here and here and more discussion here. This runs into two problems: one is permanence (there is no guarantee that the cited post will be up forever, or that the author won’t revise it later in response to criticism [as I have done with this very post!]), which can already be solved using tools such as WebCite (thanks to Cameron Neylon for bringing this to our attention in a comment on the previous post).

The other problem is that citations serve two functions, which are to establish priority and to lend authority to an argument. Citing a blog post may establish priority, but some researchers will cavil at the idea that a blog post is an authoritative source (for varying combinations of researchers and blog posts). Whether they would be right to cavil I don’t know; in the end the market will decide. The market–that is, the desire to attain professional respect and avoid censure–will also dissuade authors from larding up their papers with citations to trivial or worthless online sources.

Those who are troubled by the free discussion of papers, evidence, and hypotheses online need to realize that:

  • it’s been going on for a long time (15 years for the Dinosaur Mailing List);
  • it’s only going to accelerate in the future;
  • it’s not a problem for the vast majority of people participating in the discussions;
  • any solution must involve accommodation to the reality of how people exchange information online (immediately, freely, globally, without prior filtering).

These discussions are not going to stop, and ignoring the output of such discussions (because they “don’t count”) will eventually become prohibitively expensive as those workers who insist on playing only by the old rules are outmaneuvered by others who find ways to use all available information regardless of its provenience or “respectability”.

Paper journals will die when online journals stop sucking

Most online publications are hampered by having to be identical to the dead-tree versions (no links, no embedded video, no rotating 3D PDF images, etc.). Eventually people will realize that it is counterproductive to keep hobbling the new medium to make it as slow, flat, and inefficient as the old medium. Once one journal takes the hobbles off, others will do the same rather than lose contributors to cutting-edge outlets. A few boutique journals may still produce flattened, gutted versions of the online publications on paper. People still fly biplanes, too. Paper-based journals will never be popular again and their existence will not stop people from doing whatever technology allows them to in the online venues.

Note that this does not even refer to the economic argument against dead-tree publishing, which has already relocated encyclopedias and newspapers from ubiquity to marginality or extinction.

I’m surprised that the revolution isn’t farther along already. The cage is open.

Whither peer review and editing?

This is all part of the Big Flip in publishing generally, where the old notion of “filter, then publish” is giving way to “publish, then filter.” There is no need for Slashdot’s or Kuro5hin’s owners to sort the good posts from the bad in advance, no need for Blogdex or Daypop to pressure people not to post drivel, because lightweight filters applied after the fact work better at large scale than paying editors to enforce minimum quality in advance.

Clay Shirky, 2003, “The Music Business and the Big Flip”

PLoS ONE is already going gangbusters, without peer-review prior to publication in many cases. The only holdup there is that the post-hoc review by commenters is not working out quite like they’d hoped, because few people are commenting. Not everyone agrees that there is a dearth of commenting at PLoS ONE; the larger point is that people publish there a lot and the community treats those pubs like they count, even though in many cases they are essentially un-reviewed.

[Update: I misunderstood peer review at PLoS ONE. Papers may be reviewed externally by people unconnected to PLoS, or by one or more unpaid Academic Editors, or by a combination. I had thought of the review by Academic Editors only, which accounts for 13% of papers, as a form of internal review, but according to Bora (down in the comments) it should count as external review. If you’re happy with that–and the system is not without its critics–then all papers at PLoS ONE are externally reviewed prior to publication; even if you’re not, pre-publication review by someone is still in place across the board at PLoS ONE, and 87% of papers are externally reviewed by people unaffiliated with PLoS. Post-publication commenting supplements rather than replaces pre-publication review.]

People do comment on blogs, all the time. Post-hoc review will work, in fact already does work, just fine on blogs. I predict that PLoS ONE clones of the future (PLoS TWO?) will emulate whatever features of blogs make people willing to comment on them but not on PLoS ONE v1.0.

Alternatively, the paucity of post-hoc commenting at PLoS ONE could be taken as further evidence that journal-mediated peer review, whether before or after publication, is dying just off to a slow start. I think that editorial control is not far behind. Both are locally extinct in some parts of the science publishing ecosystem, since people are already citing blogs.

Q: But–but–but? What about protecting the sanctity of the process? What about about guaranteeing respectability? What about prestige?

A: Hey, those questions would make a terrific opinion piece for your local newspaper–oops, too late.

I don’t deny that editors and peer reviewers often make significant contributions to the quality of published work. I just think that people will learn to get along without them if doing so allows faster and easier exchange of information. That was never possible on paper; it’s long been possible here.

A priori peer review and editorial control were invented because publications were scarce (in the Econ 101 sense of being limited) and there needed to be a barrier to entry. Now publication is instant, free, and global. Error correction and the assignment of value will still happen, but they’ll happen after publication rather than before, and they’ll be distributed rather than centralized.

Creeping blogification

Clay Shirky described the problem for newspapers and the recording industry as the existence of “cheap perfect copies”. An expanded but by no means exhaustive list for science publication includes:

  • cheap perfect copies
  • editable (but also archivable)
  • sharable
  • linkable (both incoming and outgoing)
  • globally distributed
  • instantly
  • for free
  • without pre-publication filtering
  • with multimedia embeds (as opposed to including video etc. separately in the suppl. info.)

Online open-access journals currently take advantage of all of those capabilities except the last two. Newsgroup posts cover all the bases except the last one (so do tweets, despite the severe length limitations).

What covers everything? Blog posts. Which have the added advantage that people will comment on them without being asked.

But that’s not the whole simple story.

The center cannot hold–or can it?

So we’re looking at total chaos, right–a world where anyone posts anything they want, no one has any control, and no one knows how to find the good stuff? Well, two out of three, at least. I’m not worried about that last point, for two reasons.

First, thanks to search engines, aggregators, tags, tweets, links, etc., we already have pretty good tools for finding the good stuff. Those direction finders will get better even as the map gets more complicated.

Second, prestige will always be a motivator, so people will always compete to get into exclusive venues. Nature is not going away, although I think that in the near future they will decouple their online and print publications so that the former can take advantage of all the possibilities the web offers.

If I have a really good idea backed up with lots of data, I’ll keep trying to get it into the most prestigious outlet I can. I won’t put my best stuff on a blog just because it’s faster and less encumbered. Blogs probably won’t replace journals, at least not anytime soon. Rather, the spectrum of publishing possibilities will expand; below the category of Least Publishable Unit we’ll add Most Bloggable Unit and so on down to Least Tweetable Unit, and the new categories will interpenetrate with the old over time.

How nice for me

Well, what a striking coincidence that Mr. Paleo Blogger looks into the ole digital crystal ball and sees “bloggy with a 90% chance of exactly-what-he’s-already-doing”.

I can’t claim to be either uninterested or unbiased in all of this. But I am new to actually thinking about the implications. I hadn’t been to most of the above links or had any of these thoughts as of a week ago. When Casey first e-mailed me six days ago, I replied:

If you’re curious, here’s the short short version of my thoughts: science bloggers critique published papers and blog about unpublished observations all the time. Our post-paper run of posts might be an extreme or even vulgar example, and it might fire more discussion about “what counts?”, but I don’t see it as being different in kind from what many science bloggers do. Papers are papers and blogs are blogs, and I never intended to blur the lines. If people feel that all the blog posts only count as “crap some guys wrote on the internet” and that they can be safely ignored, that’s fine with me. If they think the blog posts deserve some higher level of recognition a la “what counts?”, then I’m honored, but that’s extra value that others are investing in our blog, and not anything that we’ve knowingly sought. I suppose you could turn around and say that I’m trying to have my cake and eat it, too, first with all the pro-paper blogging and now with this “I’m innocent” schtick. I don’t know what the answer is, but I know that I’m too tired to figure it out tonight. All the more reason to have an open conversation about this stuff.

Now I realize that the lines between papers and blog posts are blurring, and whether we mean to or not, we SV-POW!sketeers are contributing (Darren’s doing double duty thanks to Tet Zoo). I still think that the investment of blog posts with respectability, value, citability, or whatever rests entirely with readers, and always will. Options range from treating posts like papers to treating them like bar conversations to treating them like spam. You decide.

Also, I tried to keep the writing above value-neutral but probably failed. It’s hard not to get a bit evangelistic about the potential advantages of online publication and online everything else, a tendency I call DISSUADE: Da Internet Shall Save Us All Dead-trees Excepted. Getting published in science hasn’t always been easy up until now, but the process has been relatively clear and familiar. And stable, on decadal and even centennial timescales. Everything about scientific publication is about to get much more fluid and much less clear, and it will probably stay that way for a long time, and it may stay that way forever. Not all of the changes will be for the better, and it may be hard to decide what’s better and what’s worse until we look back with some perspective. Mechanical looms were bad for weavers but good for everyone else. I think many of the changes discussed in this post and the previous comment thread are likely, and some are inevitable.

Set against the shiny digital future is the inertia of the academy and those of us who roost there. I’m not going to stop publishing papers in dead-tree journals (although I will never publish in a journal that doesn’t provide PDFs to authors). Heck, I’m not even going to stop publishing in closed-access journals, some of which are run by societies I admire and want to participate in (after all, everything is open anyway). At the same time I will keep blogging, and while I will frequently bring up technical stuff I don’t want to publish more formally (at least not yet), I will try not to deliberately blur the lines any more than I already have. I don’t need to; the web is already blurring them faster than most of us can keep up.

Hang on.

Oh, about that mystery vert…

Metapophyses, I haz them

Metapophyses, I haz them

…at the end of the post Necks Lie. Nima called it–good spot on the split neural spine. It’s a mid-cervical of Barosaurus, AMNH 6341, in the big bone room (well, one of many big bone rooms) at the American Museum of  Natural History in New York. A cast of this vertebra makes up part of the neck in the awesome mounted skeleton in the museum rotunda. Here’s that skeleton, with Mike for scale.

Mike with Baro 480

Thanks for slogging through all this. We’ll get back to perforated postcentrodiapophyseal laminae, sacralized caudal transverse processes, and the air space proportions of pneumatic vertebrae soon.

Addendum

Matt is much more ready than I am to throw away peer-review, editorial control, and journals in general.  Sometimes, the reasons that things are the way they are, are good ones; it’s not in the interests of professional iconoclasts like Clay Shirky and Cory Doctorow to point that out or to discuss the strengths of how things are today, but that doesn’t mean we have to accept their arguments as uncritically as (say, to pick a name out of the air completely at random) Matt.

Anyway, happily, G. K. Chesterton foresaw the abolition of journals in favour of blogs, and commented thus:

Suppose that a great commotion arises in the street about something, let us say a lamp-post, which many influential persons desire to pull down. A grey-clad monk, who is the spirit of the Middle Ages, is approached upon the matter, and begins to say, in the arid manner of the Schoolmen, “Let us first of all consider, my brethren, the value of Light. If Light be in itself good–” At this point he is somewhat excusably knocked down. All the people make a rush for the lamp-post, the lamp-post is down in ten minutes, and they go about congratulating each other on their unmediaeval practicality. But as things go on they do not work out so easily. Some people have pulled the lamp-post down because they wanted the electric light; some because they wanted old iron; some because they wanted darkness, because their deeds were evil. Some thought it not enough of a lamp-post, some too much; some acted because they wanted to smash municipal machinery; some because they wanted to smash something. And there is war in the night, no man knowing whom he strikes. So, gradually and inevitably, to-day, to-morrow, or the next day, there comes back the conviction that the monk was right after all, and that all depends on what is the philosophy of Light. Only what we might have discussed under the gas-lamp, we now must discuss in the dark.

– Heretics (1905).