Regular readers will know that, as part of a broader strategy favouring open-access publishing, I no longer perform peer-reviews for non-open journals.  (I mentioned a recent example in a comment on the last article.)  I’ve had support for this stance from some impressive quarters; but also a fair bit of criticism from people who I respect.  That includes some strong open-access advocates who agree with me on where we want to land up, but don’t like the tactics I’m using to get there.

The most detailed of those criticisms in an article entitled Should we review for any old journal? by Andy Farke, and I think it deserves a detailed response.  Andy’s open-access credentials are impeccable — he writes about the issue in detail on his blog, and is an editor for PLoS ONE, by most metrics the leading open-access journal.  So when he has a criticism, it’s worth hearing.

Andy has several concerns.  Let’s look at them in turn.

I argue that, unless carefully constructed, such reviewing boycotts may never be noticed by some of the concerned parties. A typical journal editor will think “oh, Reviewer 1 refused to review. . .on to Reviewer 2.” Even if the refusal to review is accompanied by a note explaining the reasoning behind the refusal, only the editor will ever see it (and potentially the publishing admins – who have little vested interest in changing the status quo).

This is an excellent point.  A protest that no-one knows about is not going to be an effective protest.  From now on, whenever I turn down a non-open review, I will send a message to the editor, the publisher and the authors.  (Andy suggests this as one candidate strategy later on in his article.)

Second, when the pool of qualified reviewers is small to begin with, this could have the consequence of letting some really bad stuff slip into publication.

I’m not sure I buy this.  If a journal can’t find reviewers for an article, the only honourable thing for them to do is return it to the author and say so, not give it a free pass.  At any rate, it looks like a purely hypothetical problem to me.  If and when the day comes that a paper comes out that I was asked to review and declined, and I see that it’s bad and should have been blocked in review — on that day I will start to try assessing the damage.  At the moment, though, the apparent damage is zero.

I am not — not quite — going to say “never”.  For example, suppose someone found a more complete specimen of Xenoposeidon and submitted the description to Cretaceous Research, a non-open Elsevier journal that is actually a good match for the subject matter.  That truly is a paper that would benefit most from being reviewed by the person who has spent an order of magnitude more time looking at and thinking about NHM R2095 than anyone else on the planet.  In such a situation I might waive my policy.

But I’m hesitant about even admitting that.  Once you start to admit that there may be extra-special circumstances, it’s easy to start making more and more exceptions.  I’m not going to do that.

Anyway …  Back to Andy:

Third, the journals are not the ones hurt most directly by review boycotts; it is the authors. The journal will almost always find someone else to review the paper (with a delay as these reviewers are recruited); and if not, the manuscript will be returned for lack of qualified reviewers (with a delay as the paper is prepared for submission elsewhere). Rightly or wrongly, publications are a primary currency of academia. If getting that publication delayed means my friend or colleague doesn’t get a job, or a grant, or tenure, I have hurt them, not just the profits of the journal.

Here we come to the real issue — the “collateral damage” that Andy mentioned in his title.

First, let’s say that he’s right — there is damage.  A reviewing boycott is going to hurt authors.  It’s regrettable.  If I could hurt the non-open journals without hurting the authors, I surely would.  So this is a tough situation.  It’s a tough decision.

But as Matt has ably pointed out, we’re in a war.  A combination of historical accidents have manoeuvred us into a position where the interests of authors are directly opposite to those of publishers: in short, authors want their papers to be read by everyone with maximum convenience, and publishers want to prevent them from being read except by an elite few who are able and willing to pay.  My judgement is that whatever damage I may do to authors through a reviewing boycott is a tiny, tiny proportion of the damage that non-open publishers do to them every time they give away their work to a corporation that hides it away in a walled garden.

In short: there is no wholly good solution here.  It’s a matter of finding the least bad solution.  In the long term it is, unquestionably, to the advantage of all authors for open access to become ubiquitous.  Without a doubt we will need to make sacrifices to reach that future, including passing up opportunities to place our work in higher impact venues.  This is one more such sacrifice.

… and at this point, I’m a bit nonplussed.  What did we expect?  That it would just fall into our laps?  That the gigantic multinational corporations that eat our work would happily hand it all back to us?  That they would cheerfully give up the anti-science business model that has made them record profits year on year?  Did we think there would be no fight?  That we wouldn’t have to give anything up along the way?

And so on to Andy’s constructive suggestions.

1) Refuse to review the paper, but fully explain why in a letter submitted directly and separately to the editor, journal, and authors. This way everyone gets the message – not just a select few.

This is definitely the way to go.  To be clear: it’s not the only strategy we should be pursuing, but it’s the best way I’ve heard to handle the problem of reviewing.

(Might journals object to an invited reviewer contacting the authors directly?  I can’t think of a legitimate reason why they might, but I suppose it’s possible.  Anyone have any experience of this?)

2) Review the paper, but include a message with the review (perhaps both in the review text and in a direct letter to the authors) on the shame of the work being locked behind a paywall. Make the authors think twice about whether or not the intended audience will ever see the paper.

This strikes me as weak sauce.  I think of it as an emergency backup plan for the very rare cases where there really is a compelling reason to review something in a non-open journal, such as the Xenoposeidon example above.

But even then, aren’t there better alternatives?  Like simply contacting the authors directly, and explaining why you think it’s important that they send the work elsewhere?  Realistically, no author having gone successfully through peer-review is then going to pull the paper on a reviewer’s recommendation and submit it elsewhere.  Better to raise that possibility before the review has happened.

3) Submit your own work to open access journals, cite work in open access journals, and encourage your colleagues to do the same.

Oh!  Let me be very clear here: I certainly never meant to suggest a reviewing boycott as a substitute for a submission boycott!  No, it’s meant to accompany a proper open-access submission policy.

Again, I am not going to say “never”.  There are situations where no doubt I will be more or less forced to allow my work to appear in non-open venues — for example, when I speak at a conference, contribute a paper for the proceedings volume, and find that the volume is going to be non-open.  But even then, there are other approaches to be taken.  For example, when exactly this happened with my sauropod history paper being published in a non-open and ludicrously expensive Geological Society special volume, I found a way to retain the right to freely redistribute copies of my chapter.  (I have not used the SPARC Addendum yet, but may be useful in such situations … even if it does sound like a John Grisham novel.)

OK, last lap.  Here we go.  Andy says:

I sympathize with the sentiment that we academics shouldn’t be propping up the questionable practices of some publishers, but we also need to avoid shooting ourselves (and our colleagues) in the foot as a result.

I have to disagree.  Foot damage is regrettable, but it’s better than slavery.  What’s maybe got lost in this pragmatic discussion of ways and means is that the status quo is wrong.  Everyone has to make their own moral choices, but for me it would be Just Plain Wrong to perpetuate the corporate incarceration of publicly funded science.

It’s hard to write about these things without coming across as overwrought and hysterical, but let me try an analogy here.  The economic sanctions against South Africa in the 1980s, intended to bring about the end of apartheid, most certainly hurt the very citizens that they were intended ultimately to help.  But most people would agree that history has vindicated those sanctions.  It was a hard decision to make.  No doubt there were plenty of anti-apartheid activists who, with the best intentions, opposed the sanctions because of their immediate negative effect on people on the ground.  But, happily, longer-term thinking won out.  We need to be similarly far-sighted.

Is it hyperbole to compare paywalled research with institutionalised racism?  Yes, of course.  But maybe not by so much as you think.  The developing world is beset by appalling diseases that we in the West don’t even need to think about, and suffers constant famines.  Who knows what fruitful research might have been done — both by professional scientists in those countries and by unaffiliated amateurs in the West — if only the foundational research was available to them?  Open Access isn’t just a First World Problem: it potentially affects health and access to food and water for millions, or even billions, of people.

So, yeah.  I am cool with a bit of collateral damage.

I was directed to an article entitled Rookie Review on Nature Jobs by a tweet from Andy Farke (author of the Open Source Palaeontologist and an editor at PLoS ONE).  It has a lot of good stuff in it, once you get past the opening section.  But getting past that opening was difficult for me, because my blood was boiling by the time I reached the end of the third paragraph.

Here, then, is the opening of the article, with my translation.

Claudio Casola had no idea that journal editors had consistently rated his manuscript reviews highly. Then he received an award from Amsterdam-based publisher Elsevier for his “exceptional contribution to the quality of the journal Gene”.

Translation: Casola has been suckered into investing a huge amount of time and expertise, over and over again, into improving the work of other scientists, funded from the public purse, in order to increase the profits of a foreign-owned corporation that locks away the resulting science from the people who funded it.  He has done this so often and so well, that the corporation has very generously given him “an award”.  Anyone care to guess the cash value of that award?

(Notice by the way that most reviewers don’t even get the courtesy of feedback from the publisher.  Casola is a very rare exception.)

Casola, a postdoc in evolutionary genetics at Indiana University in Bloomington, says that his first review, in 2006, was typical of rookie referees. He spent more than 10 hours on the manuscript, poring over the details and asking faculty members for advice. After reviewing more than two dozen papers in the past five years, he has been able to cut the process down to three hours, quickly assessing the originality and merit of a paper. “Reviewing manuscripts makes me feel like I’m a fully fledged member of the scientific community,” says Casola.

There is it, folks.  The actual reason he gives all this work to a profiteering corporation?  They’ve managed to persuade him that they are the Scientific Community rather than a parasite that clings to it.  Fished in.

 “Young scientists should get involved in the process as they start building their careers, particularly since reviewers are harder and harder to find,” says Bart Wacek, an executive publisher in charge of Elsevier’s genetics portfolio based in Cambridge, Massachusetts.

Translation: “Young scientists should give us free professional work, and establish the habit early in their careers”, says Bart Wacek, an executive publisher at Elsevier.  “Only by getting started young can researchers hope to develop fully-fledged Stockholm Syndrome.  We need them to put in enough effort early on that the sunk cost fallacy begins to pervade their thinking: then they will invent reasons to justify to themselves why it’s a good thing to give this work to profiteers instead of to the wider scientific community.  Better still, in some cases they will even evangelise on our behalf!”

Young reviewers are certainly sought after. “The best referees are postdocs,” says Leslie Sage, a senior physical-sciences editor at Nature in Washington DC. “They are at the top of their game, well versed in the literature and politically naive enough to tell the truth.”

“… and sufficiently in awe of Real, Grown-Up Journals that they will do whatever we tell them in exchange for the oxygen of acceptance.  Catch ‘em while they’re young!”

Despite all this, the Nature Jobs article is worth reading because it does contain some useful hints about what makes a good review — especially this nugget: “Reviewers should avoid concentrating on what the study could show in principle. The focus should be on what it actually shows.”  A big amen on that.  Nothing is more frustrating than getting back a review that says “Well, you should have written this other paper instead.”

Still and all, folks.  You can choose where to direct your reviewing effort.  You can give it to open-access journals that let the whole world benefit from your work (and more important, from the author’s work and the nation’s funding).  Or you can give it to Elsevier shareholders.

It’s on the record that I think it’s stupid to do the latter — immoral, even, in an “all that is necessary is for good men to do nothing” way, because donating to paywalled journals helps to prop up their corrupt business and therefore keeps research out of the hands of the people who pay for it.  (Who are these people who want access but can’t get it?  See Peter Murray Rust’s excellent ongoing series on “The Scholarly Poor” — Dentists, Industry, The Climate Code Foundation, Patient groups, so many different types.)

So again I urge you — join me in refusing to do free work for paywalled journals.

Update (Sunday 16th October 2011)

Andy Farke offers a counterpoint over on the Open Source Paleontologist.  He raises important points that deserve to be properly addressed: I’ll probably do that in a new post here rather than as a comment.  Stay tuned!

 

Smoking Kraken

October 12, 2011

Folks.  Just don’t do this.  Just don’t.

McMenamin and Schulte McMenamin’s crack-smoking GSA abstract Triassic kraken: the Berlin ichthyosaur death assemblage interpreted as a giant cephalopod midden isn’t going to do anything for them except attract well-deserved ridicule; and it’s not going to do anything for the field of palaeontology except attract undeserved ridicule.  It’s a lose-lose.

So just don’t, OK?

Oh, and, Geological Society of America?  Don’t do this, either.  A reputation is a valuable and fragile thing.

And mainstream media: we understand that you feel you should be able to trust the Geological Society of America, but can please have just a little common-sense?

(Actual analysis, if anyone wants it, can be found here on Brian Switek’s Wired blog.)

Acknowledgements: public domain Brachiosaurus altithorax and Histioteuthis reversa images from Wikipedia.  Originals here and here.

There’s recently been a rash of requests for PDFs on the VRTPALEO mailing list.  Or maybe “plague” would be a better word.  What invariably happens is that a new paper comes out, and someone emails the list saying “Please can someone send me a PDF of this?”; then another half-dozen or so people all reply to the list saying “I’d like a copy, too”.  (The situation is exacerbated by the VRTPALEO list’s utterly advanced policy of forcing all replies to go to the whole list instead of just to the person being replied to, but that’s a whole nother rant.)

The result is of course that several thousand people get half a dozen spams.  Yes, it’s true that it only takes a couple of seconds to recognise and delete such messages.  But when two thousand people each take two seconds to delete a message, that’s 4000 seconds of time that could have been used for something useful.  In other words, to save yourself a couple of minutes’ work, you’ve wasted more than an hour of other people’s time.

Folks, this has to stop.

So what should you do when you want to get hold of a paper?  It’s a simple three-stage process.  And before you ask, yes, this is good for hobbyists as well as professionals.

Step 1: Google

Just search for the title of the paper.  You’d be surprised how often it just turns up.  Sometimes  it’s in an open-access journal, such as Acta Palaeontologica Polonica, Palaeontologia Electronica or PLoS ONE.  Sometimes the author has posted a copy, as for example I do with all my stuff and Matt does with his.  Sometimes, there just happens to be a copy lying around somewhere — for example, because a lecturer made it available to his students.

Often, though, the paper you want is out there, but paywalled.  So go on to …

Step 2: ask the author

Nine times out of ten, the abstract pages that the big commercial publishers put up include the author’s email address.  So just drop him or her a line asking for a copy.

Dear Dr. Haddockwhittler,

I was interested to see the abstract of your new paper on eroded non-diagnostic ornithopod pedal phalanges in the Journal Of Small Boring Fossils. I would be very grateful if you would send me a PDF. Many thanks.

And you’ll almost always get the PDF back within a day or two.  Sometimes authors don’t respond at all — most likely because they’ve not seen the message; and very occasionally they don’t have the PDF themselves.  But these are very rare situations.  And I have never, ever, known an author to just flatly refuse to send out a PDF.

I’ve had a few people telling me that they’re nervous about cold-contacting an Actual Credentialled Professional, and that they fear getting the brush-off because of their own amateur status.  Put this foolish idea out of your mind. Every professional is always delighted when anyone, professional or not, is interested in their work.

SPECIAL BONUS FRINGE BENEFIT: every now and then, you may find that as a by-product of such a request, you strike up a conversation with the author.  If you and they are interested in the same stuff, you sometimes find that you each have light to shed on the others’ thoughts.  As a matter of fact, this is precisely how I met and became friends with Matt (which in turn is how I became a palaeontologist — a story that I must tell some time in Tutorial 10: how to become a palaeontologist).  Usually this won’t happen: you’ll just have a brief, courteous exchange, and move on.  But sometimes it might.

But suppose you can’t find the author’s email address?  (This is much more common with older papers.)  Or suppose it’s a really old one — a classic Janensch paper or something — and the author is dead?  Or suppose you send an email, but the author never responds?  Then on to …

Step 3: ask a friend

If you know someone who’s at an institution that has good access to subscription resources, drop them a line as ask whether they’d mind pushing a copy your way.  If you’re friends already it’s probably because you’re interested in the same stuff, which means that they’ve likely already downloaded the paper in question — or, if not, they’ll be grateful to you for the heads-up.  Even if not, you’re only wasting one person’s time instead of two thousand.

And if all else fails …

… then fall back to the original: email the list and ask whether anyone can help.  Sure, there’s a place for this: it’s part of what the list is there for, and it can be absolutely invaluable when you’re trying but failing to track down an obscure old paper.

If you do this, then please use a meaningful subject for your email.  If you just write “PDF request” than I will delete it without even opening it, and I bet most other people will, too.  Do yourself a favour and write something terse but informative, like “Looking for PDF of Haddockwhittler 2010 on ornithopod phalanges”.

Another situation where mailing the list with a PDF request is appropriate: when you don’t know exactly what it is that you’re looking for, and you need expert guidance.  For example, I did this when looking for an ostrich osteology: I didn’t know of a good one (and hadn’t been able to discover the existence of one using Google), so I asked.  Not a problem.

But, people, this should be the last resort, not the first.

(There are those that say Inter-Library Loan should be on the List Of Things To Do Before Spamming VRTPALEO, but that’s not usually an option for amateurs with no formal affiliation.)

Well, I hope that’s helpful.  Now go forth and obtain papers!

This post is an expanded version of an email that I have written many, many times to individuals.  I got bored of writing it over and over, and figured that it would be quicker and easier to post this, and then be able to point people to it.

In an interesting comment on Matt’s “Amphiocoelias brontodiplodocus” post, an anonymous commenter wrote (among much else):

As for the paper itself, it does point out something that may become a future problem for paleontologists. I know of several amateur and commercial paleontologists who believe they aren’t allowed to write peer-reviewed papers to be published in journals because they aren’t professional paleontologists or work at a university (in fact, this even applies to a couple museum paleontologists who work at non-university public museums).

I started to write a reply to this, then realised it was important enough to merit its own post — so here it is.

The amateur and commercial palaeontologists alluded to in the comment are wrong, plainly and simply. Anyone can submit a manuscript to any journal[*]. And the evaluation of submitted manuscripts is supposed to be done strictly on the basis of the scientific content of the manuscript itself, not on the reviewers’ opinions of the individuals involved. [I'm not saying that ad hominem reviews never happen -- I've had one myself, when my very first submission was rejected in part because I had no publication track-record, which introduces an obvious chicken-and-egg problem. But this is very, very much the exception rather than the rule, and in fact in 40 or so reviews that I've had up to this point, I think that was the only example of this happening.]

So the commenter’s amateur friends should just go right ahead and start participating in the world of professional palaeontology. They’re welcome, so long as their stuff is good. Thing is, “participating in the world of professional palaeontology” entails things like copy-editing the careless mistakes out of your manuscript, getting your citations and references to match, reading and understanding the existing literature to recognise where your work fits in and what actual evidence supports the position you’re setting out to overturn, submitting the manuscript to a recognised journal, and putting it through peer-review. The brontodiplodocus manuscript is being dismissed by the professional community because it didn’t do any of these things — not because the authors aren’t professionals.

 

Galiano and Albersdorfer 2010:fig. 11A. Right lateral view of "Amphicoelias brontodiplodocus" specimen DQ-TY, dorsal, sacral, and anterior caudal vertebrae articulated with ilium, partially exposed in field jacket.

 

The anonymous comment continues:

Or that if they donate their specimens to a public institution so they can be publicly available they will be barred from studying the specimens and/or they will go to someone else to name. It doesn’t help that some paleontologists actively cultivate this view towards amateur and commercial paleontologists.

Who does? I have never heard of a professional palaeontologist denigrating an amateur or commercial for donating their scientifically significant specimens to a public institution. Never.

If an amateur or commercial paleontologist dots all their i’s and cross their t’s, subject their papers out to peer review, and place the holotype fossils in a publicly available institution, then why shouldn’t they be allowed to publish stuff?

They are allowed.

I don’t want to keep bashing on and on with the obvious example here, but I myself am an amateur: in the seven years since I started to work seriously on palaeo, I’ve been generated a total palaeontology income of £215, for an annual income of £30 p.a. (That’s a £40 interview fee and a 200 Euro travel grant.) I do all my work in my spare time, fitted in around a demanding day-job. I am in fact the very model of an “amateur”, i.e. one who does it for love rather than for money. That’s not stopped me from getting my work published — some of it in very good venues. It needn’t stop anyone else, either, if they’re prepared to do the work.

A better example, and one that Matt mentioned last time, is the man who is arguably the most respected in the whole field of sauropod palaeontology: Jack McIntosh, whose careful, detailed work over the last few decades has all been done in his spare time, and which constitutes a legacy of important papers that are still much referred to today.

The bottom line in the professional-vs.-amateur dichotomy is not in fact whether you get paid for what you do; it’s whether you conduct yourself according to your discipline’s professional standards or not. And that is a choice that everyone in the field (whether paid or not) makes for themselves. I know of people who are paid to do palaeo and who do not conduct themselves like professionals (though, thankfully, not many of them); and I know of unpaid people who are functional as professionals.

For this reason, I actually think that professional/amateur is unhelpful nomenclature when discussing these matters.  But  we’re stuck with it, and I’m not going to try to change the world.  Just remember, everyone: in the field of palaeontology, you’ll be considered professional if and only if you conduct yourself as a professional.

That is all.

[*] OK, “Anyone can submit a manuscript to any journal” is a very slight oversimplification.  There are a few journals that don’t accept unsolicited submissions, or that only accept them from members of a specific society, or what have you.  But these area vanishingly small proportion of the whole journal-space, and no-one should be put off from submitting to the other 99% of journals because of the existence of this 1%.

I wasn’t going to write about this, partly because it’s so darn depressing, but mostly because in the wake of this comment it seemed like the “Amphicoelias brontodiplodocus” paper was being withdrawn, and to quote something Mike said off-list, I was happier about the retraction than I was sad about the implied revisionism. But then Henry Galliano wrote:

Although the paper has still not been completed, no changes have been made altering it conclusions. Interestingly, despite the 4000 recent hits and downloads from our website, it is surprising no evidence has been submitted challenging our claims.

If it’s really supposed to be an internal manuscript/press release type thing, why brag about the lack of criticism? Did it ever occur to you that we might be holding off out of respect, to give you an avenue of retreat where you could perhaps salvage a few scraps of dignity? But if you’re going to call us out for not tearing apart this joke of a paper, then stand by.

In the previous post, Mike wrote:

In other words, we’re being asked to believe that the new specimens are more different from all other Morrison diplodocids than any of them are from each other.  And yet we’re brought to this conclusion by the very animals that are apparently not as similar.  It’s as though I discovered dogs, and thereby concluded that lions, cheetahs and house-cats are are all the same species.

No, it’s way, way worse. Because, claims of the authors to the contrary, “Amphicoelias brontodiplodocus” is not some kind of morphological outlier among Morrison diplodocids. From where I stand, it looks like it’s right in the middle. So it’s as though I discovered ocelots and thereby concluded that lions, cheetahs, and housecats were all the same thing.

If no apatosaurs had ever been found, and they got the first one, and then concluded that all the apatosaurines were one taxon and all the diplodocines were another, that would at least make some kind of sense, in that they’d be drawing their taxonomic distinctions along actual phylogenetic lines. Then it would be a fairly straightforward lumper/splitter fight. In the actual event, I’m sad to say that it’s the “A. brontodiplodocus” proponents against the reality-based community.

Back to Henry’s statement about the “surprising” lack of evidence to the contrary: dude, don’t do this to yourself. We thought you were on the right track with the implied retraction from your earlier comment. You’ve been one of the white hats, but if you go down this dark path, forever will it dominate your destiny. Consume you it will!

It’s not at all “surprising” that no one has submitted evidence to the contrary. The evidence is in the 133 years’ worth of careful morphological and phylogenetic work that you blew right past on the way to nominating your new animal, at least implicitly, as TEH MOSTEST IMPORTANT DIPLODOCID EVAR!!11eleventy! Your material is awesome, and I don’t doubt that you’ve got a new animal on your hands, but the idea that it is one of only two diplodocids in the Morrison–or worldwide–and all the others are morphs of the same thing, is both suspiciously convenient for you, and so outrageously extreme that it would take a mountain of work (that is not presented in the paper) to demonstrate. In addition to the gross, obvious morphological differences, it would be really nice to know why there are geographic, stratigraphic, and paleoecological differences among the other Morrison diplodocids. Doesn’t the work of Dodson et al. (1980), Turner & Peterson (1999), and Foster (2003, 2007), just for starters, count for anything? Instead of boasting about the uncontested status of your claims, how about doing enough work to convince us to take them seriously in the first place? People who take the time to do reasonable morphological comparisons and phylogenetic work that doesn’t hail from an opium den have better things to do than exhaustively smack down every act of Hoser taxonomy that leaks onto teh intarwebz in the first two days. Give us a minute to get over our collective shock, and in the meantime, make up your mind about what the document is. Is it supposed to be considered published, or not? If so, it’s fair game for criticism, but don’t deny that you’re at least attempting acts of taxonomy. If not, don’t beg us to criticize it. You may get a lot more than you wished for.

Sadly, this will probably go down in popular opinion as a clash between academic and commercial paleontologists, or between credentialed paleontologists and hobbyists.  It shouldn’t. I don’t care if someone is employed by a university or a rock shop, or whether they have any degrees in the field. All I care about is the quality of the work. (Repeatability, which necessitates that specimens be properly curated in accredited museums to ensure perpetual access to future researchers, is an inherent component of that quality.) Jack McIntosh is a physicist, and as far as I know never got any formal training in paleontology. But that’s irrelevant, because he taught himself by looking at literally thousands of specimens and reading everything he could get his hands on, and because his papers are as exhaustively researched as one could hope for. As Robert McKee wrote of Steven Pressfield, you can’t read Jack’s papers without being overwhelmed by “the work, the work, all the work” behind them. In contrast, I couldn’t read the “A. brontodiplodocus” paper without be overwhelmed by the complete disregard–and indeed implicit contempt–for all of the work that people from Cope and Marsh to Jerry Harris and David Lovelace have done on the admittedly knotty problem of Morrison sauropod diversity.

Taxonomy is facing a crisis, brought on by two things: at least for some charismatic clades, Hoser taxonomists potentially outnumber actual taxonomists (although even one is bad enough, as herpetologists have found); and there is essentially no filtering on what counts. Anyone in the world can whip up whatever uninformed BS they want and send a certain number of hardcopies off to libraries, and according to the ICZN their crappy work counts and the rest of us just have to deal with it. And the problem is only going to get worse in the shiny digital future as electronic publication removes the already minor inconvenience associated with “publishing” acts of taxonomy. I can think of a handful of possible outcomes:

  • Working scientists are going to bog down in endlessly putting out the fires of Hoser taxonomy.
  • We’ll install some kind of de jure filter to deal with Hoser taxonomy.
  • We’ll collectively decide to ignore acts of Hoser taxonomy, which will constitute a de facto filter.

For my part, I think the ICZN’s policy of noninterference in cases like this is taking a sound principle to the point of lunacy. It’s like I walked up to a policeman, punched him in the nose, and told him he couldn’t arrest me because my assault counted as protected speech (on reflection, I’ll bet this actually happens in Berkeley). Of the options above, I suspect that we’ll end up with the third, and I won’t be entirely happy about that, because I also suspect that some credentialed academics will want to ignore the work of commercial paleontologists and hobbyists just because they’re not credentialed academics. Which would be wrong. We want to sort the work based on its quality, not who produced it.

Which is an interesting position for me to come to, given what I’ve said here in the past about filters. It was easier to deal with the thought of completely open publication when the waste products weren’t landing on my lawn. But I still think that this is the way things are going. In which case, post-hoc criticism of self-published works is often going to be the only filter we get. The comment thread is open. Filter away!

References

  • Dodson, P., Behrensmeyer, A.K., Bakker, R.T., and McIntosh, J.S. 1980. Taphonomy and paleoecology of the dinosaur beds of the Jurassic Morrison Formation. Paleobiology 6:208-232.
  • Foster, J.R. 2003. Paleoecological analysis of the vertebrate fauna of the Morrison Formation (Upper Jurassic), Rocky Mountain Region, U.S.A. New Mexico Museum of Natural History and Science. Bulletin 23.
  • Foster, J.R. 2007. Jurassic West: The Dinosaurs of the Morrison Formation and Their World. Indiana University Press. 389pp.
  • Turner, C.E., Peterson, F., 1999. Biostratigraphy of dinosaurs in the Upper Jurassic Morrison Formation of the Western Interior, U.S.A. Pp. 77–114 in Gillette, D.D. (Ed.), Vertebrate Paleontology in Utah. Utah Geological Survey Miscellaneous Publication 99-1.

Well, this is frustrating.  Over on the VRTPALEO mailing list, all the talk at the moment is of the new paper by Henry Galiano and Raimund Albersdörfer (2010), describing their rather comically named new species Amphicoelias brontodiplodocus.  And to be fair, the material they’re describing is sensational, and the photographs in the paper are pretty good.

 

Galiano and Albersdorfer (2010:fig 10A-B): Above, cervical vertebrae 7-10 of Amphicoelias brontodiplodocus specimen DQ-TY; below, corresponding cervical vertebrae of Diplodocus carnegii holotype CM 84, modified from Hatcher (1901: plate III)

 

But I don’t want to talk about that.

There are other things I do want to talk about, but I can’t help feeling that whatever else we cover here at the moment, everyone is going to be thinking “Yes, but what about Amphicoelias brontodiplodocus?”  So I don’t think I can go on to write about the things I want to before we’ve at least acknowledged the existence of this paper.

And yet, and yet …  I have so many problems with this paper, even before we get to the controversial part, namely the conclusion that Diplodocus, Barosaurus, Apatosaurus, SupersaurusSuuwassea, Tornieria and Eobrontosaurus are all congeneric with Amphicoelias — more precisely, conspecific with the single species Amphicoelias altus.

Aside from the a priori unlikelihood of that, we have these problems:

  • First, and maybe most important, the specimens described in this paper are all privately owned, so whatever conclusions might be gleaned from examining them are not replicable by other scientists.  For the Society of Vertebrate Paleontology, that’s a deal-breaker right there (and I am in full agreement).
  • Second, the new paper doesn’t seem to be published: at least, no-one’s yet claimed that it exists in numerous identical hardcopies, so for ICZN purposes the new name is a nomen nudum.  (That will surely change, though: I am confident that Dinosauria International, LLC are perfectly capable of printing off a hundred copies and sending them out to libraries.)
  • Third, the paper doesn’t seem to have been peer-reviewed: at least, there’s nothing in the acknowledgements that indicates that it was.  It doesn’t seem to have been edited in anything like the usual sense either.
  • Fourth, there is mechanical evidence of enormous sloppiness in the composition of the paper.  For example, many cited papers are not included in the REFERENCES CITED section, and most of the references that are included are not in fact cited in the paper.  As an example, my own Taylor et al. (2009) is cited but not referenced, while Taylor and Naish (2005) is referenced but not cited.  Lots of Upchurch papers in the bibliography are never cited.  That doesn’t give me confidence about the rest of the work.
  • Likewise, the paper is rife with typos and grammar errors, such as this from page 28: “A. louisae is by far the most widely acclaimed example, and B. excelsus skeleton mounted and exhibited in the Peabody museum. Despite the familiarity of these Apatosaurus specimens various aspects of it [sic] skeleton remain poorly known.”  Not a killer, but again it doesn’t give me confidence.
  • brontodiplodocus” is a stupid name.

Against that backdrop, consider the radical taxonomic hypothesis.  All Morrison formation diplodocids (and some from elsewhere) are considered to belong to a single species, Amphicoelias altus … except for the new specimens, which belong to the new and separate species A. brontodiplodocus.  In other words, we’re being asked to believe that the new specimens are more different from all other Morrison diplodocids than any of them are from each other.  And yet we’re brought to this conclusion by the very animals that are apparently not as similar.  It’s as though I discovered dogs, and thereby concluded that lions, cheetahs and house-cats are are all the same species.

So this is not just a matter of extreme taxonomic lumping: it’s weirder than that.  It’s “all the other stuff is just a single species except the one we’ve discovered which is different”.

The point

As Tom Holtz is fond of saying, extraordinary claims demand extraordinary evidence.  I’m not going to come out and say it’s impossible that all Morrison diplodocids except the new specimens were conspecific.  But if I were the one setting out to propose such a heterodox hypothesis, I would do myself every possible favour: I’d do it from properly accessioned specimens in public museums, I’d publish in a recognised peer-reviewed journal, I’d take care to get my nomenclature right, match up my citations and references, and generally dot the i’s and cross the t’s.

Until that’s done with this new material, I’m not sure there’s much point in investing a lot more effort in evaluating the phylogenetic/taxonomic claims.

(Henry, I know you’re an occasional reader here.  Sorry to be so negative, but I’m sure you’ll understand that I have to call ‘em as I see ‘em.)

References

I’m just back from SVPCA 2010 (the Symposium of Vertebrate Palaeontology and Comparative Anatomy), and what an amazing meeting it was.  I think it was the best I’ve been to.  That’s partly because I understand more of the talks these days — it’s the first time I’ve ever listened to every single talk, even all the mammal-tooth and fish-skull talks — and I learned something interesting and new from almost every one of them.

But as is so often the case, the best thing about the meeting was, well, meeting.  I met with Matt and Darren for the first time in a year, which is always excellent.  And for the first time, I met horizontal-sauropod-neck advocate Kent Stevens.  Kent was there to present one of two talks on horizontal necks, and UK sauropod jockey John Martin presented the other.  Their talks were part of a block of seven sauropod talks — it would have been eight had Michael Pitman not changed his scheduled sauropod-tail talk to a theropod-tail talk.  Matt and I both made presentations, although Darren wasn’t able to because he didn’t know that he’d be able to come to the meeting until the last moment.

After that block of talks, Matt, Darren and I went off to lunch with Kent and Martin.  Despite the lighthearted attempts of session moderator John Hutchinson to build the session up as a two-way fight, it was all rather peaceful and enjoyable.  After lunch we all went to have our photos taken together in front of the Zoology Museum‘s giraffe skeleton:

Sauropod Neck Posture Working Group, 2010 meeting.  From left to right: Darren Naish, Matt Wedel, John Martin, Mike Taylor, Kent Stevens.

As you can see, we were all very civilised and well behaved.

The Sauropod Neck Posture Working Group carefully considers all points of view in a detached, professional and mature manner.

In all seriousness, it’s no secret that we SV-POW!sketeers are very much advocates of a raised habitual posture, and so that we strongly disagree with Kent and John.  We had a lot of fun talking together, but we didn’t find that they presented any compelling new evidence in their talks.  (You can read the abstracts of their talks, and indeed of mine and Matt’s, in the SVPCA abstracts book.)

The case for horizontal or near-horizontal habitual pose rests on two assumptions.  First, that osteological neutral pose (ONP) was habitually adopted; and second, that we can know what ONP was.  We still feel that both of these assumptions are false.  We can’t know ONP because there is not a single sauropod neck skeleton anywhere in the world consisting of undistorted cervicals — and even if we knew what ONP was, it wouldn’t tell us much about what I am suddenly going to call mechanical neutral pose (MNP)[*], because we don’t know anything about the intervertebral cartilage.  And we know that extant animals do not habitually adopt ONP because we have X-rays that show us how they habitually rest, and we know that they don’t match what you get by articulating bones.

[* either John or Kent made the point that ONP != MNP in his talk.  I think they probably used a different name for MNP, but it eludes me for now.  If anyone can remind me, I will switch to their terminology.]


So, anyway, it was a bit frustrating watching John’s talk, and seeing him show many photographs of live animals and claiming that their necks were in ONP, when we knew perfectly well that they were not — because necks lie.  We fear he may have been tricked by the misleading soft-tissue outlines that mask the postures adopted by the neck skeleton in nearly all tetrapods.  As an example, I give you the hoatzin, which happily was on display at the Zoology Museum as both a stuffed specimen and a skeleton:

Hoatzin (Opisthocomus cristatus), stuffed specimen and skeleton.  Note the extraordinarily long cervical skeleton, almost entirely unreflected in the live animal.

Here’s another photograph from the astounding collection of the Zoology Museum (and some day I really ought to blog about the museum itself).  I took this photograph of the neck of a camel with no specific agenda, but when I looked at it again today, one aspect leapt out at me:

Head and neck of dromedary camel (Camelus dromedarius) UMZC H.14191, in right lateral view, with disarticulated C3/C4 and C4/C5 joints.

Notice how very dramatically the third and fourth cervical central fail to contact, and the fourth and fifth.  How uncomfortable this must be for the poor camel — its neck extended (or “dorsiflexed”) far, far out of ONP, to the point where the vertebrae drastically disarticulate.  And yet we all know perfectly well that habitual pose for camels is much more extended than this, and many of us have seen photos of camels leaning their necks right back so that their heads are upside down, and they can rub the top of their head against their back.  Just imagine what that does to the cervical articulations.

More on this subject another time.  For now, I leave you with more from the Sauropod Neck Posture Working Group summit.

Hey!  That hurt!

What I did on my holidays

September 25, 2009

I made brachiosaur sand-sculptures.

Brachiosaurid in sleep hypothetical posture, left anteroventrolateral view.  Juvenile Homo sapiens (Daniel Taylor) for scale.

Brachiosaurid in hypothetical sleep posture, left anteroventrolateral view. Juvenile Homo sapiens (Daniel Taylor) for scale.

(And yes, it’s that Daniel Taylor, the author of Taylor 2005 — a copy of which apparently hangs on the wall of the Padian Lab.)

But wait!  Is the brachiosaur truly asleep, as it seems, or is it actually the victim of a mighty hunter?

xx

Brachiosaurid in hypothetical death pose, left posteroventrolateral view. Mighty hunter (Michael P. Taylor) for scale. Note bemused bystander in middle distance.

No, it turns out it was just asleep after all; and I joined it.

xx

Brachiosaurid in hypothetical sleep pose after all, left posteroventrolateral view. Brachiosaur's new best friend for scale.

… and finally: your obligatory sauropod-vertebra shot:

Obligatory sauropod vert shot: the Copehagen copy of Mamenchisaurus hochuanensis

Cast of Mamenchisaurus hochuanensis holotype CCG V 20401, in right lateral view. Need I draw your attention to the truly absurd neck? This cast is owned by the Homogea Museum in Trzic, Slovenia, and was on loan in the car-park of the Geological Museum in Copenhagen.

References

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.
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