We jumped the gun a bit in asking How fat was Camarasaurus? a couple of years ago, or indeed How fat was Brontosaurus? last year. As always, we should have started with extant taxa, to get a sense of how to relate bones to live animals — as we did with neck posture.

So here we go. I give you a herd of Indian elephants, Elephas maximus (from here):

056-Elephant-c-Gehan-de-Silva-Wijeyeratne-Minneriya-2004-07-27-165-Gathering

You will notice, from this conveniently-close-to-anterior view, that their torsos bulge out sideways, much further than the limbs.

Now let’s take a look at the skeleton of the same animal in the Oxford University Museum of Natural History (downloaded from here but for some reason the photo has now gone away):

4795746797_575d1f0ce6_b

The rib-cage is tiny. It doesn’t even extend as far laterally as the position of the limb bones.

(And lest you think this is an oddity, do go and look at any mounted elephant skeleton of your choice, Indian or African. They’re all like this.)

What’s going on here?

Is Oxford’s elephant skeleton mounted incorrectly? More to the point, are all museums mounting their elephants incorrectly? Do elephants’ ribs project much more laterally in life?

Do elephants have a lot of body mass superficial to the rib-cage? If so, what is that mass? It’s hard to imagine they need a huge amount of muscle mass there, and it can’t be guts. Photos like this one, from the RVC’s televised elephant dissection on Inside Nature’s Giants, suggest the ribs are very close to the body surface:

01020162576700

I’m really not sure how to account for the discrepancy.

Were sauropods similarly much fatter than their mounted skeletons suggest? Either because we’re mounting their skeletons wrongly with the ribs too vertical, or because they had a lot of superficial body mass?

Consider this mounted Camarasaurus skeleton in the Dinosaur Hall at the Arizona Museum of Natural History (photo by N. Neenan Photography, CC-BY-SA):

Camarasaurus_skeleton

Compare the breadth of its ribcage with that of the elephant above, and then think about how much body bulk should be added.

This should encourage palaeoartists involved in the All Yesterdays movement to dramatically bulk up at least some of their sauropod restorations.

It should also make us think twice about our mass estimates.

London T rex snack

Here at SV-POW!, we are an equal-opportunity criticiser of publishers: SpringerPLOS, Elsevier, the Royal Society, Nature, we don’t care. We call problems as we see them, where we see them. Here is one that has lingered for far too long. PLOS ONE’s journal information page says:

Too often a journal’s decision to publish a paper is dominated by what the Editor/s think is interesting and will gain greater readership — both of which are subjective judgments and lead to decisions which are frustrating and delay the publication of your work. PLOS ONE will rigorously peer-review your submissions and publish all papers that are judged to be technically sound.

Which is as we would expect it to be. But their reviewer guidelines page gives more detail as follows (emphasis added):

[Academic Editors] can employ a variety of methods, alone or in combination, to reach a decision in which they are confident:

  • They can conduct the peer review themselves, based on their own knowledge and experience
  • They can take further advice through discussion with other members of the editorial board
  • They can solicit reports from further referees

As has been noted in comments on this blog, this first form, in which the editor makes the decision alone, is “unlike any other first-tier academic journal”. When I submitted my own manuscript to PLOS ONE a few weeks ago, I did it in the expectation that it would be reviewed in the usual way, by two experts chosen by the editor, who would then use those reviews in conjunction with her own expertise to make a decision. I’d hate to think it would go down the easier track, and so not be accorded the recognition that a properly peer-reviewed article gets. (Merely discussing with other editors would also not constitute proper peer-review in many people’s eyes, so only the third track is really the whole deal.)

The problem here is not a widespread one. Back when we first discussed this in any detail, about 13% of PLOS ONE papers slipped through on the editor-only inside lane. But more recent figures (based on the 1,837 manuscripts that received a decision between 1st July and 30th September 2010) say that only 4.2% of articles take this track. Evidently the process was by then in decline; it’s a shame we don’t have more recent numbers.

But the real issue here is lack of transparency. Four and half years ago, Matt said “I really wish they’d just state the review track for each article–i.e., solo editor approved, multiple editor approved, or externally reviewed […] I also hope that authors are allowed to preferentially request ‘tougher’ review tracks”.

It seems that still isn’t done. Looking at this article, which at the time of writing is the most recent one published by PLOS ONE, there is a little “PEER REVIEWED” logo up at the top, but no detail of which track was taken. PLOS themselves evidently take the line that all three tracks constitute peer-review, as “Academic Editors are not employees […] they are external peer reviewers“.

So I call on PLOS ONE to either:

A. eliminate the non-traditional peer-review tracks, or

B1. Allow submitting authors to specify they want the traditional track, and

B2. Specify explicitly on each published paper which track was taken.

Suppose that, for some good and sane reason, you need to place a paper in a paywalled journal.

You do some research. You write a paper and prepare illustrations. You send it off to a journal, and a volunteer editor sends it out to volunteer peer-reviewers. You handle the reviews, revise your manuscript, write rebuttals as necessary, send in the revised version, and the editor accepts it.

Congratulations! You are now the proud owner of a peer-reviewed, revised, accepted manuscript which will shortly become a published paper that you can put on your CV and show to grant reviewers and job-search committees and tenure boards.

Note the key point here: you are the owner of the accepted manuscript. Not the journal, not the publisher. You, the author.

Any minute now the publisher is going to ask you to sign a copyright transfer agreement. Once you do that (if for some reason you decide to acquiesce) they will own your work. From that moment on, whatever you’re allowed to do with your own work, if anything, is only by their grace.

Here’s the point: in between getting your acceptance and signing away all your rights, you have a window in which you own a completed scientific work, lacking only copy-editing (if any) and typesetting. So that is your moment to make sure the world sees it. Release it now. Put it it up on arXiv or on PeerJ Preprints or on FigShare or on your institutional repository or on your own web page. There are lots of places you can post it — take your pick. Either place it in the public domain or licence it as CC BY, and do it explicitly: both options make work available for the world to use, and either way academic norms will ensure that you get credit for your work.

Of course, once you sign over copyright, you’re playing by the publisher’s rules. They may well have crazy, complex, self-contradictory rules such as Elsevier’s you-can-deposit-it-unless-mandated-to rule — they can forbid you from making the accepted manuscript available.

That’s why it’s so important to release it to the world, with a clear statement of licence, before signing the copyright transfer. Once it’s out there in the public domain or as CC BY, it can’t be rescinded. The world can see and read and use and benefit from your work, and the “publisher” can’t prevent it.

So you can ignore Elsevier’s crazy requirements — just so long as you do it before you sign up to them.

(Once your work is out there for the world to use on liberal terms, you can of course go right ahead, sign the transfer, and let the publisher publish your article behind their paywall. That’s OK: the work is out there fore people to use. And if the publisher adds significant value in their copy-editing and typesetting, people will keep buying their subscriptions.)

 

As part of the progressive erosion of RCUK’s initially excellent open-access policy, barrier-based publishers somehow got them to accept their “open-access decision tree“, which you can now find on page 7 of the toothless current version of the policy. The purpose of this manoeuvre by the Publishers Association is to lend an air of legitimacy to continuing to deny citizens access to the research they funded for up to 24 months after publication. It’s to the House of Lords’ enduring shame that they swallowed this, when they must know that there is no justification for embargoes of any length.

More recently, as commentary on the Australian Research Council’s open access policy, the Australian Open Access Support Group (AOASG) published its own rather better decision tree.

But it still doesn’t go nearly far enough. So here is the SV-POW! decision tree, which we encourage you to print out and hang on your office door.

open-access-decision-tree

 

 

… and don’t forget, when depositing your peer-reviewed accepted manuscripts in a repository, to specify that they are made available under the CC BY licence, which most benefits the field as a whole.

 

Back in February last year, in a comment section, we got to discussing arXiv, the free-to-use open-access preprint repository that pretty much every physicist, mathematician and astonomer deposits their papers in. At the time, I wrote:

The immediate answer is that arXiv doesn’t accept palaeontology papers — the closest it comes is “computational biology”.

After a bit more discussion, I emailed the arXiv administrators and promised to report back when I heard from them. And I did hear back, but failed to report it because Life happened. Here, belatedly, is that report.

Date: 19 February 2012 16:51
From: Mike Taylor <mike@indexdata.com>
To: www-admin@arxiv.org

First: arXiv is awesome! Many thanks for creating and maintaining it.

I am a palaeobiologist and open-access activist. I, along with several of my colleagues, would very much like to use arXiv to deposit preprints of our journal papers, but can’t do so as it’s limited as to subject. I wonder why that is, and whether there are plans to expand? (I did read the FAQs, but didn’t see an answer there.)

My guess was that it is probably because the organisations providing funding are mostly maths/physics-oriented, but when I checked the list for 2011 it seemed that most funding organsations are discipline-neutral:

http://arxiv.org/help/support/2011_supporters

so is there another reason besides history?

Many thanks,

Dr. Michael P. Taylor
Research Associate
Department of Earth Sciences
University of Bristol
Bristol BS8 1RJ

Date: 20 February 2012 15:42
From: Don Beyer
To: Mike Taylor <mike@indexdata.com>

Dear Michael P. Taylor,

arXiv does a periodic review the subject categories to ensure the subject categories and descriptions are appropriate. At this time arXiv is not in a position to add any new subject categories. In order to add a new subject category there would have to be a significant sized community, potential moderator(s) and arXiv resources to add the new subject category. We may re-visit this request at a later date.

arXiv admin

Date: 20 February 2012 15:54
From: Mike Taylor <mike@indexdata.com>
To: Don Beyer

Many thanks for this response. Two followups: first, may I post your reply on my blog (https://svpow.wordpress.com/)? And second, is there anything that we as a community of palaeontologists, or more broadly biologists, can do to help encourage this expansion?

Date: 20 February 2012 17:50
From: Don Beyer
To: Mike Taylor <mike@indexdata.com>

Dear Mike,

You may post my email. Please note you may poll the community and put together a list of interested community members and appeal to arXiv moderation for requesting a potentially new subject category. Also, it would be helpful to have a couple of individuals that would be interested in moderating such a subject category.

Please direct all questions and concerns regarding moderation to the moderation@arxiv.org address. More information about our moderation policies can be found at:

http://arxiv.org/help/moderation

Date: 20 February 2012 17:58
From: Mike Taylor <mike@indexdata.com>
To: Don Beyer

Many thanks. Do you have a rough sense of how many biologists registering an interest might be enough to provoke some serious discussion? (I won’t hold you to it! Just so I know if, say, I don’t get more than 100, then I should forget about it.)

Date: 20 February 2012 18:33
From: Don Beyer
To: Mike Taylor <mike@indexdata.com>

Dear Mike,

Each research community is unique so even guessing what an appropriate number would be is pure speculation. You should attempt to gather as many interested individuals as possible within a reasonable time frame and simply submit your request to arXiv when you believe you have enough interested community members.

And there the matter rested, for more than a year.

But of course, during that year, I went right ahead and submitted a preprint to arXiv anyway (and then blogged about it, naturally). Which is the very thing I’d assumed I wasn’t able to do.

Why did I do that? One thing that seems to have changed between the exchange of correspondence above and our paper being posted is that arXiv’s “computational biology” category quietly changed to “quantitative biology”, which seems a bit less forbidding. After all, our paper must have been quantitative, it had measurements in it. But I think the big shift was discovering that a fellow biologist, Casey Bergman, was already posting on arXiv. Proof by example that it can be done.

So where does that leave us?

I know of at least two other palaeontologists who have posted on arXiv since me: Matt Wedel (no surprise) and Bristol MSc graduate Matt Cobley. I’ve never yet heard of someone submitting a biology paper and being told that it’s out of scope. So I think the conclusion is that arXiv does accept palaeontology after all, and probably always did. My advice now is that if you find yourself wishing there was an arXiv for palaeo, just use arXiv.

… and now of course there’s also PeerJ Preprints. But we’ll talk about that another time.

 

Jeffrey Beall’s fatuous pronouncement that The Serials Crisis is Over has been nagging away at me since it was posted yesterday. I admit my first reaction was that it was some kind of parody or satire, but Beall’s subsequent comments seem to rule out that charitable interpretation.

I’m pleased to see that the comments on that post have shared my bafflement: Karen Coyle cited Walt Crawford’s new book, The Big Deal and the Damage Done; and an important comment by Joe Kraus of the University of Denver cites a BMJ editorial, wunkderkind Jack Andraka and the Who Needs Access? site [disclosure: which I helped build]. So far no-one’s mentioned that Harvard can’t afford its subscriptions — or maybe they have but the comment was silently moderated into oblivion, as has happened with three separate comments that I posted there.

(It is of course because my comments have been repeatedly censored that I’ve given up trying to contribute to the original post’s comment thread, and am writing this instead. I can promise anyone who wants to comment here, Beall included, that we allow all comments except spam and direct repeated personal attacks.)

Beall’s response to Joe Kraus’s comment was simply an attack on the university that he works for — an attack that Joe took rather graciously. But what about all the other people that he mentions? It’s hard to avoid the conclusion that the lines are as follows: those who say that the serial crisis is over are the hugely profitable incumbents; those who say it is not are scholars, librarians, editor, doctors, students, and in fact every single group that doesn’t stand to gain financially from the continuation of the status quo. Doesn’t that look just a tiny bit suspicious? (I asked Beall this: that was one of the comments that was censored.)

But leave all that aside. The part that I really want to comment on is this, from the original article:

I declare that the serials crisis, the event that gave birth to the open-access movement, is over. I base my declaration on my observations as an academic librarian and on the scholarly literature, selections from which I include here:
[…]
“Publishers, through the oft-reviled “Big Deal” packages, are providing much greater and more egalitarian access to the journal literature, an approximation to true Open Access.”

That quote is from Odlyzko (2013), “Open Access, library and publisher competition, and the evolution of general commerce”, which is freely available on arXiv. So let’s look at the whole abstract that Beall quoted from so we can see the context of the quote that he used. (My emphasis added.)

Discussions of the economics of scholarly communication are usually devoted to Open Access, rising journal prices, publisher profits, and boycotts. That ignores what seems a much more important development in this market. Publishers, through the oft-reviled “Big Deal” packages, are providing much greater and more egalitarian access to the journal literature, an approximation to true Open Access. In the process they are also marginalizing libraries, and obtaining a greater share of the resources going into scholarly communication. This is enabling a continuation of publisher profits as well as of what for decades has been called “unsustainable journal price escalation“. It is also inhibiting the spread of Open Access, and potentially leading to an oligopoly of publishers controlling distribution through large-scale licensing.

The “Big Deal” practices are worth studying for several general reasons. The degree to which publishers succeed in diminishing the role of libraries may be an indicator of the degree and speed at which universities transform themselves. More importantly, these “Big Deals” appear to point the way to the future of the whole economy, where progress is characterized by declining privacy, increasing price discrimination, increasing opaqueness in pricing, increasing reliance on low-paid or upaid work of others for profits, and business models that depend on customer inertia.

It could not be clearer that this paper is not evidence for Beall’s assertion that the serials crisis is over — on the contrary, it argues that things are worse than ever and getting worse.

This is a classic example of quote mining.

I’m afraid that at this point in the development of his site, Beall is looking less and less like someone offering a helpful service to researchers looking for open-access venues; and more and more like a troll.