August 28, 2014
I’m scrambling to get everything done before I leave for England and SVPCA this weekend, so no time for a substantive post. Instead, some goodies from old papers I’ve been reading. Explanations will have to come in the comments, if at all.
For more noodling about nerves, please see:
- The world’s longest cells? Speculations on the nervous systems of sauropods
- Oblivious sauropods being eaten
- Butler, A.B., and Hodos, W. 1996. Comparative Vertebrate Neuroanatomy: Evolution and Adaptation. 514 pp. Wiley–Liss, New York.
- Nieuwenhuys, R. (1964). Comparative anatomy of the spinal cord. Progress in Brain Research, 11, 1-57.
- Streeter, G. L. (1904). The structure of the spinal cord of the ostrich. American Journal of Anatomy, 3(1), 1-27.
August 21, 2014
I have often argued that given their long hindlimbs, massive tail-bases, and posteriorly-located centers of mass, diplodocids were basically bipeds whose forelimbs happened to reach the ground. I decided to see what that might look like.
Okay, now obviously I know that there are no trackways showing sauropods actually getting around like this. It’s just a thought experiment. But given how close the center of mass of Diplodocus is to the acetabulum, I’ll bet that this pose was achievable in life. If diplodocids had just pushed the CM a few cm farther back, they might have dispensed with forelimbs entirely, or done something different with them, like re-evolved grasping hands.
Image modified from Gilmore (1932: plate 6). Here’s a horizontal-necked bipedal Diplodocus and the original pose:
UPDATE the next day: I had forgotten that Niroot had already done a bipedal Apatosaurus, and a much more convincing one than mine. Go see it.
UPDATE the next week: Well, heck. Looks like the primary value of this post was so that people would remind me of all the other places the same idea has already been covered better. As you can see from the comment thread, Mike blogged about this at the WWD site, Scott Hartman drew it, and Heinrich Mallison showed that it was plausible. Sheesh, I suck.
- Gilmore, C. W. 1932. On a newly mounted skeleton of Diplodocus in the United States National Museum. Proceedings of the United States National Museum 81, 1-21.
August 15, 2014
This is an open letter concerning the recent launch of the new open access journal, Science Advances. In addition to the welcome diversification in journal choices for authors looking for open access venues, there are many positive aspects of Science Advances: its broad STEM scope, its interest in cross-disciplinary research, and the offering of fee waivers. While we welcome the commitment of the Association to open access, we are also deeply concerned with the specific approach. Herein, we outline a number of suggestions that are in line with both the current direction that scholarly publishing is taking and the needs expressed by the open access community, which this journal aims to serve.
The first of these issues concerns the licensing terms of the journal articles. The default choice of a non-commercial licence (CC BY-NC) places unnecessary restrictions on reuse and does not meet the standards set out by the Budapest Open Access Initiative. Many large funders, including Research Councils UK and the Wellcome Trust, do not recognise this as an open license. The adoption of CC BY-NC as the default license means that many researchers will be unable to submit to Science Advances if they are to conform to their funder mandates unless they pay for the upgrade to CC BY. There is little evidence that non-commercial restrictions provide a benefit to the progress of scholarly research, yet they have significant negative impact, limiting the ability to reuse material for educational purposes and advocacy. For example, NC-encumbered materials cannot be used on Wikipedia. The non-commercial clause is known to generate ambiguities and uncertainties (see for example, NC Licenses Considered Harmful) to the detriment of scholarly communication. Additionally, there is little robust evidence to suggest that adopting a CC-BY license will lead to income loss for your Association, and the $1,000 surcharge is difficult to justify or defend. The value of the CC BY license is outlined in detail by the Open Access Scholarly Publishers Association.
We raise an additional issue with the $1,500 surcharge for articles more than 10 pages in length. In an online-only format, page length is an arbitrary unit that results from the article being read in PDF format. Can the AAAS explain what the additional costs associated with the increased length are that would warrant a 50% increase in APC for an unspecified number of additional digital pages? Other leading open access journals, such as PeerJ, the BMC series, and PLOS ONE, offer publication of articles with unlimited page lengths. The extra costs create constraints that may adversely incentivize authors to exclude important details of their study, preventing replication and hindering transparency, all of which are contrary to the aims of scholarly publication. Therefore it seems counterproductive to impose this additional charge; it discriminates against researchers’ best effort to communicate their findings with as much detail as necessary.
We feel that the proposed APCs and licencing scheme are detrimental to the AAAS and the global academic community. As such, we recommend that Science Advances:
Offers CC BY as standard for no additional cost, in line with leading open access publishers, so authors are able to comply with respective funding mandates;
Provides a transparent calculation of its APCs based on the publishing practices of the AAAS and explains how additional value created by the journal will measure against the significantly high prices paid by the authors;
Removes the surcharges associated with increased page number;
We hope that you will consider the points raised above, keeping in mind how best to serve the scientific community, and use Science Advances to add the AAAS to the group of progressive and innovative open access scholarly publishers. We hope AAAS will collaborate with the academic community to facilitate the dissemination of scientific knowledge through a journal committed to fully embracing the principles of Open Access.
We kindly request that you allow your response(s) to be made public along with this letter, and look forward to hearing your response soon.
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August 13, 2014
Today for the first time I saw Saegusa and Ikeda’s (2014) new monograph describing the Japanese titanosauriform Tambatitanis amicitiae. I’ve not yet had a chance to read the paper — well, it’s 65 pages long — but it certainly looks like they’ve done a nice, comprehensive job on a convincing new taxon represented by good material: teeth, braincase, dentary, atlas, and as-yet unprepared fragmentary cervical, fragmentary dorsals, sacral spines, some nice caudals, some ribs and chevrons, and pubis and ilium.
What catches the eye immediately is the bizarre forward-curved neural spines of the anterior caudals:
Here’s the third caudal in detail. (The first is fragmentary, and the second has some minor reconstruction near the tip of the spine which sceptical readers might think is covering up a misconstruction):
And here is the right-lateral view in close-up:
A phylogenetic analysis based on that of D’Emic (2012) recovers the new taxon in a polytomy with the Euhelopus clade
that’s going to need a new name pretty soon, since it keeps growing and can’t be called Euhelopodidae for historical reasons: [that should probably be called Euhelopodidae: see discussion in comments]:
Nice to see that new sauropods just keep on rolling out of the ground faster than we can blog about them!
- D’Emic, Michael D. 2012. The early evolution of titanosauriform sauropod dinosaurs. Zoological Journal of the Linnean Society 166:624-671.
- Saegusa, Haruo, and Tadahiro Ikeda. 2014. A new titanosauriform sauropod (Dinosauria: Saurischia) from the Lower Cretaceous of Hyogo, Japan. Zootaxa 3848(1):1-66. doi:10.11646/zootaxa.3848.1.1
Fumbling towards transparency: the Royal Society’s “reject & resubmit” and submitted/published dates
July 31, 2014
Regulars will remember that nearly two years ago, I reviewed a paper for the Royal Society’s journal Biology Letters, recommended acceptance with only trivial changes (as did both other reviewers) and was astonished to see that it was rejected outright. There was an invitation to resubmit, with wording that made it clear that the resubmission would be treated as a brand new manuscript; but when the “resubmission” was made, it was accepted almost immediately without being sent to reviewers at all — proving that it was in fact a minor revision.
What’s worse, the published version gives the dates “Received August 21, 2012.
Accepted September 13, 2012″, for a submission-to-acceptance time of just 23 days. But my review was done before August 21. This is a clear falsifying of the true time taken to process the manuscript, a misrepresentation unworthy of the Royal Society, and which provoked Matt and me to declare that we would no longer provide peer-review for the Society until they fix this.
By the way, we should be clear that the Royal Society is not the only publisher that does this. For example, one commenter had had the same experience with Molecular Ecology. Misreporting the submission/revision cycle like this works to publishers’ benefit in two ways: it makes them look faster than they really are, and makes the rejection rate look higher (which a lot of people still use as a proxy for prestige).
To the Society’s credit, they were quick to get in touch, and I had what at time seemed like a fruitful conversation with Dr Stuart Taylor, their Commercial Director. The result was that they made some changes:
- Editors now have the additional decision option of ‘revise’. This provides a middle way between ‘reject and resubmit’ and ‘accept with minor revisions’. [It's hard to believe this didn't exist before, but I guess it's so.]
- The Society now publicises ‘first decision’ times rather than ‘first acceptance’ times on their website.
As I noted at the time, while this is definitely progress, it doesn’t (yet) fix the problem.
A few days ago, I checked whether things have improved by looking at a recent article, and was disappointed to see that they had not. I posted two tweets:
e.g. See this very new @royalsociety article rspb.royalsocietypublishing.org/content/281/17… and note that it has Received and Accepted dates but no Revised date.—
Mike Taylor (@MikeTaylor) July 23, 2014
Again, I want to acknowledge that the Royal Society is taking this seriously: less than a week later I heard from Phil Hurst at the Society:
I was rather surprised to read your recent tweets about us not fixing this bug. I thought it was resolved to your satisfaction.
Because newly published articles still only have two dates (submitted and accepted) it’s impossible to tell whether the “submitted” date is that of the original submission (which would be honest) or that of the revision, styled “a new submission” even though it’s not, that follows a “reject and resubmit” verdict.
Also: if the journals are still issuing “reject and resubmit” and then accepting the supposed new submissions without sending them out for peer-review (I can’t tell whether this is the case) then that is also wrong.
Sorry to be so hard to satisfy :-) I hope you will see and agree that it comes from a desire to have the world’s oldest scientific society also be one that leads the way in transparency and honesty.
And Phil’s response (which I quote with his kind permission):
I feel the changes we have made provide transparency.
Now that the Editors have the ‘revise’ option, this revision time is now incorporated in the published acceptance times. If on the other hand the ‘reject and resubmit’ option is selected, the paper has clearly been rejected and the author may or may not re-submit. Clearly if a paper had been rejected from another journal and then submitted to us, we would not include the time spent at that journal, so I feel our position is logical.
We only advertise the average ‘receipt to first decision’ time. As stated previously, we feel this is more meaningful as it gives prospective authors an indication of the time, irrespective of decision.
After all that recapitulation, I am finally in a position to lay out what the problems are, as I perceive them, in how things currently stand.
- Even in recently published articles, only two dates are given: “Received May 13, 2014. Accepted July 8, 2014″. It’s impossible to tell whether the first of those dates is that of the original submission, or the “new submission” that is really a minor revision following a reject-and-resubmit verdict.
- It’s also impossible to tell what “receipt to first decision” time is in the journal’s statistics. Is “receipt” the date of the revision?
- We don’t know what the journals’ rejection rates mean. Do they include the rejections of articles that are in fact published a couple of weeks later?
So we have editorials like this one from 2012 that trumpet a rejection rate of 78% (as though wasting the time of 78% of their authors is something to be proud of), but we have no idea what that number represents. Maybe they reject all articles initially, then accept 44% of them immediately on resubmission, and call that a 22% acceptance rate. We just can’t tell.
All of this uncertainly comes from the same root cause: the use of “reject and resubmit” to mean “accept with minor revisions”.
What can the Royal Society do to fix this? Here is one approach:
- Each article should report three dates instead of two. The date of initial submission, the date of resubmission, and the date of acceptance. Omitting the date of initial submission is actively misleading.
- For each of the statistics they report, add prose that is completely clean on what is being measured. In particular, be clear about what “receipt” means.
But a much better and simpler and more honest approach is just to stop issuing “reject and resubmit” verdicts for minor revisions. All the problems just go away then.
“Minor revisions” should mean “we expect the editor to be able to make a final decision based on the changes you make”.
“Major revisions” should mean “we expect to send the revised manuscript back out to the reviewers, so they can judge whether you’ve made the necessary changes”.
And “reject and resubmit” should mean “this paper is rejected. If you want to completely retool it and resubmit, feel free”. It is completely inappropriate to accept a resubmitted paper without sending it out to peer review: doing so unambiguously gives the lie to the claim in the decision letter that “The resubmission will be treated as a new manuscript”.
Come on, Royal Society. You’ve been publishing science since 1665. Three hundred and forty-nine years should be long enough to figure out what “reject” means. You’re better than this.
And once the Royal Society gets this fixed, it will become much easily to persuade other publishers who’ve been indulging in this shady practice to mend their ways, too.