As I was clearing out some clutter, I came across this hand-written list of projects that I wanted to get completed:

old-poop

Sadly, I didn’t put a date on the list. But I can estimate it as before 2013 (because of the reference of Why giraffes have short necks as a project still to be completed) but after 2011 (because the no necks for sex project is not listed.) So it’s probably from 2012, which means four years have passed since I wrote that list.

What have I achieved in that time? Not nearly enough.

  • ICZN checklist refers to the short set of name-a-new-animal instructions that I was crowdsourcing here on SV-POW!. We started this on 10 February 2011, had it nearly done less than two weeks later, then … stalled for no reason at all. Eighteen months later, the ICZN changed to allow electronic publication, instantly rendering the in-progress document obsolete. Now I don’t know whether to kill the project or update it. Should have just published it in 2011.
  • WTH (Why giraffes have short necks) was published in PeerJ, hurrah!
  • PBJ stands for “Pneumatic Butt on a JANGO“. It was published in the PLOS ONE’s sauropod gigantism collection, hurrah!
  • Archbishop is of course the Natural History Museum’s Tendaguru brachiosaur, which I have been planning to describe since 2004. Still not done. Shameful.
  • Apatosaurus” minimus is a descriptive project. Real work has been done, and I gave a talk about it at SVPCA in 2012. Not much progress since then. Lame.
  • Astrolembospondylus refers to the starship-shaped cervical vertebra of the Barosaurus holotype YPM 429. That project has seen daylight as both an SVPCA talk in 2013 and a PeerJ Preprint — which is great. But once the reviews were in, we should have turned it around and got it submitted as a proper paper. For some reason, we didn’t, and this project, too, is in limbo. Weak.
  • ODP is the Open Dinosaur Project. Do not get me started on that train-wreck.
  • Neck cartilage: giraffe, ostrich, croc. This refers to a comparative dissection project to determine whether sauropods had intervertebral discs. I proposed it as a Masters project twice, but no-one bit; then I offered to up to anyone who wanted it on SV-POW!, with the same (lack of) result. Looks like it’s not sexy enough for anyone to invest the time into, which is a shame because it’s important.
  • Limb cartilage limiting mass refers to the second talk I ever gave, at Progressive Palaeontology in 2004. It’s ridiculous that I never wrote this up. Ridiculous.
  • Haemodynamics refers to Matt’s and my looong-running plans to write up our thoughts about Roger Seymour’s work that suggests blood-circulation issues prevented sauropods from having habitually erect necks. I’m going to blame Matt for this one’s lack of progress. (Not because he’s any more to blame than I am — just because I’ve been taking all the blame so far, and I want to share it around a bit.)
  • Immature sauropods, pop. dynamics. Parts of this made it out in the recent Hone, Farke, and Wedel (2016) paper on dinosaur ontogenetic stages. Not as much as I’d have liked to see, but enough to make a dedicated paper about this not really feasible.
  • Ostrich skull atlas. I made lovely multi-view photos of nearly every bone in my ostrich skull. My plan was, and sort of still is, to publish them all in a text-light paper. No progress on this. I still have a few bones left to photograph, and may need to completely disarticulate the mandible before I can do that.
  • Wealden sauropod vert. analysis. I’d planned, going back to the earliest posts on this blog, to properly redescribe and analyse the many fascinating isolated sauropod vertebrae of the Wealden Formation. This is another one that I gave a ProgPal talk about before getting distracted. Not sure if this will ever happen: I’m still very interested in it, but even more interested in other things.
  • Fossils explained is a series of articles for geologists, explaining various fossil groups in laymen’s terms (here is an example). Darren’s done half a dozen of them. Once many years ago I expressed an interest in doing one on sauropods, and the editor liked the idea. Then … nothing. My bad.
  • Ventral compression bracing is a section that, heaven help us, we somehow decided we should remove from Why Giraffes Have Short Necks and make into its own paper. It got stalled on some croc-dissection work that Matt was doing with his student Vanessa and is now in limbo.

That’s fifteen projects that I had on the go, or planned to work on, four years ago. I make it that two of them (WTH and PBJ) have been published and one (Barosaurus) has made it as far as a the preprint stage. Three more are probably dead for various reasons, and that leaves nine where I’ve made woefully inadequate progress — in most cases, none at all.

Meanwhile, needless to say, I’ve added a bunch more projects to my To Do list since I scribbled this one out. (And to be fair to me, I’ve got a few other projects out in this time that weren’t mentioned in the note: neural spine bifurcation as Matt’s co-author, lead author on intervertebral cartilage and sole on its addendum; I slipped in as last author on Haestasaurus; and I wrote the SPARC briefing paper on evaluating researchers.)

What does all this mean?

I don’t know. Some of those no-progress yet projects are still very much alive in my mind — notably the Archbishop, of course. Others might never happen. Some are 90% done and I should just push them out the door.

One moral of this story is that I shouldn’t have burned 250 hours since Christmas playing Skyrim. But maybe a more constructive one is that it’s just really hard to know what projects are going to take wings and fly and which aren’t. My guess — and I’d love to hear some confirmation or denial in the comments — is that most researchers have a similar palette of half-done projects floating around their hindbrains, continually projecting low-level guilt rays. I guess I long ago gave up on the idea that I would ever finish all my projects, because the only way that would happen would be if I never started any more new ones — and that ain’t gonna happen.

Oh, here’s a better moral: ideas to work on are cheap. In fact Matt and I have so darned many that we sometimes just give them away here on SV-POW!. (I am pretty certain that there are lots more similar project-giveaway posts somewhere here, but we didn’t tag them at the time.)

Ideas are cheap; actual work is hard.

It’s hard to believe it’s been nearly seven years since the “resolution”, if you want to call it that, of Aetogate, the aetosaur plagiarism-and-claim-jumping scandal.

I was contacted privately today by someone wanting to know if I had copies of the SVP’s documents published in response to this. I didn’t — and the documents are hard to find since they have been moved at least twice from their original addresses on the SVP site. They can no longer be found by navigating that site — at least, not by me or my correspondent. (Searching doesn’t help either.)

But by suitable application of Google-fu I did manage to dig out the documents, in their third (at least) home. So I thought it would be useful to make permanent copies here, in case they vanish completely next time the SVP changes things around. Here they are:

  1. Statement from the Executive Committee about the allegations of unethical conduct from J. Martz, W. Parker, M. Taylor and M. Wedel against S. Lucas, A. Hunt, A. Heckert, and J. Spielmann.
    [SVP copy] [local copy]
  2. Best practices from the Ethics Education Committee regarding research, publication, and museum work.
    [SVP copy] [local copy]
  3. Addendum to Executive Committee’s Final Statement Concerning Allegations From Martz, Parker, Wedel and Taylor.
    [SVP copy] [local copy]

(In case anyone’s forgotten, I was not impressed by these documents. At all.)

 

Short post today. Go and read this paper: Academic urban legends (Rekdal 2014). It’s open access, and an easy and fascinating read. It unfolds a tale of good intentions gone wrong, a chain of failure, illustrating an important single crucial point of academic behaviour: read what you cite.

References

Rekdal, Ole Bjørn. 2014. Academic urban legends. Social Studies of Science 44(4):638-654. doi: 10.1177/0306312714535679

 

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:

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.

I replied:

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.

  1. 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.
  2. 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?
  3. 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:

  1. 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.
  2. 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.

Illustration talk slide 47

Illustration talk slide 48

Illustration talk slide 49

Illustration talk slide 50

That last one really hurts. Here’s the original image, which should have gone in the paper with the interpretive trace next to it rather than on top of it:

Sauroposeidon C6-C7 scout

The rest of the series.

Papers referenced in these slides:

I was astonished yesterday to read Understanding and addressing research misconduct, written by Linda Lavelle, Elsevier’s General Counsel, and apparently a specialist in publication ethics:

While uncredited text constitutes copyright infringement (plagiarism) in most cases, it is not copyright infringement to use the ideas of another. The amount of text that constitutes plagiarism versus ‘fair use’ is also uncertain — under the copyright law, this is a multi-prong test.

So here (right in the first paragraph of Lavelle’s article) we see copyright infringement equated with plagiarism. And then, for good measure, the confusion is hammered home by the depiction of fair use (a defence against accusations of copyright violation) depicted as a defence against accusations of plagiarism.

This is flatly wrong. Plagiarism and copyright violation are not the same thing. Not even close.

First, plagiarism is a violation of academic norms but not illegal; copyright violation is illegal, but in truth pretty ubiquitous in academia. (Where did you get that PDF?)

Second, plagiarism is an offence against the author, while copyright violation is an offence against the copyright holder. In traditional academic publishing, they are usually not the same person, due to the ubiquity of copyright transfer agreements (CTAs).

Third, plagiarism applies when ideas are copied, whereas copyright violation occurs only when a specific fixed expression (e.g. sequence of words) is copied.

Fourth, avoiding plagiarism is about properly apportioning intellectual credit, whereas copyright is about maintaining revenue streams.

Let’s consider four cases (with good outcomes is green and bad ones in red):

  1. I copy big chunks of Jeff Wilson’s (2002) sauropod phylogeny paper (which is copyright the Linnean Society of London) and paste it into my own new paper without attribution. This is both plagiarism against Wilson and copyright violation against the Linnean Society.
  2. I copy big chunks of Wilson’s paper and paste it into mine, attributing it to him. This is not plagiarism, but copyright violation against the Linnean Society.
  3. I copy big chunks of Rigg’s (1904) Brachiosaurus monograph (which is out of copyright and in the public domain) into my own new paper without attribution. This is plagiarism against Riggs, but not copyright violation.
  4. I copy big chunks of Rigg’s paper and paste it into mine with attribution. This is neither plagiarism nor copyright violation.

Plagiarism is about the failure to properly attribute the authorship of copied material (whether copies of ideas or of text or images). Copyright violation is about failure to pay for the use of the material.

Which of the two issues you care more about will depend on whether you’re in a situation where intellectual credit or money is more important — in other words, whether you’re an author or a copyright holder. For this reason, researchers tend to care deeply when someone plagiarises their work but to be perfectly happy for people to violate copyright by distributing copies of their papers. Whereas publishers, who have no authorship contribution to defend, care deeply about copyright violation.

One of the great things about the Creative Commons Attribution Licence (CC By) is that it effectively makes plagiarism illegal. It requires that attribution be maintained as a condition of the licence; so if attribution is absent, the licence does not pertain; which means the plagiariser’s use of the work is not covered by it. And that means it’s copyright violation. It’s a neat bit of legal ju-jitsu.

References

  • Riggs, Elmer S. 1904. Structure and relationships of opisthocoelian dinosaurs. Part II, the Brachiosauridae. Field Columbian Museum, Geological Series 2:229-247, plus plates LXXI-LXXV.
  • Wilson, Jeffrey A. 2002. Sauropod dinosaur phylogeny: critique and cladistic analysis. Zoological Journal of the Linnean Society 136:217-276.

What is an ad-hominem attack?

September 4, 2013

I recently handled the revisions on a paper that hopefully will be in press very soon. One of the review comments was “Be very careful not to make ad hominem attacks”.

I was a bit surprised to see that — I wasn’t aware that I’d made any — so I went back over the manuscript, and sure enough, there were no ad homs in there.

There was criticism, though, and I think that’s what the reviewer meant.

Folks, “ad hominem” has a specific meaning. An “ad hominem attack” doesn’t just mean criticising something strongly, it means criticising the author rather than the work. The phrase is Latin for “to the man”. Here’s a pair of examples:

  • “This paper by Wedel is terrible, because the data don’t support the conclusion” — not ad hominem.
  • “Wedel is a terrible scientist, so this paper can’t be trusted” — ad hominem.

What’s wrong with ad hominem criticism? Simply, it’s irrelevant to evaluation of the paper being reviewed. It doesn’t matter (to me as a scientist) whether Wedel strangles small defenceless animals for pleasure in his spare time; what matters is the quality of his work.

Note that ad hominems can also be positive — and they are just as useless there. Here’s another pair of examples:

  • “I recommend publication of Naish’s paper because his work is explained carefully and in detail” — not ad hominem.
  • “I recommend publication of Naish’s paper because he is a careful and detailed worker” — ad hominem.

It makes no difference whether Naish is a careful and detailed worker, or if he always buys his wife flowers on their anniversary, or even if he has a track-record of careful and detailed work. What matters is whether this paper, the one I’m reviewing, is good. That’s all.

As it happens the very first peer-review I ever received — for the paper that eventually became Taylor and Naish (2005) on diplodocoid phylogenetic nomenclature — contained a classic ad hominem, which I’ll go ahead and quote:

It seems to me perfectly reasonable to expect revisers of a major clade to have some prior experience/expertise in the group or in phylogenetic taxonomy before presenting what is intended to be the definitive phylogenetic taxonomy of that group. I do not wish to demean the capabilities of either author – certainly Naish’s “Dinosaurs of the Isle of Wight” is a praiseworthy and useful publication in my opinion – but I question whether he and Taylor can meet their own desiderata of presenting a revised nomenclature that balances elegance, consistency, and stability.

You see what’s happening here? The reviewer was not reviewing the paper, but the authors. There was no need for him or her to question whether we could meet our desiderata: he or she could just have read the manuscript and found out.

(Happy ending: that paper was rejected at the journal we first sent it to, but published at PaleoBios in revised form, and bizarrely is my equal third most-cited paper. I never saw that coming.)

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