Regular readers will remember that we followed up our 1VPC talk about what it means for a vertebra to be horizontal by writing it up as a paper, and doing it in the open. That manuscripts is now complete, and published as a preprint (Taylor and Wedel 2019).

Taylor and Wedel (2018: Figure 5). Haplocanthosaurus sp. MWC 8028, caudal vertebra ?3, in cross section, showing medial aspect of left side, cranial to the right, in three orientations. A. In “articular surfaces vertical” orientation (method 2 of this paper). The green line joins the dorsal and ventral margins of the caudal articular surface, and is oriented vertically; the red line joins the dorsal and ventral margins of the cranial articular surface, and is nearly but not exactly vertical, instead inclining slightly forwards. B. In “neural canal horizontal” orientation (method 3 of this paper). The green line joins the cranial and caudal margins of the floor of the neural canal, and is oriented horizontally; the red line joins the cranial and caudal margins of the roof of the neural canal, and is close to horizontal but inclined upwards. C. In “similarity in articulation” orientation (method 4 of this paper). Two copies of the same vertebra, held in the same orientation, are articulated optimally, then the group is rotated until the two are level. The green line connects the uppermost point of the prezygapophyseal rami of the two copies, and is horizontal; but a horizontal line could join the two copies of any point. It happens that for this vertebra methods 3 and 4 (parts B and C of this illustration) give very similar results, but this is accidental.

The preprint has all the illustrations and their captions at the back of the PDF. If you prefer to have them inline in the text, where they’re referenced — and who wouldn’t? — you can download a better version of the manuscript from the GitHub archive.

By the way, you may have noticed that what started our written in Markdown has mutated into an MS-Word document. Why? Well, because journals won’t accept submissions in Markdown. It eas a tedious and error-prone job to convert the Markdown into MS-Word, and not one I am keen to repeat. For this reason, I think I am unlikely to use Markdown again for papers.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2019. What do we mean by the directions “cranial” and “caudal” on a vertebra? PeerJ PrePrints 7:e27437v2. doi:10.7287/peerj.preprints.27437v2

Hey! Do you like what we’re doing?

If you do, you might like to think about becoming a patron, making a small monthly donation to SV-POW!. We will use your money to fund research trips; if you donate $5 per month (or more), we will formally acknowledge you in papers that result from research trips that you helped to fund.

 

I’ll have more to say about both of these in the near future, but for now suffice it to say that this (link):

and this (link):

are available for your perusal. Not just the abstracts, but the slide decks as well, just as Mike did for his talk on Jensen’s Big Three sauropods (link).

Jessie is also posting her talk a few slides at a time on her Instagram, with some helpful unpacking, so that’s worth a look even if you have the slides already. That stream of posts starts here.

My talk (Taylor and Wedel 2019) from this year’s SVPCA is up!

The talks were not recorded live (at least, if they were, it’s a closely guarded secret). But while it was fresh in my mind, I did a screencast of my own, and posted it on YouTube (CC By). I had to learn how to do this for my 1PVC presentation on vertebral orientation, and it’s surprisingly straightforward on a Mac, so I’ve struck while the iron is hot.

For the conference, I spoke very quickly and omitted some details to squeeze the talk into a 20-minute slot. In this version, I go a bit slower and make some effort to ensure it’s intelligible to an intelligent layman. That’s why it runs closer to half an hour. I hope you’ll find it worth your time.

References

As Mike noted in the last post, many (all?) of the talks from SVPCA 2018 are up on YouTube. Apparently this has been the case for a long time, maybe most of the past year, and I just didn’t know. But I’m glad I do now, because I can encourage you to take 14 minutes and watch Jessie Atterholt’s talk on air spaces inside the neural canal in birds and other archosaurs:

This will not only be interesting in itself — assuming you are interested in pneumaticity, animals, or just how weird the natural world can be at times — but it will be good homework for the Atterholt and Wedel talk at this year’s SVPCA. That talk, also to be delivered by Jessie, will be on a different weird thing about archosaur neural canals, and one that neither of us have yapped about yet on social media.

Here’s the full rundown of talks by SV-POW!sketeers and affiliates at this year’s SVPCA:

Thursday, September 12

  • 11:00-11:20 – Vicki Wedel, “Validating the use of Dental Cementum Increment Analysis to determine season-at-death in humans and other mammals”
  • 11:20-11:40 – Matt Wedel, “How to make new discoveries in (human) anatomy”

Friday, September 13

  • 10:10-10:30 – Mike Taylor and Matt Wedel, “The past, present and future of Jensen’s Big Three sauropods”
  • 15:00-15:20 – Jessie Atterholt and Matt Wedel, “Neural canal ridges: a novel osteological correlate of post-cranial neurology in dinosaurs”

Presumably most or all of these will become PeerJ Preprints in time, just like Mike’s and my presentations from SVPCA 2017 (link, link) and Jessie’s presentation last year (link). I haven’t heard anything yet about livestreaming or recording of the talks this year — fingers firmly crossed.

Anyway, we look forward to seeing at least some of you at SVPCA or at other points on our trip to England, and to having more stuff to talk about here in the near future. Stay tuned!

I’m a bit shocked to find it’s now more than five years since Robert Harington’s Scholarly Kitchen post Open Access: Fundamentals to Fundamentalists. I wrote a response in the comments, meaning to also post it here, but got distracted, and then half a decade passed. Here it is, finally. The indented parts are quotes from Harington.


I must admit to being rather tired of the fundamentalism that pervades discussions around open access policies and business models. On the one hand there are the advocates, and through the laws of conservation of energy, the equal and opposite reaction of anti-open access advocacy. There seems little room for rational debate about open access in the midst of such an antagonistic atmosphere.

It’s always a powerful rhetorical move to call your opponent a fundamentalist. It’s also a lazy one. It absolves you from the tedious responsibility of bothering to understand what the opponent actually wants: just dismiss him has a fundamentalist and call it done. I’d hope we’re better than that. At best, this seems like a fine demonstration of the principle that “there seems little room for rational debate about open access in the midst of such an antagonistic atmosphere”.

You want a rational debate? You want to talk about fundamentals? Fine, let’s do that. Here is the most fundamental question of all: what is research for? Our answer to this will profoundly affect every stance we adopt regarding publishing, OA, researcher evalution and more.

The greatest problem we have in discussing these issues is when person A assumes right off the bat that person B has the same answer to that fundamental question, and is then surprised to find that B disagrees over numerous implementation details. All those details flow from the fundamental mismatch. A and B are literally trying to solve two different problems — no wonder they can’t agree on the solution!

So what is research for? Here are three possible answers.

A. Some people believe (or maybe I should say assume) that research is for the world — for the betterment of the lot of society as a whole, the eradication of illness, the understanding of the environment, and generally the benefit of humanity. As pleasant side-effects, it also feeds publishing businesses and advances researchers’ careers.

B. Some people believe (or assume) that research is primarily for the benefit of the economy: that the principle purpose of the whole process is the financial benefit that accrues to publishers and related professions. As pleasant side-effects, it also advances the world’s knowledge and advances researchers’ careers.

C. Some people believe (or assume, or at least give the impression of assuming) that research is mostly about the careers of researchers — about giving them a way to prove their merit and advance up the career ladder. As pleasant side-effects, it also advances the world’s knowledge and feeds publishing businesses.

All of these fundamental positions exist. (There may be others that I missed.) We could probably all classify various individuals into these groups (but I’ll resist the temptation to throw in examples, as that would surely result in an epic sidetrack).

Notice that one can’t reach one of these three positions by any amount of thought about what happens within the research/publication ecosystem. It’s more fundamental than that. That decision has to come from somewhere outside. For example, my own position is no secret: I am an “A”, and the reason is because I feel it follows from the Golden Rule (“Do to others as you would have them do to you”, Luke 6:31) — probably the most universally agreed ethical principle in any religion (and among those who profess none).

And so when Robert Harrington asks:

The real debate here is to understand more about the motivations and needs of a researcher, who may or may not be funded directly. What is the best business model that will allow a researcher to publish work effectively and allow readers access to that work?

That is really two ——quite separate questions that may have completely different answers: 1, what business model will allow a researcher to publish work effectively?; and 2, what business model will allow readers access to that work? If you are an “A”, you’ll care most about the second question; if you’re a “C” you’ll care about the first question; and if you’re a “B” you might still be thinking about the business model mentioned at the start of the question.

It’s fruitless to expect “A”s, “B”c and “C”s to agree on an answer to a question when each group is hearing a different question.

Here’s another example:

The real story here is that the rights and desires of academics are being represented by organizations that do not reflect their needs, and that perhaps do not even understanding them. There is a form of fundamentalism that dictates to academics that this is what you need; just let us lead the way and we will make things right for you.

This statement suggests a “C” mindset: that the rights and desires of researchers are paramount. But if the organisations in question are “A”s (as for example you’d expect the Alliance for Taxpayer Access or RCUK to be), then this complaint is a non-issue. Of course they don’t reflect researchers’ desires — that’s not what they’re there for. They reflect the needs of broader society (which are often aligned with those of researchers, but by no means always).

That’s not a bug. That’s a feature.

And similarly:

I would suggest that there is nothing fundamentally wrong with a subscription model.

This may be true for “B”s (who might prefer the subscription model because they think it yields the most revenue) and for “C”s (who might want to place their work in a specific paywalled journal that is well regarded in their field). But it’s much less likely for “A”s, who see great public benefit in free access, and conversely great harm in arbitrary barriers.

So there you go. Fundamentals.

 

 

I’ve been on vacation for a couple of weeks, hence the radio silence here at SV-POW! after the flood of Supersaurus posts and Matt’s new paper on aberrant nerves in human legs.

But the world has not stood still in my absence (how rude of it!) and one of the more significant things to have happened in this time is the announcement of RVHost, a hosted end-to-end scholarly publishing solution provided by River Valley Technologies.

It’s not so long ago that scholarly publishing remained technically difficult, and could only be achieved by using expensive proprietary technologies. Journals that rolled their own tended to make rather creaky systems that were not much fun to use — and come to that, the commercial systems were mostly pretty wretched, too. But now there are a lot more options. I’ve surely missed some, but among the low-cost, open-oriented hosted publishing solutions out there are:

These platforms (and others that I have no doubt missed — do remind me, in the comments) provide a range of service levels and price points so that every journal should be able to find a service that suits it. Editorial boards wanting to move away from exploitative publishers have all sorts of options these days, and it’s ever easier to go open access.

Since the rather surprising apppointment of Mike Eisen as the new Editor-in-Chief of eLife, I’ve found myself thinking about this journal again. At its inception in 2012, it was explicitly intended to be the open-access alternative that would “compete with publishing powerhouses such as Nature, Science and Cell“.

A few years ago, in an article about eLife‘s £25M additional cash injection from its three original funders, Nature News reported a doubling down on its original mission, citing an interview with founding Editor-in-Chief Randy Schekman:

But it won’t, he says, establish other open-access journals that accept more papers and have lower selectivity — a strategy that some organizations, such as the Public Library of Science, or PLoS, has turned to in an attempt to shore up finances. “We have no interest in creating other lesser journals with lower standards,” he says.

This makes no sense to me.

Four years ago, I was already saying “It’s a real shame that the eLife people have fallen into the impact-chasing trap and show no interest in running an eLife megajournals.” Now that eLife’s funding is running out and it’s having to introduce APCs, it makes even less sense to refuse to run a review-for-correctness-only journal alongside its flagship.

I do see why some people think it’s desirable to have an OA alternative to Science and Nature. But I can’t understand at all why they won’t add a second, non-selective journal — an eLIFE ONE, if you will — and automatically propagate articles to it that are judged “sound but dull” at eLIFE proper (or eLIFE Gold, as they may want to rename it). Way back in I think 2012 I spoke separately to Randy Schekman and executive director Mark Patterson about this: both of them were completely uninterested then, and it seems that’s still the case.

This is why Mike Eisen’s appointment is such a surprise. In a recent interview regarding this appointment, he commented “Our addiction to high-impact factor journals poisons hiring and funding decisions, and distorts the research process” — which I agree with 100%. But then why has he taken on a role in a journal that perpetuates that addiction?

We can only hope that he plans to change it from within, and that eLife ONE is lurking just beyond the horizon.

 

Appendix

This isn’t a new drum for me to be banging. Way back when eLife launched in 2012, I left a comment on its Reviewer’s Charter. Seven years on, all the comments seem to have vanished (I hate it when that happens), but happily for posterity I saved what I wrote. Here it is:

This charter is an excellent start. But I would like to see a Guideline Zero that lays out what the purposes (plural) of peer-review are. I see three very distinct purposes, and much of the frustration with peer-review comes from reviews that blur these.

1. Assessing whether the paper is sound, i.e. does it express a coherent argument that is backed up by data?

2. Assessing “importance” or “impact”, i.e. is the paper likely to be seen as a significant advance in its field, and to gather many citations?

3. Helping the author improve the paper by constructively suggesting changes that can be made without altering the fundamental nature of the paper.

All of these are important contributions, but they are quite separate and should be kept so. In category 3, for example, if a reviewer suggests that a sentence would be easier to parse if changed around, that should certainly not affect the gatekeeping decisions in categories 1 and 2.

PLoS ONE has shown the importance of separating caterories 1 and 2. In that journal, and those that now emulate it, the “impact” criterion is explicitly ignored, and all good papers are published however important or unimportant they are considered to be. (This means, among other things, that replication studies are welcome.)

This inclusive strategy is not appropriate for all journals — I understand that eLife is actively aiming to reject most submissions on “impact” criteria, in the hope of attaining prestige similar to that of Science and Nature. But even in journals that evaluate for impact, it’s important to separate the two assessment criteria. One important practical implication of this separation is that a subsequent high-volume “eLife ONE” journal could publish all eLife submissions that passed criterion 1 but failed criterion 2 without the need for further review.

I don’t think there was ever a response to that comment back in the day (though I can’t be certain due to the comments’ having vanished.) I hope that’s set to change under the new regime.