If you check out the Shiny Digital Future page on this site, where we write about scholarly publishing, open access, open data and other such matters, you will see the following:

  • 2009: 9 posts
  • 2010: 5 posts
  • 2011: 9 posts
  • 2012: 116 posts! Woah!
  • 2013: 75 posts
  • 2014: 34 posts
  • 2015: 31 posts
  • 2016, up until the end of June: 34 posts
  • 2016, July onwards: 8 posts
  • 2017: 12 posts
  • 2018: 6 posts
  • 2019: 4 posts
  • 2020: nothing yet.

In four and a half years up to the end of June, Matt and I (but mostly I) posted 290 times in the Shiny Digital Future, for an average of 64.4 posts a year (one every 5.6 days). Since then we’ve posted 30 times in a bit more than three and a half years, for an average of 8.6 posts a year (one every 42.6 days).

Shiny Digital Future posts by year (2016 split into halves)

Something happened half way through 2016 that cut my Shiny Digital Future productivity to 13% of what it was before. (And, no, I wasn’t bought off by Elsevier.)

Here’s another funny thing. My eldest son was taking his A-levels in the summer of 2016. He had got so good at the Core 4 paper in maths that he was reliably scoring 95–100% on every past paper. He took the actual exam on the morning of 24th June, and scored 65% — a mark so low that it prevented him getting an A* grade.

Well, we all know what happened on the 23rd of June 2016: the Brexit referendum. I know that opinions differ on the desirability of Brexit, but for our family it was emotionally devastating. It’s the reason Dan was so knocked sideways that he botched his Core 4 paper. It’s hung over us all to a greater or lesser extent ever since, and it’s only with the recent triumph of the “Conservative” Party1 in the 2019 General Election that I’ve finally attained the ability to think of it as Somebody Else’s Problem. There is something gloriously liberating about being so comprehensively beaten that you can just give up.

I’m not going to rehearse all the reasons why Brexit is awful — not now, not ever again. (If you have a taste for that kind of thing, I recommend Chris Grey’s Brexit Blog, which is dispassionate, informed and forensic.) I’m not going to follow Brexit commentators on Twitter, and read all the desperately depressing analysis they highlight. I’m certainly not going to blog about it myself any more. More importantly, I’m not going to let the ongoing disintegration of my country dominate my mind or my emotions. I’m walking away: because obviously absolutely nothing I say or do about it can make the slightest bit of difference.

But there is an area of policy where I can hope to make some small difference, and that is of course open science — including but not limited to open access, open data, open reviewing and how research is evaluated. That’s where my political energy should have been going for the last three years, and it’s where that energy will be going from now on.

Because so much is happening in this space right now, and we need to be thinking about it and writing about it! Ludicrously, we’ve never even written anything about Plan S even though it’s nearly eighteen months old. But so much more is going on:

Each of these developments merits its own post and discussion, and I’m sorry I don’t have the energy to do that right now.

What I offer instead is an apology for letting my energy by stolen for so long by such a stupid issue; and a promise to refocus in 2020. I’ll start shortly by writing up the R2R debate that I was involved in on Monday, on the proposition “The venue of its publication tells us nothing useful about the quality of a paper”.

 


1The more right-wing of the two large political parties in the UK is called the Conservative party, and traditionally it has adhered to small-c conservative ideals. But at the moment, it’s the exact opposite of what it says on the tin: it’s been hijacked by a radical movement that, contra Chesterton’s Fence, wants to smash everything up in the hope that whatever emerges from the chaos will be better than what we have now. It may be exciting; it may even (who knows?) prove to be right, in the end2. What it ain’t, is conversative.

2Spoiler: it won’t.

 

Matt and I are about to submit a paper. One of the journals we considered — and would have really liked in many respects — turned out to use the CC By-NC-SA license. This is a a very well-intentioned licence that allows free use except for commercial purposes, and which imposes the same licence on all derivative works. While that sounds good, there are solid reasons to prefer the simpler CC By licence. I wrote to the journal in question advocating a switch to CC By, and then I thought the reasoning might be of broader interest. So here’s what I wrote, lightly edited.


First, CC By neatly expresses the one requirement all academics have of their work: that they get credit for it. When we publish papers, we are happy for them to be freely distributed, but also want people to build on them, re-using parts in whatever way helps, provided we’re credited — and that is exactly what CC By enables.

Second, because of this, many funders that require the work their grantees do to be published open access specifically require the CC By licence, in the expectation that it will provide the greatest societal benefit in exchange for their investment. Most famously, this is the case for the Gates Foundation (the largest private foundation in the world), but for a partial list of the many other funders with this policy, see https://www.springernature.com/gp/open-research/funding/funders-requiring-cc-by-for-articles — funders whose grantees, as things stand, are not allowed to publish their work in your journal.

Third, CC By is almost universal among well established and respected open-access journals, including all the PLOS journals, PeerJ, the BioMed Central journals, the Hindawi journals, eLIFE, Nature’s Scientific Reports, and palaeo journals such as Acta Palaeontologica Polonica and Palarch’s Journal of Vertebrate Paleontology. This is important because CC By-licenced journals can’t freely use material published under more restrictive licences such as your journal’s CC By-NC-SA. Instead, authors of such articles must labouriously seek exemptions from the copyright holders of the material they wish to reuse or adapt.

Fourth and last, other online resources also use CC By (or optionally CC By-SA in the case of Wikipedia), which means that, while material from PLOS ONE, Scientific Reports et al. can be freely used in Wikipedia articles, text and illustrations from articles in your journal cannot, limiting its use in outreach. Similarly, even on our own palaeontology blog, we would have concerns about using By-NC-SA materials as we use Patreon to solicit donations and our blog is arguably therefore commercial. (Part of the problem with the NC clause is that there is no rigorous definition of “commercial”.)

For all these reasons, we believe that your journal would better serve its authors, its readers, the academic community and broader society if its articles were published under the CC By licence. We hope that, if you agree, you are able to some point to help the journal make this transition. And if there’s anything Matt or I can do to assist that process, we’ll be happy to.

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.

Back in 2005, three years before their paper on the WDC Supersaurus known as Jimbo was published, Lovelace at al. presented their work as a poster at the annual SVP meeting. The abstract for that poster appeared, as usual, in the abstracts book that came as a supplement to JVP 25 issue 3. But the poster itself was never published — which is a shame, as it contains some useful images that didn’t make it into the descriptive paper (Lovelace et al. 2008).

With Dave and Scott’s blessing, here it is! Click through for full resolution, of course.

And here’s the abstract as it appeared in print (Lovelace et al. 2005):

REVISED OSTEOLOGY OF SUPERSAURUS VIVIANAE

LOVELACE, David, HARTMAN, Scott, WAHL, William, Wyoming Dinosaur Center, Thermopolis, WY

A second, and more complete, associated specimen of Supersaurus vivianae (WDC-DMJ021) was discovered in the Morrison Formation of east-central Wyoming in a single sauropod locality. The skeleton provides a more complete picture of the osteology of S. vivianae, including a surprising number of apatosaurine characteristics. The caudals have heart shaped centra that lack a ventral longitudinal hollow, and the rectangular distal neural spines of the anterior caudals are mediolaterally expanded similar to Apatosaurus excelsus. The centra of the anterior caudals are procoelous as in other diplodocids, but the posterior ball is very weakly pronounced. The robusticity of the tibiae and fibulae are intermediate between Apatosaurus and diplodocines. The cervical vertebrae demonstrate classic diplodocine elongation with an elongation index ranging from 4 to 7.5. All 7 of the new cervicals have a centrum length that exceeds 1 meter. Mid-posterior cervicals are semicamellate at mid-centra near the pneumatic foramina. The dorsal vertebrae exhibit a high degree of elaboration on laminae, and extremely rugose pre and postspinal laminae. Costal elements are robust, with complex pneumatic innervations in the rib head. Although unknown in other diplodocids, early reports described pneumatic ribs in an A. excelsus; unfortunately the described specimen is unavailable.

Inclusion of lesser-known North American diplodocids such as Supersaurus, Seismosaurus and Suuwassea in phyolgenetic studies, may provide a framework for better understanding North American diplodocid evolution.

Many thanks to Dave and Scott for permission to share this important poster more widely. (Publish your posters, people! That option didn’t exist in 2005, but it does now!)

References

  • Lovelace, David M., Scott A. Hartman and William R. Wahl. 2005. Revised Osteology of Supersaurus vivanae (SVP poster). Journal of Vertebrate Paleontology 25(3):84A–85A.
  • Lovelace, David M., Scott A. Hartman and William R. Wahl. 2008. Morphology of a specimen of Supersaurus (Dinosauria, Sauropoda) from the Morrison Formation of Wyoming, and a re-evaluation of diplodocid phylogeny. Arquivos do Museu Nacional, Rio de Janeiro 65(4):527–544.

Now that Matt and I have blogged various thoughts about how to orient vertebra (part 1, part 2, relevant digression 1, relevant digression 2, part 3) and presented a talk on the subject at the 1st Palaeontological Virtual Congress, it’s time for us to strike while the iron is hot and write the paper.

Figure A. NHMUK PV R2095, the holotype dorsal vertebra of Xenoposiedon proneneukos in left lateral view. A. In the canonical orientation that has been used in illustrations in published papers (Taylor and Naish 2007, Taylor 2018b, in blog-posts and on posters and mugs. B. Rotated 15° “backwards” (i.e. clockwise, with the dorsal portion displaced caudally), yielding a sub-vertical anterior margin in accordance the recommendation of Mannion (2018b). In both parts, the blue line indicates the horizontal axis, the green line indicates the vertical axis, and the red line indicates the slope of the neural arch as in Taylor (2018b: figure 3B, part 2). In part A, the slope (i.e. the angle between the red and green lines) is 35°; in part B, it is 20°.

We’re doing it totally in the open, on GitHub. You can always see the most recent version of the manuscript at https://github.com/MikeTaylor/palaeo-vo/blob/master/vo-manuscript.md and you can also review the history of its composition if you like — from trivial changes like substituting a true em-dash for a double hyphen, to significant additions like writing the introduction.

More than that, you can contribute! If you think there’s a mistake, or something missing that should be included, or if you just have a suggestion, you can file an issue on the project’s bug-tracker. If you’re feeling confident, you can go further and directly edit the manuscript. The result will be a tracked change that we’ll be notified of, and which we can accept into, or reject from, the master copy.

We hope, by making all this visible online, to demythologise the process of writing a paper. In a sense, there is no magic to it: you just start writing, do a section at a time, revise as you go, and eventually you’re done. It’s much like writing anything else. (Doing the referencing can make it much slower than regular writing, though!)

By the way, you may wonder why the illustration above is “Figure A” rather than “Figure 1”. In all my in-progress manuscripts, I just assign letters to each illustration as I add it, not worrying about ordering. Only when the manuscript is ready to be submitted do I take the order that the illustrations occur in (A, D, G, H, B, I, E, F, for example, with C having been dropped along the way) and replace them with consecutive numbers. So I save myself a lot of tedious and error-prone renumbering every time that, in the process of composition, I insert an illustration anywhere before the last existing one. This is really helpful when there are a lot of illustrations — as there tend to be in our papers, since they’re all in online-only open-access venues with no arbitrary limits. For example, our four co-authored papers from 2013 had a total of 69 illustrations (11 in Taylor and Wedel 2013a, 25 in Wedel and Taylor 2013a, 23 in Taylor and Wedel 2013b and 10 in Wedel and Taylor 2013b).

References

 

 

I know, I know — you never believed this day would come. And who could blame you? Nearly thirteen years after my 2005 SVPCA talkSweet Seventy-Five and Never Been Kissed, I am finally kicking the Archbishop descriptive work into gear. And I’m doing it in the open!

In the past, I’ve written my academic works in LibreOffice, submitted them for peer-review, and only allowed the world to see them after they’ve been revised, accepted and published. More recently, I’ve been using preprints to make my submitted drafts public before peer review. But there’s no compelling reason not to go more open than that, so I’ll be writing this paper out in the open, in a public GitHub repository than anyone can access. That also means anyone can file issues if they thing there’s something wrong or missing, and anyone can submit pull-requests if they have a correction to contribute.

I’ll be writing this paper in GitHub Flavoured Markdown so that it displays correctly right in the browser, and so that patches can be supported. That will make tables a bit more cumbersome, but it should be manageable.

Anyway, feel free to follow progress at https://github.com/MikeTaylor/palaeo-archbishop

The very very skeletal manuscript is at https://github.com/MikeTaylor/palaeo-archbishop/blob/master/archbishop-manuscript.md