Stop what you’re doing and go read Cameron Neylon’s blog. Specifically, read his new post, Improving on “Access to Research”.

Regular readers of SV-POW! might legitimately complain that my so-called advocacy consists mostly of whining about how rubbish things are. If you find that wearying (and I won’t blame you if you do), then read Cameron instead: he goes beyond critiquing what is, and sees what could be. Here is a key quote on this new post:

I did this on a rainy Saturday afternoon because I could, because it helped me learn a few things, and because it was fun. I’m one of tens or hundreds of thousands who could have done this, who might apply those skills to cleaning up the geocoding of species in research articles, or extracting chemical names, or phylogenetic trees, or finding new ways to understand the networks of influence in the research literature. I’m not going to ask for permission, I’m not going to go out of my way to get access, and I’m not going to build something I’m not allowed to share. A few dedicated individuals will tackle the permissions issues and the politics. The rest will just move on to the next interesting, and more accessible, puzzle.

Right! Open access is not about reducing subscription costs to libraries, or about  slicing away the absurd profits of the legacy publishers, or about a change to business models. It’s about doing new and exciting things that simply weren’t possible before.

 

Triceratops-dorsal-full

As a nice little perk–presumably for being early adopters and users of PeerJ–Mike and I each have been given a small number of referral codes, which will allow other folks to publish in PeerJ for free, as long as the papers are submitted by March 1, 2014. Here’s the scoop, straight from the monkey’s mouth:

If you have colleagues who would like to publish at PeerJ, then we want to give them the opportunity to try us out for free. Therefore, as a Published PeerJ Author, we are providing you with 5 unique ‘Referral Codes’ (which expire on March 1st) to distribute to your colleagues. Each code entitles the recipient to an entirely FREE PeerJ publication. They simply need to quote your referral code in the “Notes to Staff” field, when they submit to PeerJ, and as a result they will be able to publish that article for free (assuming it passes peer-review). Please disseminate these codes to colleagues who you feel will use them, but please make sure that they realize that this code is only valid for submissions made before March 1st, 2014.

Note that this is alongside the current promo wherein, if you post a preprint to PeerJ PrePrints (which is a smashing way of getting fast feedback, or at least it was for us), that manuscript can be published in PeerJ for free, as long as it is formally submitted before January 1, 2014. So if you can get the lead out before the end of the year and don’t have an allergy to fast feedback, you don’t actually need one of these codes.

Trex-dorsal-full

So. If you’re not a PeerJ member but you have a manuscript that you’d like to send to PeerJ before the first of next March, let us know and we’ll hook you up with a referral code. If you’re fairly sure you will use one but aren’t ready to ship yet, let me know and I’ll set one aside for you, with the proviso that I can give it away if we’re getting close to the deadline and you’re not realistically going to make it.

If we get more takers than codes, we’ll figure out some fair way of choosing who gets a code, probably randomly. I will be strongly biased toward people without big paychecks* or institutional support, like grad students and postdocs. (If you’re an undergrad, you can already publish in PeerJ for free, at least for the duration of the pilot program.) So if you’re a grad student or postdoc with a serious plan to get published, speak up and you’ll go to the head of the line. So if you let us know why getting a code would benefit you, you’re more likely to get one.

* I know in academia none of us think we have big paychecks, but compared to most grad students and postdocs, those of us with steady full-time employment are living the dream. I’m trying to reach the folks for whom the $99 lifetime membership fee would be a genuine impediment.

Smilodon-Nelson-Maniscalco-TOP-full

As is apparently the usual thing now when I’m writing about PeerJ and don’t have any images of my own queued up, I’ve borrowed images from Brant Bassam’s astoundingly cool BrantWorks.com to spice up this post. Explicit permission to reproduce the images with credit can be found on this page, which is coincidentally where these images themselves are from. Get on over there and prepare to lose some time looking at sweet stuff.

Update! Five more Golden Tickets available!

As noted in the comment below, Heinrich Mallison also has five PeerJ vouchers to distribute to deserving causes. So if Matt and I run out, the options are still open. Feel free to contact Heinrich directly or to go through us if you prefer.

 

The LSE Impact blog has a new post, Berlin 11 satellite conference encourages students and early stage researchers to influence shift towards Open Access. Thinking about this,  Jon Tennant (@Protohedgehog) just tweeted this important idea:

Would be nice to see a breakdown of OA vs non-OA publications based on career-stage of first author. Might be a wake-up call.

It would be very useful. It makes me think of Zen Faulkes’s important 2011 blog-post, What have you done lately that needed tenure?. We should be seeing the big push towards open access coming from senior academics who are established in their roles don’t need to scrabble around for jobs like early-career researchers. Yet my impression is that in fact early-career researchers are doing a lot of the pro-open heavy lifting.

Is that impression true?

We should find out.

Here’s one possible experimental design: take a random sample of 100 Ph.D students, 100 post-docs, 100 early-career researchers in tenure-track jobs and 100 tenured researchers. For each of them, analyse their last ten years of publications and determine what proportion are paywalled, what proportion are free to read (e,g, on arXiv or in an all-rights-reserved IR), and what proportion are true (BOAI-compliant) open access.

An alternative approach would be to randomly sample 1000 open-access papers (from PLOS and BMC journals, for example), and 1000 paywalled papers (from Elsevier and Springer, say) and find the career-stage of their authors. I’m not sure which approach would be better?

Who is going to do this?

I think it would be a nice, tractable first project for someone who wants to get into academic research but hasn’t previously published. It would be hugely useful, and I’m guessing widely cited. Does anyone fancy it?

Update

Georg Walther has started a hackpad about this nascent project. Since Jon “Protohedgehog” Tennant has now tweeted about it, I assume it’s OK to publicise. If you’re interested, feel free to leap in!

I was very pleased, on checking my email this morning, to see that my and Matt’s new paper, The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines, is now up as a PeerJ preprint!

Figure6-vertebra-q-composite

Taylor and Wedel (2013b: figure 6). Barosaurus lentus holotype YPM 429, Vertebra Q (C?13). Top row: left ventrolateral view. Middle row, from left to right: anterior view, with ventral to the right; ventral view; posterior view, with ventral to the left. Bottom row: right lateral view, inverted. Inset shows diapophyseal facet on right side of vertebra, indicating that the cervical ribs were unfused in this individual despite its great size. Note the broad, flat prezygapophyseal facet visible in anterior view.

I was pleased partly because of the very quick work on PeerJ’s part. I submitted the preprint at 1:22am last night, then went to bed. Almost immediately I got an automatic email from PeerJ saying:

Thank you for submitting your manuscript, “The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines” (#2013:09:838:0:0:CHECK:P) – it has now been received by PeerJ PrePrints.

Next, it will be checked by PeerJ staff, who will notify you if any alterations are required to the manuscript or accompanying files.

If the PrePrint successfully passes these checks, it will be made public.

You will receive notification by email at each stage of this process; you can also check the status of your manuscript at any time.

Lots to like here: the quickness of the response, the promise of automatic email updates, and the one-click link to check on progress (as opposed to the usual maze of Manuscript Central options to navigate).

Sure enough, a couple of hours later the next automatic email arrived, telling me that Matt had accepted PeerJ’s email invitation to be recognised as the co-author of the submission.

And one hour ago, just as I was crawling out of bed, I got the notification that the preprint is up. That simple.

xx

Taylor and Wedel (2013b: Figure 9). Partial reconstruction of the Barosaurus lentus holotype YPM 429, cervical vertebra R, approximating its undamaged state by allowing for dorsoventral crushing, shearing and loss of some extremities. Anterior and posterior views scaled to 125% of uncorrected width and 80% of uncorrected height. Dorsal view scaled to 80% of uncorrected height; condyle moved forward and cotyle scaled to 50% of uncorrected width to allow for shearing. Lateral view scaled to 125% of uncorrected height, and sheared backwards 15 degrees. Metapophyses and postzygapophyses drawn in multiple views based on vertebrae Q and S and AMNH 6341 material.

I’m also pleased because we managed to get this baby written so quickly. It started life as our talk at SVPCA in Edinburgh (Taylor and Wedel 2013a), which we delivered 25 days ago having put it together mostly in a few days running up to the conference — so it’s zero to sixty in less than a month. Every year we promise ourselves that we’ll write up our talks, and we never seem to get around to it, but this year I started writing on the train back from Edinburgh. By the time I got home I had enough of a hunk of text to keep me working on it, and so we were able to push through in what, for us, is record time.

Now here’s what we’d like:

We want this paper’s time as a preprint to be time well spent — which means that we want to improve it. To do that, we need your reviews. Assuming we get some useful comments, we plan to release an updated version pretty soon; and after some number of iterations, we’ll submit the resulting paper as a full-fledged PeerJ paper.

So if you know anything about sauropods, about vertebra, about deformation, about ecology, or even about grammar or punctuation, please do us a favour: read the preprint, then get over to its PeerJ page and leave your feedback. You’ll be helping us to improve the scientific record. We’ll acknowledge substantial comments in the final paper, but even the pickiest comments are appreciated.

Because we want to encourage this approach to bringing papers to publication, we’d ask you please do not post comments about the paper here on SV-POW!. Please post them on the PeerJ preprint page. We’ve leaving comments here open for discussion of the preprinting processes, but not the scientific content.

References

  • Taylor, Michael P., and Mathew J. Wedel. 2013a. Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is based on erroneously referred specimens. (Talk given as: Barosaurus revisited: the concept of Barosaurus (Dinosauria: Sauropoda) is not based on erroneously referred specimens.) pp. 37-38 in Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston and Vicen Carrió (eds.), Programme and Abstracts, 61st Symposium on Vertebrae Palaeontology and Comparative Anatomy, Edinburgh, UK, 27th-30th August 2013. 33 pp.
  • Taylor, Michael P., and Mathew J. Wedel. 2013b. The neck of Barosaurus was not only longer but also wider than those of Diplodocus and other diplodocines. PeerJ PrePrints 1:e67v1 http://dx.doi.org/10.7287/peerj.preprints.67v1
Brachiosaurus sp. BYU 12866 c5? in left lateral view with CT slices, some corrected for distortion.

Brachiosaurus sp. BYU 12866 c5? in left lateral view with CT slices, some corrected for distortion.

Last Tuesday Mike popped up in Gchat to ask me about sauropod neck masses.  We started throwing around some numbers, derived from volumetric estimates and some off-the-cuff guessing. Rather than tell you more about it, I should just paste our conversation, minimally edited for clarity and with a few hopefully helpful links thrown in.

Mike: Dud. Neck masses.
Matt: What about ‘em?
Mike: Taylor (2009:803) measured the neck of Giraffatitan by GDI as 4117 liters.
Matt: k
Mike: I didn’t convert that to a mass, but I guess density of 0.5 is as good as any, which gives us (say) 2 tonnes.
Matt: That works for me.
Mike: That’s for an 8.5 m neck. So Supersaurus at 15 …
Matt: Yep. Almost twice as long, and not much more slender, and from what I’ve seen, ASP about the same.
Mike: Is 1.76 times as long. If it was isometric with the G. neck, it would be 5.5 times as heavy, which is 11 tonnes.
Matt: Oh.
Mike: So first: yeesh. Like, that is the mass of a whole freaking Diplo. Now we surely have to say isometry is unlikely.
Matt: Prolly.
Mike: But just multiplying out by length is unrealistic too. So maybe I should guess at mass =~ l^2? If I went with that, I’d get 6410 kg, which is elephant mass.
Matt: Something just occurred to me. Like, just now. For my 2006 poster, I calculated the mass of the cervical series in Giraffatitan, by summing over the CT slices from Brachiosaurus sp. BYU 12866 and multiplying by appropriate scale factors for the rest of the verts. We could “skin” that in muscle, and actually figure this out, for various muscle thicknesses, for one sauropod.
Mike: We should totally do that … if we had some idea how heavily muscled it was.
Matt: Well, obviously the thing to do is what Hutch et al. did for the tyrannosaurs, and put on several soft tissue envelopes. Crazy skinny, our best guess, markedly unfit, OMG, etc. It’s not that much more work. In fact, that could be my SVPCA talk this year.
Mike: Sure, but that’s just how to mitigate our ignorance. All we’d be doing at this point is taking n guesses instead of one. But, yeah, we should do it. Or you should if you prefer.
Matt: Let’s make it a Wedel and Taylor. I’ll crunch the numbers, but I want your input.
Mike: Works for me!
Matt: Good. Now let’s file it until April at least.
BYU 12613, a posterior cervical probably referable to Diplodocus, in dorsal (top), left lateral (left), and posterior (right) views. It compares most favourably with C14 of D. carnegii CM 84/94 (Hatcher 1901: plate 3) despite being less than half as large, with a centrum length of 270 mm compared to 642 mm for C14 of D. carnegii. From Wedel and Taylor (in press).

BYU 12613, a posterior cervical probably referable to Diplodocus, in dorsal (top), left lateral (left), and posterior (right) views. It most closely resembles C14 of D. carnegii CM 84/94 (Hatcher 1901: plate 3) despite being less than half as large, with a centrum length of 270 mm compared to 642 mm for C14 of D. carnegii. From Wedel and Taylor (in press).

Matt: Oh!
Matt: Also.
Matt: You know that little Diplo cervical from BYU that we figure in our in-press paper?
Mike: I think I know the one, yeah.
Matt: I am SUCH a moron. I have CT scans of the whole thing.
Mike: Good.
Matt: I forgot that Kent and I scanned it back in 2008. Even blogged about it, fer cryin’ out loud.  So I can do the sum-over-slices, scale-for-other-verts thing for Diplodocus, too. Which is at least closer to Supes than JANGO is.
Mike: Remind me, is it from a juvenile?
Matt: Maybe, maybe not. It IS tiny, but the neural spine is fused, the internal structure is crazy complex, and it doesn’t have any obvious juvenile characters other than just being small. The ASP is about as high as it gets in diplodocids. Which, as you may remember, is not nearly as high as it gets in titanosauriforms–that’s another paper that needs writing. Damn it. To know all this stuff and not have told it yet is killing me.
Mike: PeerJ!
Matt: I know!
Mike: Bottom line, it’s nuts that no-one has ever even tried to weigh a sauropod neck.* We should definitely do it, even if we do a really crappy job, if only so that others feel obliged to rebut.
Matt: Quite. Let’s do it. For reals.
Mike: In April. Done.

* R. McNeill Alexander (1985, 1989) did estimate the mass of the neck of Diplodocus, based on the old Invicta model and assuming a specific gravity of 1.0. Which was a start, and waaay better than no estimate at all. Still, let’s pretend that Mike meant “tried based on the actual fossils and what we know now about pneumaticity”.

The stuff about putting everything off until April is in there because we have a March 31 deadline to get a couple of major manuscripts submitted for an edited thingy. And we’ve made a pact to put off all other sciencing until we get those babies in. But I want to blog about this now, so I am.

Another thing Mike and I have been talking a lot about lately is the relation between blogging and paper-writing. The mode we’ve seen most often is to blog about something and then repurpose or rewrite the blog posts as a paper. Darren paved the way on this (at least in our scientific circle–people we don’t know probably did it earlier), with “Why azhdarchids were giant storks“, which became Witton and Naish (2008). Then last year our string of posts (starting here) on neural spine bifurcation in Morrison sauropods became the guts–and most of the muscles and skin, too–of our in-press paper on the same topic.

But there’s another way, which is to blog parts of the science as you’re doing them, which is what Mike was doing with Tutorial 20–that’s a piece of one of our papers due on March 31.

Along the way, we’ve talked about John Hawks’ model of using his blog as a place to keep his notes. We could, and should, do more of that, instead of mostly keeping our science out of the public eye until it’s ready to deploy (which I will always favor for certain projects, such as anything containing formal taxonomic acts).

And I’ve been thinking that maybe it’s time for me–for us–to take a step that others have already taken, and do the obvious thing. Which is not to write a series of blog posts and then decide later to turn it into a paper (I wasn’t certain that I’d be writing a paper on neural spine bifurcation until I had written the second post in that series), but to write the paper as a series of blog posts, deliberately and from the outset, and get community feedback along the way. And I think that the sauropod neck mass project is perfect for that.

Don’t expect this to become the most common topic of our posts, or even a frequent one. We still have to get those manuscripts done by the end of March, and we have no shortage of other projects waiting in the wings. And we’ll still post on goofy stuff, and on open access, and on sauropod stuff that has nothing to do with this–probably on that stuff a lot more often than on this. But every now and then there will be a post in this series, possibly written in my discretionary blogging time, that will hopefully move the paper along incrementally.

References

How disruptive is PeerJ?

February 21, 2013

Matt and I were discussing “portable peer-review” services like Rubriq, and the conversation quickly wandered to the subject of PeerJ. Then I realised that that seems to be happening with all our conversations lately. Here’s a partial transcript.

Mike: I don’t see portable peer-review catching on. Who’s going to pay for it unless journals give an equal discount from APCs? And what journal is going to do that when they get the peer-review done for free anyway? If I was Elsevier, I wouldn’t say “OK, we’ll accept your external review and give you a $700 discount”, I’d charge the full $3000 and get two more free reviews done.

Plus, you know, I can get all the peer-review I want, free of charge, at PeerJ.

Matt: Yeah, that was pretty much my take. Even as I was sending that I thought about adding, “I wonder if this is one more thing that PeerJ will kill.” Only ‘abort’ is more the verb I want, in that I don’t see this ever getting off the ground anyway.

Mike: I think the world at large has yet to realise what a black hole PeerJ is, in the sense that it’s warping all the space near it. Pretty much every time I have any thought at all about scholarly publishing now, that thought it swiftly followed by “… or, wait, I should just use PeerJ for that.”

Matt: Exactly. It makes me think that we may be discovering the contours of that space-warping effect for some time, in that we’re used to one model, and that, among all the other things PeerJ does, it quacks something like that old model so we tend to think of it as a very cool duck, and not the freakin’ tyrannosaur that is going to eat scholarly publishing.

Also makes me think of that Paul Graham thing about noticing that the door is open, and there being a lag between the freedom to do something and the adoption of that newly facilitated action or behavior.

Interesting times.

New thought: assuming PeerJ does not implode, will the established powers try to start PeerJ-alikes, and if so, what will they charge (amount), and what will they charge for (lifetime membership? decadal? annual? per 1000 pages published?).

Mike: Sweet metaphor. It’s true. It’s qualitatively different from other journals in two respects.

First, the APC is literally an order of magnitude less — and at that point, a quantitative difference becomes qualitative. Someone like [NAME REDACTED] would worry about paying $1350 to PLOS ONE, but didn’t even stop and think before saying, yeah, I’ll do that.

Second, the lifetime membership changes the game for all subsequent submissions. Now when you have a manuscript ready to go, your question isn’t going to be “where shall I send this?”, it’s going to be “is there are compelling reason not to send this to PeerJ?”

Legacy publishers won’t start PeerJ-alikes because they can’t. As noted in many SV-POW! posts, Elsevier takes about $5000 for each article they put behind a paywall. Slice away the 40% profit and you get $3000 which not coincidentally is what they charge as an APC. They have old, slow, encumbered systems and processes and top-heavy organisation. At $3000 they are only breaking even. They can’t compete at a PLOS-like $1350 level and they can’t even think about competing at PeerJ levels. If they offered a lifetime membership they’d have to ask $10k or something stupid.

I don’t think it’s that they don’t want to change. They can’t. They’ve ossified into 1990s companies running on 1990s software. It’s hard to steer a ship with a $2bn turnover, and impossible to replace the engines while still cruising.

Matt: I think it is probably a mistake to think that PeerJ will only encroach “upward”, onto the territory of more traditional journals (which is “all of them”). We’ve already talked about it taking business from arXiv (at least ours, although there is the large non-overlap in their respective subject domains–for now, anyway).

But my point is, the question, “Why wouldn’t I send this to PeerJ?” may not only kick in for papers that you might conceivably send elsewhere, but also for manuscripts that you might not conceivably send anywhere.

Mike: There are plenty of historical SV-POW! posts that could have been PeerJ articles on their own — for example, the shish-kebab post that ended up as part of Why Giraffes Have Short Necks.

Matt: Right. And if one is on the fence, shove it on the PeerJ preprint server and see what people have to say.

Mike: I think it’s the first megajournal to have an associated preprint server, and that may yet prove the most important of all its innovations.

Matt: It feels almost … struggling to find the right word, in part because it’s late and I need to go sleep. “Seditious” is not quite it, and neither is “seductive”.

At that point we started talking about something else, so I never did find out what word Matt was groping for. But what’s only gradually become clear to us is how much PeerJ is changing how we think about the academic publishing process. It’s shaking us out of mental ruts that we didn’t even know we were in. Exciting.

 

Wire skull

Big news yesterday. Identical bills were introduced into the US House of Representatives and Senate that, if passed, will make federally-funded research freely available within six months of publication. Here’s the exact wording, from the press release on Mike Doyle’s (D-PA) website:

The Fair Access to Science and Technology Research Act (FASTR) would require federal agencies with annual extramural research budgets of $100 million or more to provide the public with online access to research manuscripts stemming from funded research no later than six months after publication in a peer-reviewed journal.

As Peter Suber explains here and here, FASTR is a stronger version of FRPAA, the Federal Research Public Access Act, which has been introduced in Congress three times before (2006, 2009, and 2012) but never come up for a vote. However, momentum for open access is gathering, both on the supply side with progressive new outlets like eLife and PeerJ, and on the demand side of, well, citizens demanding access to the research they’ve already paid for, and legislators increasingly agreeing with them. So FASTR  has a real shot at getting to a vote, and if voted on, could well pass. Which would be awesome, because we all need access.

Raptor skull in cardboard

I am especially happy that FASTR has bipartisan sponsorship in both houses of Congress. The sponsoring representatives in the House are Mike Doyle (D-PA), Kevin Yoder (R-KS), and Zoe Lofgren (D-CA). The identical Senate bill was introduced by John Cornyn (R-TX) and Ron Wyden (D-OR). So we’ve got Democrats from deeply blue states and Republicans from deeply red states, which is awesome and totally appropriate, because this issue really does cut across party lines. And, hell, last year Elsevier managed to hire bipartisan sponsorship for their toxic–in more ways than one–and rapidly-killed Research Works Act, so it’s nicely symmetrical that politicians from both sides of the aisle have come together to sponsor that bill’s near-opposite.

What can you do? If you live in the US, contact your legislators and tell them to support FASTR! It takes almost no time at all and it makes a big difference. This afternoon I called all five of the sponsoring legislators to thank them, and I called my representative and both California senators to encourage them to support the bill, and all told it took just a little over half an hour. If you skipped the thank yous and just got in touch with the legislators who represent you, it could be done in 15 minutes, and you’ve probably wasted more time than that today daydreaming about dinosaurs. Here’s what you’ll need.

Encourage your legislators:

Thank the bills’ sponsors:

This is big. This matters. Send an email, pick up the phone, make a difference.

Rexy skeleton

I didn’t have any really motivational “contact your legislators!” artwork so the photos in this post are of papier mache dinosaurs–all stinkin’ theropods, I’m afraid–that I’m building with my son. More to come on that soon, but in the meantime, check this out and give it a whirl–after you contact your legislators!

The Three Machesketeers

Follow

Get every new post delivered to your Inbox.

Join 390 other followers