I think it’s fair to say that this “bifurcation heat-map”, from Wedel and Taylor (2013a: figure 9), has been one of the best-received illustrations that we’ve prepared:
Back when the paper came out, Matt rashly said “Stand by for a post by Mike explaining how it came it be” — a post which has not materialised. Until now!
This illustration was (apart from some minor tweaking) produced by a program that I wrote for that purpose, snappily named “vcd2svg“. That name is because it converts a vertebral column description (VCD) into a scalable vector graphics (SVG) file, which you can look at with a web-browser or load into an image editor for further processing.
The vertebral column description is in a format designed for this purpose, and I think it’s fairly intuitive. Here, for example, is the fragment describing the first three lines of the figure above:
Taxon: Apatosaurus louisae
Specimen: CM 3018
Taxon: Apatosaurus parvus
Specimen: UWGM 155556/CM 563
Taxon: Apatosaurus ajax
Specimen: NMST-PV 20375
Basically, you draw little ASCII pictures of the vertebral column. Other directives in the file explain how to draw the various glyphs represented by (in this case) “Y”, “V”, “u”, and “n”.
It’s pretty flexible. We used the same program to generate the right-hand side (though not the phylogenetic tree) of Wedel and Taylor (2013b: figure 2):
The reason I mention this is because I released the software today under the GNU General Public Licence v3.0, which is kind of like CC By-SA. It’s free for anyone to download, use, modify and redistribute either verbatim or in modified form, subject only to attribution and the requirement that the same licence be used for modified versions.
vcd2svg is written in Perl, and implemented in part by the SVG::VCD module, which is included in the package. It’s available as a CPAN module and on GitHub. There’s documentation of the command-line vcd2svg program, and of the VCD file format. Also included in the distribution are two documented examples: the bifurcation heat-map and the caudal pneumaticity diagram.
Folks, please use it! And feel free to contribute, too: as the change-log notes, there’s work still to be done, and I’ll be happy to take pull requests from those of you who are programmers. And whether you’re a programmer or not, if you find a bug, or want a new feature, feel free to file an issue.
A final thought: in academia, you don’t really get credit for writing software. So to convert the work that went into this release into some kind of coin, I’ll probably have to write a short paper describing it, and let that stand as a proxy for the actual program. Hopefully people will cite that paper when they generate a figure using the software, the way we all reflexively cite Swofford every time we use PAUP*.
Update (12 April 2014)
- Swofford, D. L. 2002. PAUP*: phylogenetic analysis using parsimony (* and other methods). Sinauer Associates, Sunderland, MA.
- Wedel, M.J., and Taylor, M.P. 2013. Neural spine bifurcation in sauropod dinosaurs of the Morrison Formation: ontogenetic and phylogenetic implications. Palarch’s Journal of Vertebrate Palaeontology 10(1): 1-34. ISSN 1567-2158.
- Wedel, Mathew J., and Michael P. Taylor. 2013. Caudal pneumaticity and pneumatic hiatuses in the sauropod dinosaurs Giraffatitan and Apatosaurus.PLOS ONE 8(10):e78213. 14 pages. doi:10.1371/journal.pone.0078213 [PDF]
March 25, 2014
How should scientists, and reporters, discuss work that has failed to replicate? The original Barr and colleagues article remains in the scientific literature; failed replication alone is not grounds for retraction.
He’s right, of course: we certainly don’t want to retract every paper whose conclusions can’t be replicated, for all sorts of reasons: they may subsequently be replicated after all; the paper may contain other useful information even if the experiment in question was flawed; the replication studies themselves probably rely on the original’s Methods section; authors should not be punished for unfortunate outcomes unless they were fraudulently obtained.
What we want is for that Barr et al paper, whenever anyone looks at it, to be displayed with a prominent header that says “The following studies attempted to replicate this finding but failed:”, and a list of references/links. And, for that matter, another header saying that the following other studies did replicate it.
For web-sites to automatically produce that kind of annotation, they need articles that cite the original to include an additional piece of metadata, along with the author/year/title/journal/etc. metadata that identifies the cited paper. That additional ingredient is the citation’s type, which should be one of a small set of defined values.
What values are relevant? I won’t try to come up with an exhaustive list at this point, but obvious ones include:
- Replicates — the current paper replicates work done in the cited paper (and so provides evidence, though not proof, that the cited paper’s conclusion is correct).
- FailsToReplicate — the current paper attempts to replicate work done in the cited paper, but fails (and so provides evidence that the cited paper is mistaken).
- Falsifies — the current paper shows definitely that the cited paper is wrong. This is a stronger statement than FailsToReplicate, and would be used for example when the new work shows conclusively that the experimental protocol of the original was critically flawed.
- DependsOn — the current paper depends on information from the cited paper, such as the phylogeny that it proposes or the vertebral formula that it gives. For these purposes, the cited paper is treated as an authoritative source.
- Acknowledges — the current paper uses ideas proposed in the cited paper, and gives credit to the original.
There are all sorts of practical issues that will impede the adoption of this idea (not least the idiot fact that the citation graph is a trade secret rather than a freely available database), but let’s ignore those for now, and figure out what taxonomy of citation-types we want.
February 9, 2014
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.
February 3, 2014
From the files of J. K. Rowling.
Dear Ms. Rowling,
Thank you for submitting your manuscript Harry Potter and the Half-Blood Prince. We will be happy to consider it for publication. However we have some concerns about the excessive length of this manuscript. We usually handle works of 5-20 pages, sometimes as much as 30 pages. Your 1337-page manuscript exceeds these limits, and requires some trimming.
We suggest that this rather wide-ranging work could usefully be split into a number of smaller, more tightly focussed, papers. In particular, we feel that the “magic” theme is not appropriate for our venue, and should be excised from the current submission.
Assuming you are happy to make these changes, we will be pleased to work with you on this project.
Esteemed Joenne Kay Rowling,
We are delightful to recieve your manuscript Harry Potter and the Half-Blood Prince and we look forword to publish it in our highly prestigious International Journal of Story Peer Reviewed which in 2013 is awarded an impact factor of 0.024.
Before we can progression this mutually benefit work, we require you to send a cheque for $5,000 US Dollars to the above address.
Dear J.R.R. Rowling,
We are in receipt of your manuscript Harry Potter and the Half-Blood Prince. Unfortunately, after a discussion with the editorial board, we concluded that it is insufficiently novel to warrant publication in our journal, which is one of the leading venues in its field. Although your work is well executed, it does not represent a significant advance in scholarship.
That is not to say that minor studies such as yours are of no value, however! Have you considered one of the smaller society journals?
Dear Dr. Rowling
Your submission Harry Potter and the Half-Blood Prince has passed initial editorial checks and will now be sent to two peer-reviewers. We will contact you when we have their reports and are able to make a decision.
Dear Dr. Rowling
Re: Harry Potter and the Half-Blood Prince.
We agree that eighteen months is too long for a manuscript to spend in review. On making inquiries, we find that we are unfortunately no longer able to contact the editor who was handling your submission.
We have appointed a new handling editor, who will send your submission to two new reviewers. We will contact you as soon as the new editor has made a decision.
Dear Dr. Rowling
Re: Harry Potter and the Half-Blood Prince.
Your complaint is quite justified. We will chase the reviewers.
Dear Dr. Rowling
I am pleased to say that the reviewers have returned their reports on your submission Harry Potter and the Half-Blood Prince and we are able to make an editiorial decision, which is ACCEPT WITH MAJOR REVISION.
Reviewer 1 felt that the core point of your contribution could be made much more succinctly, and recommended that you remove the characters of Ron, Hermione, Draco, Hagrid and Snape. I concur with his assessment that the final version will be tighter and stronger for these cuts, and am confident that you can make them in a way that does not compromise the plot.
Reviewer 2 was positive over all, but did not like being surprised by the ending, and felt that it should have been outlined in the abstract. She also felt that citation of earlier works including Lewis (1950, 1951, 1952, 1953, 1954, 1955, 1956) and Pullman (1995, 1997, 2000) would be appropriate, and noted an over-use of constructions such as “… said Hermione, warningly”.
Dear Dr. Rowling
Thank you for your revised manuscript of Harry Potter and the Half-Blood Prince, which it is our pleasure to accept. We now ask you to sign the attached copyright transfer form, so we can proceed with publication.
Dear Dr. Rowling
I am sorry that you are unhappy about this, but transfer of copyright is our standard procedure, and we must insist on it as a prerequisite for publication. None of our other authors have complained.
Dear Dr. Rowling
Thank you for the signed copyright transfer form.
In answer to your query, no, we do not pay royalties.
Dear Dr. Rowling
Sadly, no, we are unable to make an exception in the matter of royalties.
Dear Dr. Rowling
Your book has now been formatted. We attach a proof PDF. Please read this very carefully as this is the last chance to spot errors.
You will readily appreciate that publishing is an expensive business. In order to remain competitive we have had to reduce costs, and as a result we are no longer able to offer proof-reading or copy-editing. Therefore you are responsible for ensuring the copy is clean.
At this stage, changes should be kept as small as possible, otherwise a charge may be incurred for re-typesetting.
Dear Dr. Rowling
Many thanks for returning the corrected proofs of Harry Potter and the Half-Blood Prince. We will proceed with publication.
Now that the final length of your contribution is known, we are able to assess page charges. At 607 pages, this work exceeds our standard twenty free pages by 587. At $140 US per page, this comes to $82,180. We would be grateful if you would forward us a cheque for this amount at your convenience.
Dear Dr. Rowling
Thank you for you prompt payment of the page charges. We agree that these are regrettable, but sadly they are part of the reality of the publishing business.
We are delighted to inform you that Harry Potter and the Half-Blood Prince is now published online, and has been assigned the DOI 10.123.45678.
We thank you for working on this fine contribution with us, and hope you will consider us for your future publications.
Dear Dr. Rowling
You are correct, your book is not freely downloadable. As we explained earlier in this correspondence, publishing is an expensive business. We recover our substantial costs by means of subscriptions and paid downloads.
In our experience, those with the most need to read your book will probably have institutional access. As for those who do not: if your readers are as keen as you say, they will no doubt find the customary download fee of $37.95 more than reasonable. Alternatively, readers can rent online access at the convenient price of $9.95 per 24 hours.
Dear Dr. Rowling
I am sorry that you feel the need to take that tone. I must reiterate, as already stated, that the revenues from download charges are not sufficient for us to be able to pay royalties. The $37.95 goes to cover our own costs.
If you wish for your book to be available as “open access”, then you may take advantage of our Freedom Through Slavery option. This will attract a further charge of $3,000, which can be paid by cheque as previously.
Your attitude is really quite difficult to understand. All of this was quite clearly set out on our web-site, and should have been understood by you before you made your submission.
As stated in the copyright transfer form that you signed, you do not retain the right to post freely downloadable copies of your work, since you are no longer the copyright holder.
We must ask you not to contact your handling editor directly. He was quite shaken by your latest outburst. If you feel you must write to us again, we must ask you to moderate your language, which is quite unsuitable for a lady. Meanwhile, we remind you that our publishing agreement follows industry best practice. It’s too late to complain about it now.
IP Lawyer #1
Dear Pyramid Web-Hosting,
We write on behalf of our client, Ancient Monolith Scholarly Publishing, who we assert are the copyright holders of Harry Potter and the Half-Blood Prince. It has come to our attention that a copy of this copyrighted work has been posted on a site hosted by you at the URL below.
This letter is official notification under the provisions of Section 512(c) of the Digital Millennium Copyright Act (“DMCA”) to effect removal of the above-reported infringement. We request that you immediately issue a cancellation message as specified in RFC 1036 for the specified posting and prevent the infringer, Ms. J. K. Rowling, from posting the infringing material to your servers in the future. Please be advised that law requires you, as a service provider, to “expeditiously remove or disable access to” the infringing material upon receiving this notice. Noncompliance may result in a loss of immunity for liability under the DMCA.
Please send us at the address above a prompt response indicating the actions you have taken to resolve this matter.
Examination of Ms. Rowling’s personal effects established that she had written most of a seventh book, Harry Potter and the Deathly Hallows. However, Rowling never sought to publish this final book in the series.
January 21, 2014
Regular readers will remember Jennifer Raff’s guest post on the PeerJ blog, How To Become Good At Peer-Review; and my response to it, Three points of disagreement. Today I read a very different take on this piece by Chorasimilarity, who is a frequent commenter here at SV-POW!: Two pieces of all too obvious propaganda.
Chorasimilarity starts by taking the original piece to task — fairly, I think — for its opening statement that “peer review is at the heart of the scientific method”. It’s true that the scientific method is something rather different. But as I argued in Science is enforced humility, peer-review is part of the scaffolding that prevents individual scientists from running away with their own ideas, unchecked by consensus wisdom.
Chorasimilarity then goes on to make a stronger criticism of peer-review:
Peer review is an idea based on authority, not on science [...] the quote mentions that “one’s research must survive the scrutiny of experts before it is presented to the larger scientific community as worthy of serious consideration”, which would be just sad, dinosaurish speaking, if it would come from an old person who did not understood that today there is, or there should be, free access to information.
As we’ve discussed here before, having been through peer review certainly does not mean we can trust a published paper. People do sometimes talk as though this is the case, and it’s an absolutely fallacy that we should be quick to rebut whenever we encounter it.
But it does have a weaker, yet still non-negligible, value.
The real value of peer-review not as a mark of correctness, but of seriousness. Back in the original SV-POW! series on peer-review (Where peer-review went wrong, Some more of peer-review’s greatest mistakes, What is this peer-review process anyway?, Well, that about wraps it up for peer-review), I likened peer-review to hazing:
The best analogy for our current system of pre-publication peer-review is that it’s a hazing ritual. It doesn’t exist because of any intrinsic value it has, and it certainly isn’t there for the benefit of the recipient. It’s basically a way to draw a line between In and Out. Something for the inductee to endure as a way of proving he’s made of the Right Stuff.
So: the principle value of peer-review is that it provides an opportunity for authors to demonstrate that they are prepared to undergo peer-review.
When I first wrote that, I wrote it in a spirit of cynicism and in frustration that so much of the effort that goes into the process is thrown away and that the results are so arbitrary. Those are real and serious complaints, but I’ve since come around to the idea that peer-review is useful in that the hazing aspect enables it to clear a much lower bar. Being prepared to undergo peer-review really is a mark of seriousness.
I would imagine that everyone involved in dinosaur research occasionally gets unsolicited emails from cranks and from as-yet unpublished amateurs. One of the most reliable ways to distinguish the two groups is this: serious amateurs are trying to figure out how to get their work into peer-review, while cranks are either actively avoiding it or not even aware of it. That’s why the web is full of sites like Dinosaur Home, with all its fine pictures of pebbles, which can continue on their merry way free of scrutiny.
I do think that the benefits of traditional peer-review are usually greatly overstated and the costs (both direct and indirect) underestimated. But I’m coming down on the side that its barrier-to-cranks effect might just tip the balance in favour of retaining it.
Think your work has scientific value? Good. Prove it, by showing it to professionals. If you won’t do that, then the rest of us don’t need to expend mental energy on taking you seriously.
January 20, 2014
Jennifer Raff wrote a useful guest post on the PeerJ Blog: How To Become Good At Peer-Review. Most of its advice is excellent, and I’d heartily recommend it to anyone starting out on reviewing. But there are three points where I disagree with it. Here are the three things Jennifer said, and my counter-points.
1. Communicating with authors
“Don’t communicate with the authors about their manuscript. All thoughts and comments on it should only go to the editor.”
This may be different in different academic fields, but I’ve been contacted by reviewers of my material, and contacted the authors of papers I’m reviewing, too. Palaeo may be less formal in this respect than fields such as medical research. It’s often useful, for example, to get the authors to send higher resolution versions of the specimen photographs than the downscaled ones the journal passes on; or to get the manuscript in a read-write format that lets you more easily add notes and corrections. Most importantly, I’ve sometimes had to send my marked-up copy of the manuscript directly to the corresponding author because the journal’s automated system has no way to attach it to the formal response.
Perhaps the idea that you shouldn’t communicate with authors comes from confidentiality concerns. But I know who the authors are. (There are no palaeo journals that do double-blind reviewing, and it would be impossible any in a field small enough that you pretty much know who everyone is and what they work on.) And since I never review anonymously, I don’t mind them knowing who I am while I am still doing the review.
In the end, one of the main goals of peer-review — I would say the main goal — is to help the authors make their work the best it can be. Often contacting them directly is the more effective way to do that.
“Ask yourself whether the questions the authors are addressing are really advancing the field in a meaningful way. This does not mean that an article has to be completely novel, but it does mean that the work contributes to the sum of knowledge in the field and does not, for example, simply repeat well known results.”
I only agree with this for certain values of “well known”. In experimental sciences, replication is hugely important, and it’s one of the worst consequences of the prestige-obsessed journal system that it’s so hard to get a replication published. You could almost say that an experimental result that’s only been published once is worthless.
Equally important, or maybe even more important than replication, is the failed replication. When Doyen et al. (2012) tried and failed to replicate the findings of Bargh et al. (1996) on psychological priming, it was an important check on the influence of an article that has been cited more than 2,500 times. Bargh himself was not happy about it, but to quote a much-loved SV-POW! maxim due to Tom Holtz, “Sorry if that makes some people feel bad, but I’m not in the ‘make people feel good’ business; I’m a scientist.”
So a reviewer should only complain about lack of novelty if the experiment has already been replicated several times. (There’s no value in a research paper showing that large and small cannonballs fall at the same speed from the top of the leaning tower of Pisa.)
3. Changing the subject
“Can you think of a better way to address the research questions than what the authors did?” … “You have every right to ask the authors to do a different experiment.”
Ugh. I just hate this. There is literally nothing I detest more in a review than “You should have written this different paper instead”. Please reviewers, review what’s in front of you, not what you would have done instead.
If you think of another approach that you think is promising, by all means suggest it as a followup project. But please in the name of all that we hold dear, don’t let it be a roadblock that delays this work from being published.
January 13, 2014
So, I’ve been thinking a lot about this interesting situation with Elsevier, which David Tempest’s remarks at the Oxford Evolution or Revolution debate highlighted: they can’t afford (literally or figuratively) to tell us how much they charge different institutions for the same stuff.
And I had this thought, which Mike tweeted:
When simply telling the truth can blow up your business model, you need a new business model.
Mash that up with “information wants to be free” and “if all else fails, someone will show up to liberate it”, and you get this:
When a single person of good conscience can blow up your business model simply by telling the truth, you need a new business model.
If we’ve learned anything in the past few years, it is that humans are the weak link in any campaign of secrecy.
We know that all of the big barrier-based publishers have these bundling deals with libraries, and that no-one on either side is allowed to say what the terms of those deals are. But there must be a lot of people with access to that information. And at least some of them must know how much libraries are getting screwed, precisely because they have access to that information. Seems unlikely that information will stay secret forever.
So, should we be expecting a Snowden-type leak from one or another barrier-based publisher? It doesn’t have to be Elsevier, but I think if it happens they’re the most likely target, because they are so single-minded about cultivating the ill-will of the people they allegedly serve (most recently with this and this). Sometimes I wonder if the other barrier-based publishers are getting too much of a free pass precisely because Elsevier is so good at tossing grenades and then jumping on them.
Corollary: barrier-based publishers, what are you doing to prepare for such a leak? “More secrecy” and “harsher penalties” will probably not work out well in the long run. But do feel free to keep scoring own goals if you must.