A pre-print experiment, continued

Over a year ago, I uploaded a preprint into bioRxiv. When people upload preprints, bioRxiv sensible puts on a disclaimer that, “This article is a preprint and has not been peer-reviewed.”

A little over a week ago, the final, paginated version of the paper that arose from the preprint was published. Now, bioRxiv is supposed to update its notice automatically to say, “Now published in (journal name and DOI).”

Perhaps because the final paper was substantially different than the preprint – in particular, the title changed – bioRxiv didn’t catch it. I had to email bioRxiv’s moderators through the contact form asking them to make the update.

The preprint was making more work for me. Again. It wasn’t a lot of work, I admit, but people advocating preprints often talk about them as though they take effectively zero time. They don’t. You have to pay attention to them to ensure things are being done properly. I want people to cite the final paper when it’s available, not the preprint.

Some journals are talking about using bioRxiv as their submission platform. This would be a good step, because it would remove work duplication.

I’m glad I’ve been through the preprint experience. But I am still not sold on its benefits to me as a routine part of my workflow. It seems all the advantages that I might gain from preprints can be achieved by other methods, notably publishing in open access journals with a good history of good peer review and production time.

Related posts

A pre-print experiment: will anyone notice?

New snail species is hard to find, in more ways than one

Last year, I tweeted:

One of today's highlights: helping a colleague photograph the holotype of an undescribed species!

I’m pleased that this species description is now out. The species in question was a little snail, now named Praticolella salina! The discovery is highlighted on the university’s home page! But the university’s article doesn’t tell you where to find the paper. Putting the name into Google Scholar didn’t help either. I finally found it because someone posted a shot of the article on Instagram:

Once I knew the journal, I went looking for its home page. I found it is still a print-only affair, with PDFs of the journal lagging three years behind the publication date.

Just remember that the next time anyone says of scientific publishing, “Everything is all online now.” No. No it is not.

External links

UTRGV professor and student researchers discover, name new species of South Texas snail
The Nautilus (journal)

Ireland vs. the pet trade

My newest paper is part of my own Pirates of the Caribbean franchise. It’s the fifth in a series, “pet crayfish on the internet.” 

The first (Faulkes 2010) used surveys; the second, Google alerts (Faulkes 2013); the third, online auctions, and (Faulkes 2015a); the fourth (Faulkes 2015b), classified ads. The fourth one was short, but I pushed it out because I thought documenting the illegal sale of marbled crayfish in Ireland would be useful for policy makers.

But there was an obvious question: if I blundered across ads for illegal crayfish in Ireland without looking, how many illegal crayfish would I find if I went looking?

While doing this paper, I was reminded was how useful it is to start writing the paper as soon as possible. This paper has a year of data from the Republic of Ireland, but only about half a year of data from the UK. That’s because I started writing the manuscript halfway through the year. I thought, “Hey, I’ve got half the data, I know what this paper is going to look like in broad strokes, so I can start putting this together.”

As soon as I started writing, I started thinking, “Uh oh.” I realized that there were gaps in what I was collecting (sigh), but that I might still have time to address (whew!). Writing forced me to articulate what I was doing, and I started imagining what the reviewers might say if I didn’t have certain things.

An advantage of having a scientific franchise is that some things get easier. I learned that it was useful to have a project run one calendar year. It’s a time frame that people get, and is manageable. You have a clearly defined end date, so you know how far along you are at all times. Data collection finished 1 January, 2016. Because I had done quite a bit of the leg work up front, I was able to finish writing and submit the paper less than two weeks later.

Where to submit the paper was tricky. Some articles have obvious homes, but there wasn’t for this one. There is no Journal of Pet Trade Studies. I looked at a lot of journals before settling on Biology and Environment. I had never published there before, but I couldn’t get a better fit than a regional Irish journal with a broad editorial mandate.

There was a cost to that good fit, though. The journal had no open access options. I’ve been trying to publish my papers open access when possible, and this is one of the first papers in a while (besides book contributions) that isn’t. In this case, I thought the fit was so good, this journal was the best chance for my paper to find its target audience, and that was worth the sacrifice.

Once the paper was submitted, I waited. I sent an email after two months, asking if I could post a pre-print while waiting for a decision. I was politely asked not to, so I didn’t. I waited some more. And waited. After six months, I sent an email making sure nobody had forgotten my manuscript. (Because that’s happened to me before.) I was assured it hadn’t been. I waited some more.

I checked in again around the nine month mark to make sure the manuscript was still a live concern for the journal. The editors really wanted a particular person to review this paper, and was just waiting on the one review to come in. So, yes, this is one of those frustrating cases where the editorial decision making was slowed by reviewers not promptly returning reviews. I was a bit miffed, since the paper was neither long nor complex, and I didn’t think it needed the many months it took to review. But I was pleased that I had learned to be more persistent in checking with the journal.

That said, once the reviews were back, I was pleased with the rest of the journal’s service. The typesetting and copy editing process was thorough and responsive, and it felt like they genuinely wanted to get everything right.

It’s funny to think that when I started my academic career as an undergraduate, I didn’t have an email address. The Internet existed, but practically nobody knew about it. The web was about a decade away. And now, I can publish papers about Ireland from my desk in Texas just by watching what people do the Internet.

Like any good franchise, I am already working on the sequel.

Update, 1 June 2017: I received a hard copy of the journal in the post today (cover above). It’s been a while since that happened! And I must say, the production is top notch. The colour pictures look bright and beautiful. The paper feels good in your hands. And there is an editor’s introduction to each article. The one to mine reads, in part:

Ain’t no barricade high (or wide) enough

Enforcing any restriction on the movement of goods or organisms is beset by problems even when physical barriers are used. We have been lucky in Ireland that the movement of many unwanted organisms has been prevented because we are separated from both the UK and continental Europe by natural water barriers. Whilst natural barriers are important these can still be circumvented often through trade-related, human assisted transportation. ...

Perhaps there is a message here–that the implementation of any barrier to the movement of an unwanted species is always likely to be too later–and that such a move has to be combined with an appropriate follow-up management plan?

This relates to a point I made on Twitter last week. It’s not fair to compare the delay in posting a pre-print to the delay in publication in a journal, as Leslie Vosshall did.

I say that knowing that I myself have complained about editors have never helped papers become more readable. But I think that was a little unfair. For one, I’m a native English speaker, and though I say it myself, a pretty good writer. My writing probably doesn’t need dramatic revision to be readable.

Since I wrote that blog post, I’ve worked with more journals. Several of them actively made my paper better after acceptance. Like this one, the improvement came in the copy editing and proofing stages. Lots of little details got detected and corrected before the final version was produced that would appear in the journal, and be the version of public record. I greatly appreciated that intense, detailed, checking of the text. That care showed up in the production of figures and tables, too.

Sometimes, it seems that some scientists are so confident of their abilities that they think their uncorrected, unreviewed manuscript cannot possibly be improved. Reviewing and editing are just unnecessary delays in getting their brilliant science out to the world .

I think that such manuscripts are extraordinarily rare.

Related posts

Can civil servants defuse a bomb? An Irish crayfish problem

Academic publishers need better defenders

The editor’s influence

References


Faulkes Z. 2010. The spread of the parthenogenetic marbled crayfish, Marmorkrebs (Procambarus sp.), in the North American pet trade. Aquatic Invasions 5(4): 447-450. http://dx.doi.org/10.3391/ai.2010.5.4.16

Faulkes Z. 2013. How much is that crayfish in the window? Online monitoring of Marmorkrebs, Procambarus fallax f. virginalis (Hagen, 1870) in the North American pet trade. Freshwater Crayfish 19(1): 39-44. http://dx.doi.org/10.5869/fc.2013.v19.039

Faulkes Z. 2015a. Marmorkrebs (Procambarus fallax f. virginalis) are the most popular crayfish in the North American pet trade. Knowledge and Management of Aquatic Ecosystems 416: 20. http://dx.doi.org/10.1051/kmae/2015016

Faulkes Z. 2015b. A bomb set to drop: parthenogenetic Marmorkrebs for sale in Ireland, a European location without non-indigenous crayfish. Management of Biological Invasions 6(1): 111-114. http://dx.doi.org/10.3391/mbi.2015.6.1.09

Faulkes Z. 2017. Slipping past the barricades: the illegal trade of pet crayfish in Ireland. Biology and Environment: Proceedings of the Royal Irish Academy 117(1): 15-23. http://dx.doi.org/10.3318/BIOE.2017.02 

Incoming: ReSearch: A Career Guide for Scientists

I just signed an author’s agreement for ReSearch: A Career Guide for Scientists. It’s been a while since I’d thought about this project.

I didn’t write it, or even a chapter. Back in 2015, one of the co-authors, Nathan Vanderford, cold emailed me asking if I would be willing to write something about “personal branding.” I said, “Sure!” So I wrote a little sidebar as a case study.

The book is slated for release next month. I’m curious to see how my little contribution is woven into the text.

External links

Publisher’s website
Amazon page

The value of editors

There is a line of thought among some scientists – and it is not a short line among a small fraction of scientists – that pre-publication peer review is useless, reviewers are useless, and editors are useless. Thus, journals are useless.

Albrecht Schulte-Hostedde was brave enough to post one of his old rejection letters this on Twitter (text follows images). Albrecht prefaced this saying, “Lessons learned as a young and arrogant graduate student.”

Canadian Journal of Zoology
17 April 1997
File Number: Y1150

Mr. A.I. Schulte-Hostedde

Department of Zoology
Umversity of Guelph
Guelph. Ontario NlG 2W1

Dear Mr. Schulte-Hostedde:

Subject: Patterns of Association in a Temperate Rodent Community

We have sent your paper out for re-review. Neither reviewer has been convinced by your rebuttal and as a consequence we have decided to reject your paper. We are returning the paper to you.

Neither reviewer has provided comments for transmission to the authors. Let me, however, add some comments of my own, since I detect that you may not understand the nature of the review process. We try to select reviewers who are knowledgeable and objective and who understand the role of the Canadian Journal of Zoology as a generalist journal. They are volunteers who support the discipline by committing some of their time to helping authors get their work into an acceptable form. In your case both reviewers had a number of substantive suggestions for improvement. We indicated that the paper was unlikely to be accepted without major revisions.

Your revisions were anything but major. So far as I can determine, they consisted of changing the title and adding a short section on predation. Under such circumstances we sometimes return the manuscript directly to the authors, asking them to try again. But in this case, there was an extensive rebuttal, and we thought that the reviewers should see that. The reviewers have, as I say, not been convinced, and they are both deeply disappointed by the nature and tone of your response. To quote one of them “if the authors do not respect the reviews I do not know why they would want to publish their research in the Canadian Journal of Zoology nor do I understand why the editors would accept it.”

You are just beginning your career. Let me take off my editorial hat and, as a person who has been publishing in the field for more than 40 years, offer some advice. Of the approximately 200 papers which I have published, only two were accepted without change. Of the remainder, I have invariably benefited from the advice of the reviewers. I think that you would be wise to regard the reviewers not so much as gate-keepers, but as persons who volunteer helpful advice.

Yours sincerely,

K.G. Davey/A.S.M. Saleuddin
Editors

You know what? This was written by people who care both about the scientific enterprise, and the professional development of the author. This is mentoring. This is humane. You are far less likely to get this sort of interaction from posting draft manuscripts on pre-print servers and hoping people click “Like” bottons afterwards.

I know that this is an unusual, dare I say, exceptional bit of editorial advice. But if more editors worked like this, fewer people who would question the value of journals.

2016: Where did the work go?

There are reasons aplenty to hate this wretched year, but I’m just going to focus on the professional side for me. 2016 was a year I felt like I just couldn’t get stuff done.

On paper, it was not a horrible year. On paper, the book Freshwater Crayfish was released, which I co-edited and had a couple of chapters in. But in reality, the physical copy of that book was released in August 2015.

I also had one other book chapter, in Science Blogging: The Essential Guide, back in February. But the production on that book had dragged on for so long (I first blogged that it was coming out late in 2014) that it certainly didn’t feel like it was something new.

My frustrations were compounded because I had submitted a couple of papers early in the year; one early January, in fact. But for reasons that do not need exploring at this juncture, the editorial process for both of them dragged out longer than usual and they won’t see the light of day until 2017.

(At least, I hope they will appear in 2017. One journal that has accepted one of my articles still has items in its pre-print queue today, 30 December 2016, that are dated 30 December 2015. A whole year as a “forthcoming” article? That sucks.)

The number of blog posts was down here on NeuroDojo, but holding reasonably steady on Marmorkrebs and Better Posters. I have a lot of blog posts that I started but wasn’t able to finish.

I did teach a lot this year. I just got through the heaviest teaching load in a semester I’ve had in a very long time (and am so pleased nobody yelled at me, which I was convinced was about to happen any day). I did two graduate classes that were new to me for the first time ever. I taught a grad course in summer. And I taught the #SciFund poster class for the second time.

For me, professionally, 2016 feels like “the one that got away.”

The open access “sting” by Science, three years on

In 2013, writer John Bohannon published a Science article where the main drawing card was an obviously bad paper that he got accepted or published in multiple junk journals. He was not the first, nor has he been the last, to set out to punk crappy journals with obviously bad papers. It’s practically a scientific genre in its own right now.

I grabbed four of the papers that made it through the production process (despite Bohannon’s efforts to keep them out of the literature) for teaching purposes. I was recently reminded of those papers, and went looking for them again.

Let’s start with Indandah et al., 7-chloronorlichexanthone inhibits the growth of murine SV40 transformed lymphoid sarcoma Cells in vitro, in Medicinal Chemistry:

The journal is still there, but there is no hint of the retraction. There’s just a gap in the page numbering.

Next, Magaya et al.,Arthogalin inhibits the growth of murine malignant prostate sarcoma cells in vitro, from Journal Of Pharmacy And Pharmacological Research.

The entire publisher website is gone. The same is true for Nonjah et al., Nephrosterinic acid inhibits the growth of murine malignant pleural sarcoma cells in vitro.

The entire Scientific Journal of Medical Science is gone, gone, gone.

With this track record, I was surprised to see one journal acting like a real journal: being transparent and taking responsibility. The Journal of Biochemical and Pharmacological Research still exists, first of all. You need to drill down to find their page for Onnoocom et al. contribution, Schizopeltic acid inhibits the growth of murine polyploid pulmonary blastoma cells in vitro. But when you do:

The journal acknowledges that the paper was there in its table of contents, but the links for the abstract and PDF both lead to a retraction notice:

JBPR has been a victim of bogus submissions; and this paper is one of those and is hereby retracted. The editor in chief takes full responsibility for accepting this bogus manuscript for publication in JBPR. We sincerely assure readers that something like this will not occur again.

The last line makes me raise my eyebrows a bit. No journal can assure readers that they won’t make this mistake again. It’s just not possible to have a 100% failsafe fraud detection system.

Yes, journals should be criticized when they publish deeply flawed papers. But how they respond to those errors matters, too. It is possible that some junk journals are actually new journals run by people with good intentions but little experience that have the potential to improve. I’m not saying a single retraction notice makes a journal reputable,

Related posts

Open access or vanity press, the Science “sting” edition
Using “journal sting” papers for teaching

The cages we scientists make for ourselves

 
“We need to change incentives!”

Ah, how many times I have heard some variation of that phrase in describing scientific publishing.

With the creation of UTRGV, my department was forced to create new evaluation documents for annual review, for merit and tenure, and so on. Creating policy documents sounds dull, but I was quite excited by this. You don’t get many opportunities the scrape away all the junk that accumulated over the past few decades that nobody could be bothered to change. This is not an opportunity that comes along every day.

I argued to change our department’s incentives structure. I had a few things I wanted to accomplish.

• I wanted us to reward open access publication and data sharing.
• I wanted to broaden the range of things that could be considered scholarly products to include more than journal articles.
• I wanted our evaluation document to reflect that the current world of scientific publishing is largely online.

My arguments did not convince my colleagues. Mostly.

People voted in favour of rewarding people for editing a book (which was previously missing from our list), or getting a patent. Progress!

People did not vote in favour of reward sharing datasets (e.g., on Figshare) or computer code (e.g., on Github), although those votes were close. Promising.

The discussion over rewarding publication was revealing.

Previously, we had given multipliers for whether a paper was published in a regional, national, or international journal. I proposed that instead, we give more weight for an open access journal article, and less weight for an article that appeared in a print only journal (e.g., not available online).

There were two arguments against rewarding open access papers.

The first was “But it costs money.” I pointed out that many open access journals charge nothing, or have fee waivers. I was also not sure why “I have to pay” was seen as a problem, since one of the legacy departments has long rewarded people for each scientific society they belong to, and that’s an out of pocket expense to get a reward, too.

The second objection was prestige. I provided links and papers to support the arguments of the benefits of open access, the pitfalls of Impact Factor, and that reprint requests don’t cut it compared to genuine open access. But they were not swayed.

Ultimately, it felt like asking my colleagues to image a world where a PLOS ONE paper was worth more in an evaluation than a Nature paper was like asking them to picture a reddish shade of green. They just couldn’t imagine it.

The department voted against the new multipliers.

So the next time you hear, “We just have to change incentives for scientists,” remember that these existing incentives are often ones that many scientists actually want. They are in a cage of their own making and could leave at any time, but won’t.

Photo by Amber Case on Flickr; used under a Creative Commons license.

Personalizing PDFs: reclaiming a personal touch on reprints

As a grad student, one of my keys to my development as a professional scientist was getting acquainted with the relevant literature. Because I be old, this was all done on paper, and largely consisted of raiding my supervisor’s files and photocopying her reprints. Some of her reprints were signed, often with short little personal notes on them.

When I started to send off reprint request cards in the mail, I started getting back a few of my own signed reprints. I liked the personal touch, and I tried to put a personal touch on my own paper reprints when I mailed them out.

Of course, email requests and PDFs supplanted posted reprints (thank goodness!). I would never want to go back to managing huge file cabinets full of photocopied reprints, but I kind of miss that personal touch. I realized, though, that there is a way to reclaim it.

If you can edit PDFs (which you can in Adobe Acrobat), you can insert test anywhere you want using the “Tools.” You can use a typeface that has a handwritten look (say, something from comic letterer Blambot) to make it distinct and separate from the main text of the paper.

You can place a signature file, like a scan of your signature on paper, using “Fill & Sign.”

It takes only a minute or two. You can make a personal message, and thank the person requesting your reprint by name. While it might not entirely capture the charm of the ink on paper, but it shows a bit of effort. And maybe it can provide some of that sense of personal connection to a community that I felt as a grad student when I was looking through my supervisor’s filing cabinets.

A pre-print experiment: will anyone notice?

In late February, there was a lot of chatter on my Twitter feed from the #ASAPBio meeting, about using pre-prints in biology.This has been the accepted practice in physics for decades.

My previous experience with pre-prints was underwhelming. I’d rather have one definitive version of record. And I’d like the benefits of it being reviewed and edited before release. Besides, my research is so far from glamorous that I’m not convinced a pre-print makes a difference.

Following the ASAPbio meeting, I saw congratulatory tweets like this:

Randy Schekman strikes again: yet another #nobelpreprint - Richard Sever

Marty Chalfie on bioRxiv! That’s Nobel #2 today - Richard Sever

Yay, Hopi Hoekstra (@hopihoekstra) just published on @biorxivpreprint - Leslie Voshall

Similarly, a New York Times article on pre-prints that appeared several weeks later focused on the Nobel laureates. I admit I got annoyed by tweets and articles about Nobel winners and Ivy League professors and HHMI labs and established professors at major research universities using pre-prints. I wasn’t the only one:

 I wish this article didn’t erase the biologists who have been posting to arXiv for years.

If pre-prints are going to become the norm in biology, they can’t just work for the established superstars. Pre-prints have to have benefits for the rank and file out there. It can’t just be “more work.”

For example, I think one of the reasons PLOS ONE was a success was that it provided benefits, not just for superstars, but for regular scientists doing solid but incremental work: it provided a venue that didn’t screen for importance. That was a huge change. In contrast, new journals that try to cater to science superstars by publishing “high impact” science (PLOS Biology or eLife and Science Advances), while not failures, have not taken off in the same was that PLOS ONE did.

I decided I would try an experiment.

I don’t do the most glamorous scientific research, but I do have a higher than average social media profile for a scientist. (I have more Twitter followers than my university does.) So I thought, “Let’s put up a pre-print on biorXiv and see if anyone comments.”

I spent the better part of a morning (Thursday, 25 February 2016) uploading the pre-print. Since I had seen people whinging about “put your figures in the main body of the text, not at the end of the paper,” I had to spend time reformatting the manuscript so it looked kind of nice. I also made sure my Twitter handle was on the front page, to make it easy for people to let me know they’d seen my paper.

I was a little annoyed that I had to go through one of those clunky manuscript submission systems that I do for journals. I had to take a few stabs at converting the document into a PDF. biorXiv has a built-in PDF conversion built into it, but the results were unsatisfactory. There were several image conversion problems. One picture looked like it came out of a printer running low on ink. Lines on some of the graphs looked like they had been dipped in chocolate. Converting the file to PDF on my desktop looked much better. I uploaded that, only to find that even that had to go through a PDF conversion process that chewed up some more time.

biorXiv preprints are vetted by actual people, so I waited a few hours (three hours and thirty-nine minutes) to get back a confirmation email. It was up on biorXiv within a couple of hours. All in all, pretty quick.

I updated the “Non-peer reviewed papers” section of my home page. I put a little “New!” icon next to the link and everything. But I didn’t go out and promote it. I deliberately didn’t check it on biorXiv to ensure that my own views wouldn’t get counted. Because the point was to see whether anyone would notice without active promotion.

I waited. I wasn’t sure how long to wait.

After a day, my article had an Altmetric score of 1. biorXivpreprints and three other accounts that looked like bots tweeted the paper, apparently because they trawl and tweet every biorXiv paper. (By the way, “Bat_papers” Twitter account? There are no bats in my paper.) The four Twitter accounts combined had fewer followers than me. Looking at the Altmetrics page did remind me, however, that I need to make the title of my paper more Twitter friendly. It was way longer than 140 characters.

Four days later (29 February 2016), I got a Google Scholar alert in my inbox alerting me to the presence of my pre-print. Again, this was an automated response. That was another way people could have found my paper.

Three weeks has gone by now. And that’s all the action I’ve seen on the pre-print. Even with a New York Times article brought attention to pre-prints and biorXiv, nobody noticed mine. Instead, the attention is focused on the “established labs,” as Arturo Casadevall calls them. The cool kids.

I learned that for rank and file biologists, posting work on pre-prints is probably just another task to do whose tangible rewards compared to a journal article are “few to none.” Like Kim Kardashian posting a selfie, pre-prints will probably only get attention if a person who is already famous does it.

Update, 18 March 2016: This post has been getting quite a bit of interest (thank you!), and I think as a result, the Altmetric score on the article reference herein has jumped from 1 to 11 (though mostly due to being included in this blog post).

Related posts

The science of asking
Mission creep in scientific publishing

Reference

Faulkes Z. 2016. The long-term sand crab study: phenology, geographic size variation, and a rare new colour morph in Lepidopa benedicti (Decapoda: Albuneidae) biorXiv. http://dx.doi.org/10.1101/041376

External links

The selfish scientist’s guide to preprint posting
Handful of Biologists Went Rogue and Published Directly to Internet
Taking the online medicine (The Economist article)

Picture from here.

Mission creep in scientific publishing

Sometimes, it feels like every proposed reform of scientific publishing involves me doing more work.

There’s significant mission creep in the checklist of disseminating scientific information. While “publish” is necessary to avoid “perish,” it is no longer sufficient. It’s “Be visible, or vanish.” And visibility requires work.

When I was in grad school, I had to write a paper and publish it.

Now, people are suggesting that I also pre-register my experiments; curate and upload all my raw data (which may be in non-standard or proprietary formats); deposit pre-prints; publish the actual paper in a peer-reviewed journal (because that’s not going away); promote it through social media; upload it into sites like Academia.edu or ResearchGate; update my publication information in databases like ORCID, ImpactStory, and institutional measures; and watch for comments on post-publication peer review sites like PubPeer and engage with them as necessary.

Now, don’t get me wrong. Those are good things to do. Individually, each one has a solid rationale. But I don’t have an army of students, or post-docs, or administrative assistants to help with any of that. It’s all me. The cumulative effect could be draining.

My approach has been to do these things when the time cost is expected to be fairly minimal. I’ve put data up for many of my papers on Figshare... usually based on whether it was already in a spreadsheet. Converting a megabytes, if not gigabytes, of physiological recordings to some sort of interoperable standard? Nope.

Similarly, after the #ASAPbio meeting, I voted “No” to a Twitter poll asking if I would commit to posting my “best” science as pre-prints. I’ll do it if it makes sense for the project (timeliness of information is important, say).

External links

Are you an  ‘academic superhero’?

The unenveloping* of Science Blogging!

It’s here!

It’s been a long time in writing and editorializing and proofing and printing (I first announced it in fall 2014), but the book is finally here! I can read Science Blogging: The Essential Guide! And you can’t yet, nyah nyah nyah!

Honestly, I’m excited not only as one of the chapter authors (first publication of 2016, I get to have some Canadian chocolate today!), but as a reader. I certainly didn’t know the complete list of chapter authors when I started writing. Looking at the other contributors to this volume is, frankly, terrifying. They are such great writers. I feel like:

I started working on my chapter on the plane to Science Online 2013. It’s almost exactly three years ago. I got 422 words written (less than many of my blog posts), which are still on my iPad. Here’s a snippet of the very start of the very first draft:

Ronin blogging
I have three science related blogs. I started what became NeuroDojo in 2002, followed by Marmorkrebs in 2007 and Better Posters in 2008,

There are advantages to belonging to a network, but they may not be as great as you think. Being on a network in and of itself does not guarantee readership.

While you are an independent blogger, you still need to develop a community.

And it goes on from there. Looking back at that first draft, it’s interesting to see how many of those first sketchy ideas survived into the final chapter.

I do have one disappointment in my chapter, though. Because this chapter references “ronin” as a metaphor extensively, I had wanted to pay tribute to Legend of the Five Rings and use this John Wick quote from one of the very first L5R promo cards, Dairya, to open the chapter:

“You call me a masterless man. You are wrong. I am my own master.”

Alas, that lead-in quote did not survive the edit, but I was able to get some L5R references in the main body of the text.

And the references to me being at The University of Texas-Pan American are also obviously out of date.

But I am so happy that this book is now out! I’m very happy with some of the turns of phrase in m contribution, and I cannot wait to work through everyone else’s chapters.

And, for the first time, something about this book has moved faster than expected! Previously, I announced it would be out 22 March, but Amazon is now showing it for sale on 1 March!

^* Normally, the reveal of a fresh new something is called “unboxing,” but since this didn’t come in a box...

Bird picture from here.

External links

Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

Related posts

Incoming: The Complete Guide to Science Blogging
Incoming: Science Blogging
Science blogging book: now with blurbs!
Science Blogging: The Essential Guide book cover reveal

Bad design used to make a good point

Michael Eisen recently took all the journal titles off descriptions of his papers on his lab website. This upset some people, which Eisen chalked it up to “the cult of the journal title.”

Alternate hypothesis: maybe it upset people because it was a bad design decision.

I’ve explored design a lot over at the Better Posters blog, and one of the most powerful lessons I’ve learned has been that good design is about empathy. Good designers empathize with their users, anticipate their needs, and fulfill their needs.

One of the things a person going to a lab publication list wants to do is to be able to find articles that interest them. Removing journal titles makes it harder for users to find articles. And while many (but, importantly, not all) articles have DOIs and links, they are not necessarily things that people relate to as much as a journal title. If you need to scribble a reference on a piece of paper, a journal, volume, and first page number is easier than a DOI link.

The argument that you don’t need journal titles because everything is on the Internet overlooks that the Internet doesn’t need journal articles. People do. People have to work with imperfect memories (some of us more than others) before starting a search on Google Scholar or PubMed. There are many papers that I look at, and I will never commit the DOI or link to memory. I remember the journal that papers were published in quite regularly, though. I don’t remember journals because of their Impact Factors, but because of the content of the journal, the layout and formatting, and other features. A PLOS ONE paper looks different than a PeerJ paper.

By removing a piece of information that users expect and want, Eisen is not meeting the user’s needs. Quite the opposite, he’s explicitly criticizing users who want this information. But good design is not about the designer. It’s about the experience of the end user.

That said, running in the opposite direction is no better:

This was a joke from Yoav Gilad (archived by Claus Wilke; it doesn’t look like that now). But for the sake of argument, let’s analyze it anyway. Here, the changes in text size for the journals (related to Impact Factor) is, for those outside of academia, pointless, and therefore confusing. For those in academia, it looks like an ego trip. (“Oooh, look at the fancy journal I published in!”)

Again: design is not about you.

Now, there is more to life than good design. Removing journal titles from a publication list is a successful act of advocacy against evaluation by “prestige,” which is a much-needed discussion to have. But it may be that users are upset not (only?) because of a cultish belief that journal titles are important signifiers of quality, but because they realize that the design effectively gives them the finger by leaving out something they want.

Update, 15 December 2015: Expanded the post with Gilad’s joke and more discussion.

External links

What’s in a journal name?
Picture from here.

Presentation Tips for people in a hurry

Batman: [reads the second riddle] What people are always in a hurry?

Robin: Rushing people... Russians!

I’m very excited to announce that my itty-bitty ebook, Presentation Tips, is now available in Russian!

You can download the Russian language PDF here.

This translation is courtesy of Maksim, who took advantage of the book’s Creative Commons license. I’m so pleased someone found this resource useful enough to translate, and I thank Maksim to no end.

This arrives on the heels of yesterday’s post (about a citation of my paper published as blog post). Both the blogged paper and this ebook were released about the same time. Both were experiments in bypassing the traditional publishing route, just to see if you could make an impact. It took a few years, but it feels vindicating to see that these projects have made ripples, and didn’t vanish without a trace.

I never thought I would see my name in Cyrillic, never mind an entire work of mine in a language other than English.

External links

Подсказки докладчикам (Зен Фолкс, 2012)

Related posts

Presentation tips compiled
Presentation Tips for Kindle
Upload the universe: validating self-publishing
2012: waiting and DIY
Fanboying

Science Blogging: The Essential Guide book cover reveal

I like it. Subdued and understated.

Related posts

Science blogging book: now with blurbs!

External links

Sci Blogging Guide Facebook Page
Yale University Press page
Amazon page

Paper published on this blog is cited because it’s a paper published on a blog

A few years ago, I published an original, data driven research paper here on this blog. As I wrote in a companion post:

I thought, “Let’s try something new.” ... I’ve also been paying attention to the people who say that scientific publishing is broken, and we should blow it up and start over. Lots of those people are basically advocating what I just did yesterday: “just blog the paper.” ...

Could blogging research work?

The acid test for whether blogging research could work is the same acid test for any academic product: do other people find it useful enough to re-use it? Usually, they show this by citing it. Admittedly, some journals are very narrow minded in what they allow you to cite, so that’s a big barrier for showing that others are using non-traditional online resources like pre-prints, blog posts, etc.

But I’m pleased to report that my crazy “self-published on a blog” paper has just got its first citation in an academic journal (Kooy, in press)!

As I expected, though, it’s being cited not because of the biology, but because it’s a paper on a blog.

Some scholars even post their research data and findings to their blogs.<sup>32

32</sup> See for example, Zen Faulkes, “The Distal Leg Motor Neurons of Slipper Lobsters, Ibacus Spp. (Decapoda, Scyllaridae)," NeuroDojo, September 6, 2012, accessed January 3, 2015, http://neurodojo.blogspot.com/2012/09/Ibacus.html.

I expected this. The paper has been viewed 3,947 times, according to Blogger. The companion post explaining why I published the paper on this blog has been viewed 11,832 times. Publishing a paper is barely worth a mention, except to the authors and a few colleagues in the field. But publishing a paper on a blog is still remarkable. In fact, more than three years on, I can’t think of (m)any other examples where people have published entire original papers on their blogs.

Instead, biology is coming around to the concept of pre-prints. I think many people think of a pre-print server as a strange sort of journal: both serve to bundle traditional research articles in a single one-stop location. Plus, pre-print servers have been long running enough in areas like physics that depositing a paper on a pre-print server is a conservative move. Blogging a paper is still a radical act.

I am very happy that my publishing experiment has been cited by others. It’s a win for the discussion of alternate ways of publishing.

But I still crave complete victory: to see the paper cited by others because of the science, not just because it’s a paper on a blog.

Reference

Faulkes Z. 2012. The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae). NeuroDojo (blog): http://neurodojo.blogspot.com/2012/09/Ibacus.html [PDF version for printing]

Kooy BK. Building virtually free subject area expertise through social media: an exploratory study. College & Research Libraries: in press. http://crl.acrl.org/content/early/2015/08/11/crl15-759.abstract


Related posts

Why I published a paper on my blog instead of a journal
Why can’t I cite Mythbusters?

External links

Pre-print power

Science blogging book: now with blurbs!

Science Blogging: The Essential Guide is now available for pre-order on Amazon!

The fun thing about the Amazon page, in comparison to the publisher’s page for the book, are a series of juicy blurbs. Here’s a couple:

“The word ‘essential’ is often overused but in this case, it suits perfectly.” — Deborah Blum, Director of Knight Science Journalism Program at MIT

“This is the guidebook science blogging deserves, and that every science blogger needs to read.” — Thomas Hayden, coeditor of The Science Writers’ Handbook: Everything You Need to Know to Pitch, Publish, and Prosper in the Digital Age

There you have it. You need a copy of this book! Make sure to order yours!

Badges for scientific paper contributors

A news article in Nature examines the latest bid to reform scientific authorship: badges.

I completely agree that the problem the badges are trying to address is one that needs addressing: clarifying author contributions. The article describes efforts to come up with a standardized list of tasks that people might perform in a scientific study. I’ve done similar exercises in my biological writing classes. Usually, we end up with about five categories, something like this:

• Concept 
• Experimental design
• Data collection
• Statistical analyses
• Writing

The taxonomy the badges are working from is more elaborate, with 14 categories, although the article mentions another group that recorded over 500 reasons (!) someone might be an author on a paper.

The Nature article links out to four papers with badges, each badge signifying an author’s contribution. The badges are standardized, appearing with the same design in both journals.

In neither journal do the badges appear in the PDF of the papers. To me, this immediately limits the usefulness of badges. I save papers as PDFs, and I consider that to be the most “official” version of the paper. If the goal is to clarify authorship, it needs to as integral a part of the paper as author affiliations or contact information.

Turning these contribution categories into badges seems like needless gamification. The article notes that software firms have used badges. This is probably why I have only heard our online learning center talk about badges. That’s been about it.

I’m hesitant about adopting trendy things from software companies. I think too often, you run the risk of investing a lot of time and effort into something nobody uses, and is quickly abandoned a few years later. For example, see this article about how universities bought into Second Life, and where that effort stands now:

I decided to travel through several of the campuses, to see what’s happening in Second Life college-world in 2015.

First, I didn’t see a single other user during my tour. They are all truly abandoned.

Second, the college islands are bizarre. They mostly are laid out in a way to evoke stereotypes of how college campuses should look, but mixed in is a streak of absurd choices, like classrooms in tree houses and pirate ships. These decisions might have seemed whimsical at the time, but with the dated graphics, they just look weird.

The work on standardizing the contributions seems very valuable to me. It moves us closer to to the movie credit model, which I think scientific authorship will ultimate evolve towards, particularly with kiloauthored papers. But I am trying to imagine having “writing,” “acting” and “special effect” badges go by at the end of movie. It wouldn’t deepen my understanding of who did what.

I do not understand how contribution badges add value that you don’t get by simply writing out the contributions in words.

Related posts

Letter in Science!
How common is “co-first” authorship?
When does authorship stop meaning anything useful?
Everybody gets to be corresponding author! 

References

Chawla DS. 2015. Digital badges aim to clear up politics of authorship. Nature 526: 145–146. http://dx.doi.org/10.1038/526145a

Photo by hyperdashery badges on Flickr; used under a Creative Commons license.

Everybody gets to be corresponding author!

Spotted in the comments section of DrugMonkey’s blog:

(C)an someone explain to me how a paper in this week’s Science is able to have 4 freaking corresponding authors?

It’s worse than that. In this week’s Science, there is one paper with two corresponding authors, one with three, and one with four corresponding authors, as mentioned above.

And that paper with four corresponding authors? It only has four authors! As Oprah might put it:

On top of that, the paper with four corresponding authors also has a note that two of the authors “contributed equally.”

DrugMonkey’s reply is on the ball:

It is because the Corresponding Author marker has now become a tick mark of academic contribution and credit instead of a mere convenience for getting in touch with the research team. So much like we’ve seen metastasis of “co-equal” first (and now last) authors, we’re seeing expansion of corresponding author credits.

We now have at least three “indicators” of relative contributions to a paper:

1. First author: this is usually assumed to be the person who did most of the “boots on the ground” work, a grad student or post-doc.
2. Last author: This is usually assumed to be the boss, the principle investigator, the person who came up with the idea and got the grant.
3. Corresponding author: Um... to me, I would take this as a signal that this person is the boss. That is, it’s the exact same assumption I make for “last author.”

If I saw a paper with different last author and corresponding author, I’d be confused. Add in multiple corresponding authors and multiple “co-last” authors and equal contribution notes, and I have no idea who’s to credit (or, if it’s bad, who’s to blame).

This is not an idle exercise for me. My new university is in the middle of trying to develop new promotion and tenure guidelines. I’m on a departmental tenure and promotion committee. Figuring out how people interpret authorship (particularly upper administration) has real implications for people’s careers. A couple of years ago, one administrator was complaining that our tenure-track faculty didn’t have enough first authored papers, apparently not realizing that in biology, the norm is that they would be last author on papers.

This is yet another indication of the phenomenon I’ve been talking about for a while. The concept of “authorship” for scientific papers isn’t the right model for assigning credit in large collaborative research projects.

Additional, 25 September 2015: Scott Edmunds on Twitter notes that “corresponsing author” has monetary value:

Chinese authors get paid (and also pay) to be corresponding, first and last author

He gave links out to China's Publication Bazaar and The outflow of academic papers from China: why is it happening and can it be stemmed?.

Related posts

When does authorship stop meaning anything useful?
Letter in Science

Incoming: Science Blogging

After being listed as “in press” on my home page for some months now, Yale University Press has moved a step closer to publication of Science Blogging: The Essential Guide.

It now has a publication date (22 March 2016), an ISBN (9780300197556 – accept no substitutes), and a price (an affordable “buy one for yourself and one for a gift” price of $24.00).

Along the way, the book has gotten a slight title makeover from The Complete Guide to Science Blogging to Science Blogging: The Essential Guide. The change is probably a good one, as it puts the book’s subject matter right up front.

The cover is not up yet, but I’ll be sure to preview it when it’s available!

External links

Science Blogging on Yale University Press
Science Blogging page of Facebook