25 November 2015

Academic boycotts

Mark Carrigan’s website poses this question as part of a lead-up to a roundtable in early December:

Why have researchers been so ready to campaign against for-profit academic publishers such as Elsevier, Springer, Wiley-Blackwell, and Taylor & Francis/Informa, but not against for-profit platforms such as Academia.edu, ResearchGate, and Google Scholar?

Because “someone’s making money” isn’t what bugs researchers. What bugs researchers is being impeded from the business of doing their research.

Paywalls and subscription fees obstruct academics trying to do research.

Platforms like Google Scholar facilitate research. I could not do my job half as effectively if Google Scholar didn’t exist. Academia and ResearchGate haven’t been as useful yet, but I have never felt the frustration in using them like I have when I’ve hit the “pay now” screen for that article I want to read..

It’s also worth noting that the original question contains an assumption: that campaigns against for-profit publishers are major academic movements. But those calls for boycotts have...well... not exactly left those business struggling. They are still highly profitable, and show no visible signs of worrying that academics are going to stop submitting papers to their journals.

External links

As Academia.edu Grows, Some Scholars Voice Concerns

24 November 2015

Tuesday Crustie: Flat footed

I’m such a sucker for digging crustaceans...

One of the matutid digging crabs, Ashtoret lunaris. Look at those lovely digging feet!

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

23 November 2015

Getting what’s paid for, scientific publishing edition

I like open access, but I think for profit publishers can continue to have a role in the scientific publishing ecosystem. But boy oh boy, some academic publishers do make it hard for a body to support them.

Recently, two independent blog posts from two separate scientists described the same problem from two separate publishers: both were downloading a lot of papers from their academic library for research purposes, and libraries were threatened by the publishers.

In both cases, the libraries had fully paid subscriptions to these journals.

Case one from Chris Hartgerink:

I started ‘bulk’ downloading research papers from, for instance, Sciencedirect. I was doing this for scholarly purposes and took into account potential server load by limiting the amount of papers I downloaded per minute to 9. I had no intention to redistribute the downloaded materials, had legal access to them because my university pays a subscription, and I only wanted to extract facts from these papers. ...

Elsevier notified my university that this was a violation of the access contract, that this could be considered stealing of content, and that they wanted it to stop.

Case two:

I was frequently obstructed by BioOne. My IP address kept getting blocked, stopping me from downloading any further papers from this publisher. I should note here that my institution (NHMUK) pays BioOne to provide access to all their papers – my access is both legitimate and paid-for. ...

I swiftly found out that downloading more that 100 full text articles in a single session is automatically deemed “excessive” and “a violation of permissible activity”.

My reaction is to give these publishers some high level side eye.

This is mind boggling. It’s so completely at odds with people’s understanding of what you should get from paying a subscription to an online resource. If your institution’s subscription fees are paid up, you should be able to access the resource. End of story.

Additional: Nature News picked up the first half of this story and covered Elsevier’s actions. Meanwhile, Elsevier has attempted to fix the situation, but Chris Hartgerink says Elsevier’s solution is not a very good one. It imposes several restrictions on the license, and doesn’t include images, which are necessary for the research.

External links

Traditional Publishers: please stop blocking research
Elsevier stopped me doing my research

20 November 2015

From spreadsheet to synthesis: my last paper from UTPA

My latest paper started as a spreadsheet.

During the writing of my last paper on the crayfish pet trade (described here), I was kind of surprised that I kept finding new papers about pet crayfish. I cited these in my paper, but mainly for the total numbers of species sold in different countries. I realized that I didn’t have a clear picture in my head of what the common species might be across all the places that had been examined.

So I made a great big spreadsheet compiling all the crayfish species sold as pets in all the countries from all the papers I could find. And I started to get a sense of the patterns. Here’s a visual (click to enlarge):

Germany was the hotspot for pet crayfish, by a long, long way. But as you can see from the map, the places that have been examined are patchy. I thought if I didn’t have a clear picture in my head, maybe others didn’t either.

So I wrote a review article.

Academics sometimes tend to view review articles as “make work” projects. Reviews are the things you write because you’ve hit a dry spell and can’t publish a data-driven experimental paper. You know, a real paper.

I get that. I’m proud of my data-driven papers. But there are a factors that can make a review very valuable.

First, when the literature is scattered, or in hard to get journals, a review provides people with a key to finding that literature. That was definitely the case here. These papers were published in were often obscure (thank goodness for Google Scholar and alerts), at least to me. There were many key papers in journals I’d never heard of before.

Second, when the literature is new, a review can draw attention to an emerging research topic. All the literature was pretty recent: 2010 and onwards. There wasn’t archival research that I could find on aquarium keeping in the twentieth century.

Third, when the research field is new, the literature is likely to be disconnected. A review of a new research topic can show where the empty spaces in knowledge are, and point ways forward. For instance, in this paper, I think one of the things that hasn’t been talked about explicitly in other papers is the supply chain from crayfish harvest to owner.

This was a fairly quick project compared to many of my papers. In some ways, I almost wish I had waited a little bit longer to submit. I didn’t think of including a couple of figures, like the map above, until it was too late. A new article about crayfish as pets in Japan appeared in the International Association of Astacology newsletter just before this article appeared.

On the other hand, I did sneak in some new data. It was data should have been in an earlier paper, but I hadn’t bothered to do the calculations until I had to give a presentation.

The journal, Crustacean Research, is a well-established society journal in Japan, but a new one to me. When I heard about it earlier this year, I kept it in mind for my papers. I like publishing in different journals, rather than going back to the same ones over and over. I like the challenge of having articles scrutinized by different sets of people, rather than going back to the same journal over and over again because you think the editor likes your work.

I liked that the journal is open access, and had moderate article charges. I had not submitted to them before, partly because their PDF production was slightly lower quality than other journals. But they just changed their production this year, and their new PDFs are as sharp as any other journal.

This paper has some personal significance for me, because it was the last I created under the auspices of The University of Texas Pan American. I completed it and submitted it two weeks before the university ceased to exist and I became a professor at The University of Texas Rio Grande Valley. The one trace of how close it was to the transition was that while I listed UTPA as my institutional affiliation, I gave UTRGV as my email. I listed my new email because I knew my UTPA email account would be dead in a few months.

And, as has been the tradition this year, I celebrated the publication of this review by dipping into my stash of Canadian chocolate:

Update, 21 November 2015: I just uploaded the spreadsheet that started this all to figshare. And I added in that newsletter article I mentioned, just for extra usefulness.

Related posts

A clone and two dwarfs
Can civil servants defuse a bomb? An Irish crayfish problem
How much is that crayfish in the window?
Tracking Crayfish Zero: The threat of pet crayfish

Throwing out the pennies

On not publishing results because they won’t end up in glam journals:

Refusing to release findings that you have already worked on, just because their most likely outlet has low standards, is like throwing all pennies out of your house because having them around make you look cheap.

Giner-Sorolla R. 2012. Science or art? How aesthetic standards grease the way through the publication bottleneck but undermine science. Perspectives on Psychological Science 7(6): 562-571. http://dxd.oi.org/10.1177/1745691612457576

Image from here.

18 November 2015

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

17 November 2015

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.32

32 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.


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

12 November 2015

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!

10 November 2015

Tuesday Crustie: Old hermit

And I mean really old... like, the Cretaceous.

Hermit crabs have a lot of flexibility in the shells they use, and different kinds of species have made shells over the millennia. So it’s surprising that we find hermits in shells of species that no longer exist, like ammonites:

Here’s a reconstruction of what that might have looked like:

The shells looks a little bigger in proportion to the crab that modern snail shells. But any ol’ port in a storm.


Fraaije RHB. 2003. The oldest in situ hermit crab from the Lower Cretaceous of Speeton, UK. Palaeontology 46(1): 53–57. http://dx.doi.org/10.1111/1475-4983.00286

Hat tip to Tim Ziegler (here) and Louise Johnson on Twitter.

05 November 2015

When you can say “There’s a lot we don’t know” (and when you can’t)

I’ve been digging Larry Wilmore’s The Nightly Show. Last night’s panel had this wonderful little exchange that was cut from broadcast, so I wanted to give it a little more visibility:

Larry Wilmore: But do you think dinosaurs were chasing Jesus?

Carl Lentz: (Laughs) Oh, man, that’s, uh… there’s a, there’s a lot we don’t know.

Neil DeGrasse Tyson: No no no we know… if… we know, if Jesus existed, if Jesus coexisted with other human beings on earth, he was not riding the back of any dinosaur. So we know that. You can’t say, “There’s a lot we don’t know” after someone says, “Was Jesus around hanging with the dinosaurs?”

Video below the fold.

03 November 2015

Tusday Crustie: Cutie

Great new crustacean species keep appearing! And this is a new genus, too!

Meet Aletheiana tenella, a new species from Indonesia. Lovely little guy!


Ng PKL, Lukhaup C. 2015. Aletheiana tenella, a new genus and new species of freshwater hymenosomatid crab (Crustacea: Decapoda: Brachyura) from Central Sulawesi, Indonesia. Zootaxa 4039(1): 118-128. http://dx.doi.org/10.11646/zootaxa.4039.1.4