06 October 2015

Tuesday Crustie: All hail the king!

When something makes normally conservative scientists put “remarkable” in the title of a paper, and name a species “king,” you stop and you open the paper.

This lovely hermit crab is Patagurus rex. This was a new genus, named after a legend in the world of crustaceans, Pat McLaughlin.

The species name is not given because it is particularly regal (sadly), but for “the extraordinary albeit superficial resemblance of this new species to some king crabs.”

This picture shows this hermit carrying not the curved snail shell you usually associate with hermit crabs, but a clam shell.

My only regret is that I didn’t stumble upon this lovely little hermit crab description when it was published a couple of years ago.


Aanker A, Paulay G. 2013. A remarkable new crab-like hermit crab (Decapoda: Paguridae) from French Polynesia, with comments on carcinization in the Anomura. Zootaxa 3722(2): 283-300. http://dx.doi.org/10.11646/zootaxa.3722.2.9

01 October 2015

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! 


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.

Comments for second half of September 2015

DrugMonkey asks how much it costs to generate a publication in something like Science or Nature or Cell. This was probably prompted by Steve Ramirez’s estimate that it took $3 million to generate one of his papers.

30 September 2015

Journals, tired of complaining about blogs, complain about PubPeer

Well, it had been a while since a journal complained about how the Internet is ruining science.

Fortunately, Michael Blatt,  Plant Physiology stepped up to the plate with an editorial re-hashing tired arguments about post-publication peer review.

How tired are they? The editorial pretty much checks off every box of arguments against post-publication peer review that I listed in my article on the subject over a year ago. It’s so familiar, Blatt could have used mine article as a template for his. “Hm. Have I complained about anonymity yet? I have. Oooh, but I haven’t said anything about the tone.”

The only wrinkle is that this time, it’s directed at PubPeer rather than blogs. Blatt goes so far as to say:

Until then, I urge scientists publishing in Plant Physiology and other reputable scientific journals not to respond to comments or allegations on PubPeer(.)

Weirdly, a very similar sentiment was expressed about the blog Retraction Watch just days before:

Mr. (Ariel) Fernández never filed the lawsuit he threatened against Retraction Watch in 2013. But he has not retracted his disdain for the blog.

“I thought about suing RW,” he told The Chronicle in an email this month, “then I quickly realized that nobody with scientific credentials takes RW seriously.”

It’s a slightly sad and desperate ploy. “Don’t look at them!”

I would do a deeper analysis of this editorial, but Paul Brookes and DrugMonkey have already done it. Go read.

Related posts

Back room science

External links

Punching down; In defense of PubPeer
Throwing punches about PubPeer


Blatt MR. 2015. Vigilante science. Plant Physiology 169(2): 907-909. http:/​/​dx.​doi.​org/​10.​1104/​pp.​15.​01443

Faulkes Z. 2014. The vacuum shouts back: post-publication peer-review on social media. Neuron 82(2): 258-260. http://dx.doi.org/10.1016/j.neuron.2014.03.032

28 September 2015

“Ideas you shall have...”

The other day, someone said to me (roughly), “You made your research career by scratching it out with your fingernails.”

Which reminded me of this classic Sandman comic (#17):

All the pictures in my head. I had to get them down, but I didn’t have any paper, or ink. So I used the wall.

And my fingertips.

Sounds about right.

25 September 2015


I saw a meteor last night!

I was lucky. I was outside for just a few minutes, and turned around at just the right time.

Now, I’ve seen meteors before. Shooting stars, like the Perseid meteor shower. But this was a big ol’ bright fireball.

At first, I thought it was a firework or something man-made. It was bright, and moving slower than I’d seen shooting stars move. It had a long trail that changed colour as it fell, although it was mostly green.

And it looked like it was headed straight for the ground. I seriously wondered if it might have landed and made an impact.

Idiot that I am, I didn’t look at my watch to get the exact time. It was too fast for video. It lasted just a few seconds.

Of course, I did what anyone would do today when they want to catch up with real-time information: I hopped on Twitter. Sure enough, there were tweets about seeing a meteor at about the same time I did. Most people didn’t have where they lived, but the timing and description matched what I saw, so I was pretty sure this was real.

I tweeted if anyone knew where I could report this, since the trajectory led me to think it might, just might, have landed. Bad Astronomer and one-time UTPA presenter Phil Plait came through and told me about the American Meteor Society’s reporting website. It’s a very cool process; very easy to give a lot of information. If you ever see a meteor, report it! For science!

The phrase “once in a lifetime” gets overused a lot, but this probably was a true once in a lifetime event.

Additional: Here’s the report page of the American Meteor Society of last night’s fireball. Quite surprised by spread out the observers were!

Do you take science to where the people are, even if they’re at a vile cesspool?

I saw this question from a Reddit “Ask me anything” (known as AMA for short) science session on Twitter:

The gist of the question is, “female Neanderthal... do you bang or do you pass?”


The answer is pretty funny, but the question comes close to encapsulating why I, personally, am less and less inclined to try to do an AMA on Reddit.

Lots has been written about Reddit’s culture of sexism (here’s one, two, three, four for starters). And yes, there is good stuff on Reddit. I have an account and post there from time to time. Some women report having never experienced sexism on Reddit. I get that.

Nevertheless, there are enough examples of problems that I ask myself: “Is this a forum I feel comfortable appearing in?”

Increasingly,  my answer to Reddit is no. Because from a distance, I’m kind of getting the impression the place is mostly a cesspool.

But I say this realizing that... there are a lot of people on Reddit. If you only go to where there are like-minded people, you can consign yourself to irrelevance.

For my fellow scientists, have you done outreach on places that are opposite to your views? Would you? Why or why not? Would you do a spot on Fox News in the U.S.? (Or, if you happen to be a politically conservative scientist, MSNBC?)

External links

Why Reddit is sexist
Sexist, racist – the web hounding of Ellen Pao shows the trolls are winning
Why Reddit Tends Towards Sexism In 1 Chart
Reddit’s woman problem

24 September 2015

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

Overly honest recruitment ad

I spotted this recruiting ad for an undergraduate research position yesterday:

“You’re Only Limited by Your Imagination!

“and funding”

I’m not sure that this level of candor is attractive, helpful, or necessary for undergraduates.

Quote of the day: Career long shots

Applies to scientific careers as well. Emphasis added:

When first starting out, did making a career of fiction writing seem possible?

Sure, it was an awfully long shot, but also I was in my 20s, and that’s the time to take your long shots — when you don’t have a mortgage, don’t have kids, don’t have anybody else who’s depending on you. Yes, of course it was a long shot, but so is being a professional athlete, being a professional actor, being a professional musician. But the world would be devoid of arts and culture (and science - ZF) if everybody said, “Ah, it’s not easy, I’d better give up now.” - Robert J Sawyer

External links

Writers on Writing: Robert J. Sawyer
Hat tip to Robert J. Sawyer on his Facebook page. 

23 September 2015

Ancient legacies promoting ancient legacies

In all the excitement about the discovery of the new fossils of Homo naledi, many of my friends in the science community have remarked on this discovery being published in the journal eLife, a new open access journal, rather than Science or Nature.

“Look, this shows that you don’t have to publish short articles in those closed access journals to get lots of attention!”

What I haven’t heard many people point out is that the discovery of Homo naledi had the advantage of being publicized by a well-oiled, well established, recognized print brand: National Geographic.

The style of coverage for Homo naledi was almost exactly what you would see for Science or Nature: simultaneous press releases, probably embargoes, cover of a magazine,and so on. The only difference is that National Geographic isn’t a peer reviewed journal, but I’m not sure that difference is one that a lot of the non-scientist crowd (maybe even including many in journalism) would recognize. I would wager that for many, National Geographic is viewed as having the same authority as Science or Nature.

Don’t get me wrong: it’s great that this kind scientific research is in an open access journal with an unlimited page count. See this post by team member John Hawks which shows how this publication compares to the scientific arguments over other fossils: short papers, long waits for descriptions, etc. And the scans of the fossils that people can print on 3-D printers are something pretty new to scientific publication. All of that is important for the science, but I’m asking more about the outreach.

If this same amount of attention had been garnered by the eLife articles alone – or, to head into complete fantasy, a bioRxiv or PeerJ pre-print (say) – then it will be safer to say the landscape for scientific publicity, news, and outreach has changed significantly. Right now, it’s just showing how much muscle the established media brands still have.

External links

New species of human relative discovered in South African cave
Is Homo naledi just a primitive version of Homo erectus?
Cover image from here.