27 April 2016

Evolution journal retracts old science because new science is better

Retraction Watch is reporting on a case where the journal Evolution is retracting a paper, against the author’s wishes, because the author’s new research was better than the old (now retracted) research.

This is a bad move by the editors, for multiple reasons. Retracted papers still get cited, though. And maybe, in this case, that’s a good thing.

05 April 2016

Tueday Crustie: Maintenant en couleur!

Here’s a treat. The Biodiversity Heritage Library has digitized one of the first books to show crustaceans in colour! It’s from 1754. As with much old work, it’s an interesting mix of the scientific and artistic. Many of the crustaceans are immediately recognizable from their general shape, but there is a lot of detail work that is... what’s the word... fanciful.

For instance, this is without a doubt a ranid crab of some sort:

Though I have never seen any crab with such a regal looking plant on its carapace before. It also appears to have four eyestalks.

Here we have a slipper lobster:

And a spiny lobster with antennae so spectacular it required a special fold-out plate!

And, oh yeah, a mermaid. With tiny little arms.

The Christie’s auction listing notes:

Renard never visited the East Indies and was completely reliant on information supplied by Fallours and other returning travellers, and, clearly worried by brilliant colours, fantastic shapes and habits of his subjects, felt it necessary to include affidavits from various eye-witnesses testifying to the accuracy of the depictions. Despite these declarations, his work was dismissed at the time as being largely fantasy. However, writing over one hundred years later, Bleeker remarked that, 'Although these figures are partly exaggerated and partly unrecognizable, it later proved that practically every one of them is based on a natural object'.

For more on this fascinating book (and the conviction that mermaids were real), see here.

Hat tip to Raven.

External links

Poissons Ecrevisses et Crabes, de Diverses Couleurs et Figures Extraordinaires, Que L’On Trouve Autour Des Isles Moluques, et Sure Les CĂ´tes Des Terres Australes
Glasgow University Library Special Collections Department Book of the Month, January 2002: Louis Renard,
Poissons, Ecrevisses et Crabes
Christie’s auction description

29 March 2016

Tuesday Crustie: Winning the war

I recently discovered the TV show Skin Wars on Hulu. It’s one of those, “Make some cool really fast” competition shows like FaceOff, Top Chef, or Project Runway. In this case, the topic is body painting. The show’s had two seasons, with a third starting up next month. But this was the last winning entry that clinched season two for Lana!

23 March 2016

The craziest recommendation form I have ever completed

As a professor, you write recommendations for student regularly. One came in this morning, so I started filling it out. First questions were pretty standard, asking you to rate students compared to others you’ce interacted with.

One struck me as oddly worded: something like, “Student will do the right thing when no one is looking.” Um... if this student does these things when no one is looking, how can anyone know?!

But then I got to the question (click to enlarge):

And you can pick “All that apply”! “I’ll be Secretary of State and run a pro sports team!” “I’ll be Fortune 500 CEO and an astronaut, becoming the first entrepreneur in space!” These are the kind of career ambitions you might have when you’re eight. But for evaluating university students? No. These achievements are so rare and capricious that it makes no sense to ask someone to say that a student is likely to achieve these.

I thought, “This is the craziest, least realistic question I have ever had to do on a scholarship recommendation.”

Then I saw the next question, and I had to throw out my previous record holder for craziest, least realistic question I’ve had to answer for a scholarship recommendation.

There are some people in that list I would use if I wanted to diss a student. Some of the politicians come to mind.

The way this recommendation was going, I expected the next question to be, “What is this student’s mutant superpower?”

These questions are dumb. I get that a scholarship organization wants students to aim high and achieve and all, but geez. These are not realistic career expectations. And it’s not a helpful way for professors to try to characterize what they think the student’s good and bad qualities are.

17 March 2016

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


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.

15 March 2016

Tuesday Crustie: Paddy

I love this design, although since the only native Irish crayfish is the what-clawed crayfish, I kind of wish this guy had some patches of white on his claws.

This design is by Jen, who has this page with a whole whacking big stack of crustacean design! I suppose my only complaint is that the “lobster” and “crawfish” look mighty similar to one another.

08 March 2016

Fewer shots, more diversity?

The National Science Foundation just announced changes to its Graduate Research Fellowship Program (GRFP) that limits the number of applications for grad students to one. The NSF lists several reasons for this:

1) result in a higher success rate for GRFP applicants

You know how else you could increase success rate? Give more awards. But the political reality is that the NSF budget is stagnant, so the best they can do is increase in success rate at the cost of limiting chances to apply.

2) increase the diversity of the total pool of individuals and of institutions from which applications may come through an increase in the number of individuals applying before they are admitted into graduate programs,

You know what else could increase the diversity of applicants? Instead of changing the applicants, change the reviewers. Change the criterion those new reviewers are judging the awards by. Let’s not forget that in the past, GRFPs have been criticized for giving awards to doctoral students in a limited number of institutions. If the review process is biased, tweaks to the applicant pool won’t create more diversity, because they’ll be going through the same filter.

And just because I run a master’s program, let me call out that in the past, only 3.5% of awards went to students in master’s programs (page 3, footnote 3 in this report). Why do you hate master’s students, NSF?!

Terry McGlynn notes, however:

Shifting the emphasis of @NSF GRFPs to undergrads will increase representation because it will recruit people. If you give a GRFP to someone already in grad school, odds are they would be successful anyway. GRFPs can get undergrads into good labs.

This is a good point, but if undergraduates are still competing against graduates, and there’s still a bias towards the advanced doctoral students as the “safer bet,” the change in the applicant pool might not achieve the desired result in diversity. This might be an argument for splitting the program: one for undergraduates transitioning to graduate programs, one for graduate students in programs.

Finally, NSF’s last reason for the change.

3) ease the workload burden for applicants, reference writers, and reviewers.

I am glad to see this listed as a reason, because it is honest. It’s a lot of hard work to review applications, and you have to keep it to a reasonable level. I think it might be even more honest if it was listed as reason #1 instead of reason #3.

External links

NSF Graduate Fellowships are a part of the problem
How the NSF Graduate Research Fellowship is slowly turning into a dissertation grant
Evaluation of the National Science Foundation’s Graduate Research Fellowship Program final report
NSF makes its graduate fellowships more accessible

Picture from here.