No mystery how invaders cross oceans

I hate it when news organizations act boggled when there is no reason to be.

Man-Eating Nile Crocodiles Found In Florida, And No One Knows How They Got There

Obviously, the “man-eating” thing is a bit overblown and lurid, but it’s that second half that bugs the heck out of me.

Nile crocodiles are large (hence, potential “man-eaters”) animals that live in Africa. There is one way, and only one way, that they got across the Atlantic Ocean to wind up in Florida.

People moved them.

They didn’t swim. They weren’t carried off by flying rocs and dropped off. They weren’t picked up in some freakish weather event. (Though Crocnado would be an awesome name for a bad SyFy movie, if sharks hadn’t got there first.)

Sure, maybe we want some more details about who did the moving and why. The article goes on to suggest someone thought a Nile crocodile would be a great pet. The technical paper notes:

Over the last decade several large groups of C. niloticus have been imported from South Africa and Madagascar for both zoological display (e.g., Disney’s Animal Kingdom) and the pet trade, with the latter being the most likely introduction pathway for these individuals.

Saying, “Nobody know how they got there” is a lame dodge of responsibility. It’s just another example of humans messing with wildlife. We need to recognize that, and not absolve people through “mystery.” A few years ago, I heard someone on a radio show say something like, “Our pets have become family, and wild animals have become our pets.” We need to get over this notion that almost any type of animal can be a pet.

Hat tip to Andrew Thaler. Update: Andrew rightfully points out:

The specific mode of each introduction is hugely important. Accidental release from a zoo? Illegal exotic trade? Unintentional transmission via shipping? Those details matter, and we don't know yet.

That’s a fair comment. Those details are important. They may be more important for those of us studying the pet trade or working on policy than it is in a general news story. In a general news story, more good might be done by spreading the message, “Don’t keep exotics.”

Reference

Rochford MR et al. 2016. Molecular analyses confirming the introduction of Nile crocodiles, Crocodylus niloticuslaurenti 1768 (Crocodylidae), in Southern Florida, with an assessment of potential for establishment, spread, and impacts. Herpetological Conservation and Biology 11(1): 80–89. http://www.herpconbio.org/Volume_11/Issue_1/Rochford_etal_2016.pdf

External links

Man-Eating Nile Crocodiles Found In Florida, And No One Knows How They Got There


Picture from here.

Research underemployment

In general, people in science get doctoral degrees because they want to do science. But the opportunities to do so after grad school and post-docs have shrunk dramatically.

Karen James wrote about the prospects of being an unsupported scientist. Shortly after, Terry McGlynn talked about the prospect of self-funding research. Both are expressions of a common frustration: more people are getting trained to do science, but after that “training period” is over, there’s less money for research per scientist than there used to be. It’s getting tighter and tighter, with no end in sight.

While I was turning this over in my mind, two questions came to me.

Who is to blame?

The answer, of course, is nobody is to blame. Funding agencies, states, and universities each have their own, often contradictory, sets of goals and incentives. On science social media, most of the talk rotates around the policies federal funding agencies, neglecting the role of the states, incentives for institutions, and that some trends occur with no help from funding agencies. (For instance, those agency policies don’t seem to account for the growth in master’s degrees.)

The last one – institutional incentives – is is not looked at enough. If I were a university president, even knowing the oversupply problem, if I had a chance to create more doctoral programs, I would do it. There are just too many advantages. You get higher university rankings and more money.

For instance, look at the Carnegie classifications of universities. Their first pass on classifying universities as research (R1, R2, R3) is based on the number of doctoral programs. In my state, the Texas Higher Education Coordinating Board groups universities by the number of graduate programs, number of graduate students, and research expenditures. (The last is another potentially corrosive influence.)

Why is number of graduate programs and students used to measure research output? It assumes that faculty perform no research outside of supervising doctoral students. Why not number of publications or scholarly products? Universities collect that data. Heck, I’ve lost count of the number of times my university has asked me for my CV.

Obviously, there are potential pitfalls in systems intended to measure academic productivity. But consider what would change if universities were classified more by what research they put out instead of how many training programs and students they have.

Using the number of doctoral programs as a proxy measurement for amount of research capacity of a university is like using the Impact Factor as a proxy measurement for the quality of research articles: deeply, if not fatally flawed for most purposes, but survives because it’s convenient. The difference is there’s no shortage of researchers, editors, and others writing articles and editorials pointing out that the limits of Impact Factors.


Why are there so few solutions suggested to address these problems? 

Everyone likes to support “training.” Nobody’s going to get fired for putting money into training, since education is one of those rare areas that pretty much everyone wants to be seen supporting.

People with doctorates have some of the lowest unemployment rates in the U.S. There’s very little concept of underemployment and no balance sheet for missed opportunities. That makes it a tough sell to convince politicians that people with a Ph.D. are a group in crisis.

Like the weather, everyone talks about Ph.D. oversupply, but nobody know what to do about it besides dressing for today and hoping it’ll chance to something nicer soon.

External links

Karen James’s Twitter rant
Self-funding your research program
Refusing to be measured
In the future, all research will be funded by Taco Bell

Building a winning trivia team

Trivia night!

A local pub, Grain to Glass, hosts trivia night every Tuesday. I got invited to join a team over a year ago now. Our team consistently does very well, thank you.

I’ve thought a lot about why our team does so well. I’ve concluded it’s because pretty much everyone on the team is different. We have Americans, an Englishman, and a Canadian who’s lived in Australia (me!). Just that geographic diversity helps a lot. Our ages from youngest to oldest covers probably 20 years. Our professions are different. We have both men and women. My strength is science and movies, but I suck at sports... which a couple of other team members know very well.

If we had someone who kept up with current pop music, we’d be unstoppable. (Why are there so many questions about One Direction?!)

This same applies to departments and institutions, too. Diversity can build a better team.

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.

And the cycle repeats

Today is the last day of class for the Spring semester, which kind of means it’s the end of the first regular academic year at UTRGV. Okay, sure, there is summer session, but really, most of us faculty have a nine month salary, so our pay stubs say this is the end.

Where are we with UTRGV? Ugh. It’s still in beta testing. There are still many weird, unsettled (and unsettling) things going down for my liking. There’s an obsession with instant growth, and a lot of parachute candidates for administrative positions. Could it have been better? Sure. I suppose it could have been worse, though.

Meanwhile, speaking of education, Texas is set to review its science standards again. Slate has the story. Notably, author Zack Kopplin writes:

Via public records request, Slate obtained the full list of 545 applicants. Many seem up for the task, including the employees of the Perot Museum of Nature and Science in Dallas, scientists from Houston’s energy industry, the president of the Micropaleontology Press, science-assessment specialists from the textbook publisher Pearson, and hundreds of K-12 science teachers or college professors.

I was one of those hundreds of educators who applied, by the way. I’ll let you know if I get picked, but I think the odds are long. As the article says:

Members of the Texas State Board have full discretion over whom they want to appoint to the review panels—and history shows they often pick creationists.

In other words, here we go again. At least because this is happening in summer, I should have time to blog about it.

And it’s also Star Wars day! I won this glass at the pub last night during trivia.Thanks, Grain to Glass! They made both Light Side and Dark side glasses. Only Dark Side glasses were left, but I would have picked that one anyway. I’m definitely a Sith.

I won it knowing what “AT-AT” stands for. (Gloss for the non-Star Wars fans: The AT-ATs were these things, introduced so memorably in The Empire Strikes Back.)

“AT-AT” stands for “All Terrain Armored Transport.”

External links

Scientist vs. Creationist: Who will get to update Texas’ science standards?

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.

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 Côtes 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

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!

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):

Which of the following achievements may be applicable to your student's future: Select all that apply.

Options include “Astronaut,” “Nobel prize,” “US Supreme court justice.”

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.

If you fast forward 10-20 years, who would these student most closely resemble?

Options on the first screen include Barack Obama, Elon Musk, and Charles Darwin.

Options on second screen include Marie Curie, Mother Theresa, and Oprah Winfrey.

Options on third screen include Rosa Parks, Thomas Edison, and Rita Moreno.

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.

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.

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.

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.

A light touch or hands on? Monday morning quarterbacking a retraction

Things moved fast last week. I blogged about a paper with strange references to “The Creator”. Within hours, the story exploded on social media (the main hashtag was #HandOfGod on Twitter), and even garnered some tech news coverage before the paper was retracted. I was teaching and traveling when a lot of this went down, so didn’t have much change to follow up until now.

PLOS ONE deserves credit for not dawdling on this. A concern was identified, and by the next day, they arrived at a decision.

PLOS ONE loses the points they just earned, however, for the lack of transparency in their retraction notice.

Our internal review and the advice we have received have confirmed the concerns about the article and revealed that the peer review process did not adequately evaluate several aspects of the work.

Which means... what, exactly? PLOS ONE claims it will publish any technically sound science. What’s the basis for retraction, then? What about the paper is not technically sound? You can’t find it in the retraction notice. I haven’t seen any criticisms about the paper’s scientific content beyond, “It’s not news; we know hands grab things.” But no comments like, “The wrong statistic was used,” or “The authors didn’t account for this uncontrolled variable.”

The retraction notice says the editorial process wasn’t very good, but that should not be the basis for a retraction. If an editor screwed up, a competent paper shouldn’t suffer. A good result shouldn’t be punished for a bad process.

PLOS staffer David Knutsen wrote more for this blog post, but we still only get vague references to:

(T)he quality of the paper in general, the rationale of the study and its presentation relative to existing literature(.)

It still doesn’t answer what technical flaw the paper had. PLOS ONE comes out looking like it might have swatted a flay with a sledgehammer, and facing accusations of racism.

This situation is not a bug in the PLOS ONE system: it’s a feature. Ph.D. Comics published this cartoon about PLOS ONE back in 2009, which takes on new relevance:

“Let the world decide what is important.” PLOS ONE was designed from the get go to:

1. Have a light editorial touch. “Is it technically competent? Then publish.” The high volume of papers (PLOS ONE is the biggest single scientific journal in the world) pretty much ensures you cannot have the same level of editing that happens at other journals.
2. Encourage post-publication peer review.

When you combine those two things, things like the “hand of god” paper are practically inevitable. The question becomes whether the benefits of light editing (authors having more direct and potentially faster communication of what they want) outweighs the potential downsides (disproportionate criticism for obvious things that could have been fixed).

Related posts

A handy new Intelligent Design paper

External links

Follow-up notification from PLoS staff
A Science Journal Invokes ‘the Creator,’ and Science Pushes Back
Hand of God paper retracted: PLOS ONE “could not stand by the pre-publication assessment”
The “Creator” paper, Post-pub Peer Review, and Racism Among Scientists
This Paper Should Not Have Been Retracted: #HandofGod highlights the worst aspects of science twitter

A handy new Intelligent Design paper

Back on January 5, PLOS ONE published an Intelligent Design paper containing numerous references to “the Creator.” Judging from the consistent use of capitals, this would mean the Judaeo-Christian God.

I have no idea how this went unnoticed by science social media. The paper didn’t bury this, but announced it right in the abstract:

The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way.

The Introduction marks it as an Intelligent Design paper:

Hand coordination should indicate the mystery of the Creator’s invention.

And again in the discussion:

In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years.

Judging from the rest of the text,the paper probably has other credible information, which is probably why PLOS ONE published it. PLOS ONE reviews for technical competence, not importance.

From my point of view, these three sentences should have been removed as a condition of publication. Random references to a “Creator” do not advance the argument of the paper. It is not at all clear what predictions flow from the “Creator” hypothesis. The authors do not support the “Creator” hypothesis with relevant literature from the biomechanical field. In short, references to a “Creator” mark the paper as not competent science, and thus unfit for publication under PLOS ONE’s standards.

This might be one of the few times that a peer-reviewed journal has published an Intelligent Design paper. The best known was a paper by Stephen Meyer in the Proceedings of the Biological Society of Washington, over ten years ago. It was much more explicit about its Intelligent Design aspirations than this one, and it got in by... suspect methods of dodging peer review.

PLOS ONE made a mistake. It’s not a big one, as far as mistake go. Reasonable people can disagree over how big a mistake it is. It’s probably not as bad as running an entire journal devoted to homeopathy (say). It’s not surprising that the biggest journal in the world, handling thousands of papers annually, makes mistakes. They’re far from the only journal to have published texts with religious overtones.

It’s an embarrassing mistake because it would have been so easy to fix. Change three sentences, and this paper would be uncontested. Good editing is valuable, not disposable.

Hat tip to James McInerney and Jeffrey Beall.

Update: Oh yeah, this story is now burning up my Twitter feed. PLOS ONE tweeted that they are looking into this paper.

Update: Grant pointed out that even one of the paper’s own authors doesn’t seem to buy into their references to “the Creator”:

Update: Terry McGlynn notes that the lab page of one of the authors doesn’t appear to have any overt religious overtones. Several people are suggesting that this is a mistranslation. I’m not convinced (nor are others). Even if it is “just” a mistranslation, the journal doesn’t come out looking much better, because it highlights weak editing.

The hashtag for this has been deemed #HandOfGod.

Update, 1:12 pm: PLOS ONE writes:

The PLOS ONE editors apologize that this language was not addressed internally or by the Academic Editor during the evaluation of the manuscript.

Reference

Liu M-J, Xiong C-H, Xiong L, Huang X-L. 2016. Biomechanical characteristics of hand coordination in grasping activities of daily living. PLOS ONE 11(1): e0146193. http://dx.doi.org/10.1371/journal.pone.0146193

External links

The shroud of retraction: Virology Journal withdraws paper about whether Christ cured a woman with flu
Hands are the “proper design by the Creator,” PLOS ONE paper suggests

Tuesday Crusty: Fuzzy vizzie

Jessica Waller took this gorgeous picture of a juvenile American lobster (Homarus americanus). It’s the People’s Choice award winner in this year’s Vizzies for excellence in scientific visualization!

Good photos do not come easily. The page notes:

This image of a live three-week-old specimen was one of thousands Waller took.

When this went around on Facebook, friend of the blog Al Dove mentioned he got an honorable mention in a different competition for a picture of these beasts, but even younger:

External links

2016 Vizzies

Open access paper, closed data

A new paper in Science Advances by Kicheli-Katz and Regev (2016) is interesting in several ways. It’s a very interesting look at gender bias using eBay auction data.

I’ve used data from eBay myself (Faulkes 2015), and it was hard going. I visited the website roughly daily and pulled auction data into a spreadsheet by hand for each listing. Nothing was automated.

Kicheli-Katz and Rege, however, got data directly from eBay. And they got over one million transactions to analyze. That’s an awesome sample that gives them a lot of statistical power. I was curious to know more, but found this text in several places in the paper.

According to our agreement with eBay, we cannot use, reproduce, or access the data.

I raised my eyebrows at that a bit. All sorts of questions bubbled into my mind. The acknowledgements section provided more detail, however:

eBay has provided written assurance that researchers wishing to replicate the work would be afforded access to the data under the same conditions as the authors.

Okay. That’s more helpful information, and I wish it was in the main body of the text, rather than buried at the end of the acknowledgements. On the Science Advances webpage, it is the second to last thing on the page (the last is the copyright notice).

Clearly, social media companies realize that their data is scientifically valuable and want to use that for their own gain. OKCupid used to write amazing blog posts based on their data that give you a hint of how rich the kinds of questions and answers you can tackle are using large social media datasets. (Although OKCupid also got flak for running unregulated experiments on its users, and rightfully so.)

The eBay disclaimer runs counter to the major trends we are seeing in scientific publication: more transparency, more access to raw data. I am not sure how confident I am with eBay’s promise to share the data with other researchers. From the point of view of reading this paper, eBay is mostly a big black box.

Update, 12 April 2017: I emailed the eBay representative listed as a contact in the paper on 26 February 2016, inquiring about working with eBay’s research lab.

I never got a reply.

References

Kricheli-Katz T, Regev T. 2016. How many cents on the dollar? Women and men in product markets. Science Advances 2(2): e1500599. http://dx.doi.org/10.1126/sciadv.1500599

Faulkes Z. 2015. 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

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’?

Tuesday Crustie: Beer

“It’s okay, we can regrow the claw!”

Hat tip to John Wares on Twitter.

Steampunk open access

Consider a world much like our own. Scientists do research, and publish their findings in academic journals, made of paper and ink and glue and leather.

Except... that the concept of open access took hold in the early days of academic publishing. Authors paid article processing fees to pay for printing costs. The resulting print journals and books were sent to libraries and to archive free of charge. People who wanted copies merely had to ask.

This system continues until the late twentieth century, when the Internet becomes readily available to researchers and the public alike. Now, all those centuries of research (still freely available, mind you) are in an antiquated, inconvenient format. People want get digital copies of research papers that interest them.

Who would put in all the hours of work to digitize those open access articles? Who would pay the costs? Who would create the websites? Who would assign the DOIs?

There used to be a complaint that younger scientists’ reference lists rarely went back before the 1990s because papers weren’t online. Imagine how much worse the problem would be in the steampunk open access scenario.

In our world, a lot of the world’s scientific back catalog got digitized by those bad guys, commercial publishers.

It is short-sighted to think that electronic text, and particular PDFs, are the final form of academic communication. When the next transition of formats occurs, how will open access papers make the jump?

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

Science Blogging: The Essential Guide companion website up!

 

We’re exactly two weeks out from the launch of Science Blogging: The Essential Guide. When I got my review copy, one of the first things I did was to look for the online resource mentioned in the book, and was a bit nervous not to find it. But that is now remedied, and it is up for you to check out today at The Open Notebook!

Among the goodies is a Q&A with the editors here, with some good thoughts on the past and future of blogging.

Scicurious put together a Twitter list of all the authors and editors for your following pleasure.

Meanwhile, I noticed that Amazon will be offering a Kindle edition of the book for those of you who already have enough physical stuff lining your bookshelves. It’s also up for sale at other vendors, such as Barnes and Noble, although they don’t seem to have an ebook version available yet.

Update, 23 March 2016: Joanne Manaster interviewed the editors, Bethany, Christie, and Jason on her Read Science hangout series.


Update, 24 March 2016: Editor Jason Goldman is interviewed on Science Writing Radio, Episode 31!

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
The unenveloping* of Science Blogging!
Science Blogging: The Essential Guide already making waves!

External links

The twain shall meet
Science Blogging on Yale University Press
Science Blogging page of Facebook
Science Blogging on Amazon

Tuesday Crustie: Lobsterworthy

We can thank Queen B for the latest crustacean meme.

External links

After Beyoncé Shout Out, Red Lobster Makes “Lobsterworthy” Shirts For Valentine’s Day

Another UTRGV teachable moment

UTRGV tweeted this image from our Brownsville campus:

I’ve walked through this lobby a few times, but it never clicked that the spiral is supposed to represent DNA, the molecule of life. It is in the lobby of the Life and Health Sciences Building.

I realized there’s a problem.

The spiral is going the wrong way.

It’s twisting to the left (counterclockwise). DNA twists right.

It’s not the only problem with the image. The two strands of DNA are not evenly spaced, for one, but I am willing to let that one slide because of limitations of the medium (bricks and tile). But it would have been as easy to build it twisting the other way. Indeed, this seems to be such a common mistake that I wonder if there are more incorrect depictions than correct ones out there.

I knew that DNA strands have a particular direction. Pretty much all biological molecules are “handed” in some way. But I am not a molecular biologist, and was never able to remember which was the right way around. Thanks to this pillar, I’ll probably never forget now. Even it that knowledge is tinged with a little embarrassment that a new research university is displaying something factually wrong.

External links

DNA's twist to the right is not to be meddled with, so let's lose the lefties 
Graphic design, error, and accidental learning

Editors are responsible when you get a bad review, too

Jon Tennant, writing at Science Open, has me thinking about the ongoing issue of anonymity in science again, particularly in peer review. My thinking on this matter has changed a lot. I sign my reviews, but I’m much more sympathetic to those who don’t sign their reviews than I used to be.

Jacquelyn Gill recently provided a useful reminder of how unhelpful and downright crappy some reviews can be:

I recently had an NSF proposal reviewer say outright that I was only on a proposal to check the gender diversity box, and that I am a “competent palynologist” (sic) and don’t need “pity support” from male colleagues. ... the implication that I wasn’t deeply involved in the conception and writing of the proposal was insulting to me and my colleagues, and there was zero evidence of that in the proposal.

When you get a bad review, the first thing you’re tempted to do is lay blame on the reviewers. After all, the words originated there. This carries through to most of the writing and research on peer review: most arguments center on anonymity of the reviewers, and to some degree, the authors.

If an author gets such a bad, biased review, it is not solely the fault of the reviewer. An editor passed that along. An editor decided that stupid review was worth conveying to the author.

An editor who did that should have her or his feet put to the fire. Part of the job of an editor is to provide oversight. An editor who blindly forwards all reviews regardless of their content, regardless of how blindingly unhelpful or even blatantly sexist they are, is incompetent.

While most journals allow anonymous peer review, they don’t allow anonymous editors. Until scientific culture changes to make reviews more open (and it may not), editors should be pressure points of accountability. We need to publicize cases where editors pass on the dumbass reviews.

This can work. There’s been at least one case of an associate editor being relieved of duties after passing on a bad review.

External links


Peer review: open sesame?
Over-proved, but fantastic flavor: The Great British Baking Show as a model for writing reviews

Science Blogging: The Essential Guide already making waves!

We’re still more than two weeks away from the official release of Science Blogging: The Essential Guide, but the book has already racked up its first citation, in the New York Times Sunday Book Review.

It’s kind of a throwaway reference at the end of a longer book review (on atheism and religion, by James Jones, but it’s exciting. Early references to the book bode well for its reception.

Harker’s book, though of interest to anyone looking for a guide to such controversies, is aimed at college students in an introductory philosophy of science course. Should he ever decide to communicate these views more broadly — which is to say, to blog about them — he might consider picking up a copy of SCIENCE BLOGGING: The Essential Guide (Yale University, paper, $24), edited by Christie Wilcox, Bethany Brookshire and Jason G. Goldman, which offers practical advice on such matters as “blogging about controversial topics” and “persuading the unpersuadable.” For example: Always link to the relevant research, avoid “muppet flailing” (excessive fervor, I gather) and “don’t let the trolls get you down.” Words not just to blog but to live by.

“Words not just to blog but to live by.” That’s not a bad pull quote for a book blurb!

Additional, 8 March 2016: I guess I’ll use this post to compile reviews and features of the anthology. This article just in from Times Higher Education! It also has a very brief cameo at the end of this Canadian Science Press post, Science Blogging 101.

Additional, 17 March 2016: Andrew David Thaler, himself no slouch at blogging, reviews the book in Science magazine.

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
The unenveloping* of Science Blogging!

External links

The twain shall meet (New York Times)
How to set up a blog about science (Time Higher Education)
Science Blogging 101
Blogging for beginners (Science, paywalled)

Sales links

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

Tuesday Crustie: Colour your own crustacean!

Colouring books for adults are popular now, so I applaud the BioDiversity Library for making this outreach tool! They have a whole big big available here.

Hat tip to Ely Wallis.

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

Setting an agenda

Despite the title, committee chairs don’t have all that much power, particularly in academia. The whole point of having committees is that committees vote, and responsibility is diffused.

Committee chairs do have one actual power: to set an agenda.

I’m only a few days into my term as chair of the Student and Post-doc affairs committee at SICB, but I just want it to be known publicly that preventing sexual harassment of students and trainees has jumped to the top of the agenda.

This went to the top this morning when I opened my Twitter feed and saw, over and over, people discussing this article in the New York Times about an individual who harassed students at multiple institutions. This comes on the heels of other examples in recent months. This blog post could easily turn into a litany of harassment, so let’s just say this: there’s too much of that crap going on.

I don’t know whether harassment has been a topic of conversation for the committee before, but I look forward to finding out. If it hasn’t, it’ll be new. If it has, I plan to keep it front and center.

And I’m blogging this because I want to be accountable. I want people to know that this is what I want to try to do, so they can see if I succeed or not.

Related posts

Okay, SICB students and post-docs, I’m your guy

External links

Chicago professor resigns amid sexual misconduct investigation
Here’s how Geoff Marcy’s sexual harassment went on for decades
Work in progress: changing academic culture
You are worthy.

Photo by A Syn on Flickr; used under a Creative Commons license

Who is Jingmai O’Connor, and why is she saying nasty things about science blogggers?

We’re less than two months away from an entire book about science blogging dropping from a major university press (disclaimer: which I have a chapter in), and here we have a reminder that many believe blogs are not a legitimate form of academic writing:

What’s your view on social media and science? For example, the role of science blogs in critiquing published papers? Those who can, publish. Those who can’t, blog. I understand that blogs can be useful in affording the general public insights into current science, but it often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves. If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form. The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet. Thus, I find that criticism in social media is damaging to science, as it is to most aspects of our culture.

This quote is from an interview with Jingmai O’Connor, a paleontologist currently in China.

Let’s break down the problems here.

“Those who can, publish. Those who can’t, blog.” There are many researchers who do both, productively.

“I understand that blogs can be useful in affording the general public insights into current science...” It’s nice that we bloggers got tossed a bone (no pun intended). But science blogs do not just help the general public; there are many technical comments on papers that help provide needed context for other scientists, whose own research is tangential to published research: close enough to see the relevance, but without the deep expertise needed to pick out specific problems.

“(I)t often seems those who criticize or spend large amounts of time blogging are also those who don’t generate much publications themselves.” O’Connor is hypothesizing that there is an inverse correlation between blogging and primary literature. This an interesting empirical question. It’s true that time spent blogging is time that cannot be spent writing primary peer-reviewed journal articles, so prima facie, there might be truth to this. But as far as I know, there is no actual peer-reviewed literature on this. Will update this post if I find any.

“If there were any valid criticisms to be made, the correct venue for these comments would be in a similar, peer-reviewed and citable published form.” The venue a claim is published in does not determine the validity of the claims. She is correct that certain journals are averse to citing non-peer reviewed material, and that putting material in the literature helps to assure the long-term findability of the critique. But these matters are not central to the main issue: is the criticism valid? Then it does not matter where it was published.

“The internet is unchecked and the public often forgets that. They forget or are unaware that a published paper passed rigorous review by experts, which carries more validity than the opinion of some disgruntled scientist or amateur on the internet.” Some things on the Internet are unchecked. Some things on the Internet are rigoruously checked. It should also be noted that some journals that call themselves peer reviewed provide checks that are, at best, cursory (see here and here, for instance). Even “top” journals have published papers that made pro scientists ask, “How did this get published?” Has Dr. O’Connor not heard of arsenic life or STAP cells?

“I find that criticism in social media is damaging to science, as it is to most aspects of our culture.” I’ve written a whole article (Faulkes 2014) about why I find that criticism in social media generally valuable. To name just two: it is rapid, and provides a way to bypass powerful gatekeepers with vested interests.

I have no idea what damaging effects of social media on culture she is referring to. It’s off topic, in any case.

Not surprisingly, as soon as someone on social media found this, this quote began spreading like wildfire. But there is apparently a backstory that is not spreading as fast. Jon Tennant wrote:

In this situation, she’s actually right. There's a core of semi-pro bloggers who attack her work/never formally publish anything.

I went digging. And I was surprised, because my first impressions are that Dr. O’Connor is not a stereotypical stick in the mud, conservative older scientist that is sort of the stereotype for critiques of blogging and social media. Honestly, she seems... kind of... awesome.

I went through the first ten pages of Google results, and found tons of positive stuff about her, including tons of stuff on blogs. She’s had lots of high profile papers. She’s done some science outreach. She strikes me as smart, outspoken, and a little unconventional. Jingmai O’Connor seems like exactly the sort of person I’d use a counter-example to the “scientists are old white dudes” stereotype.

I did a Google search for her name plus “blog.” Went through multiple pages and still found nothing negative about her, or controversies around her work. Tried her name plus “controversy.” Still nothing.

Maybe the blogging criticism is behind the Great Firewall of China.

Even when intentionally looking for the backstory that might have motivated her comment, I can’t find it. Whoever the bloggers are who have criticized her, they didn’t appear to make a big dent in her online reputation to an outsider like me. Which makes me all the more puzzled why she would paint all bloggers with such a broad brush.

It’s unfortunate. I hope that the criticism of her ill-advised comments don’t cement her “The Internet is bad” opinions. If she had a blog, I would be reading it.

Additional: Lengthened the blog post with a line by line fisking of the quote.

References

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

O’Connor J. 2016. Jingmai O’Connor. Current Biology 26(1): R11–R12. http://dx.doi.org/10.1016/j.cub.2015.11.046

External links

Jingmai O’Connor home page
Interview with Dr. O’Connor
A teacher can never tell where his influence stops
Fashionista: Jurassic Jingmai
Jingmai Kathleen O'Connor: Badass archeologist (sic)
Society for Vertebrate Paleontology 2014

Blogging is wonderful for science. More scientists should blog and tweet.
Chill out about Jingmai O’Connor’s criticism of bloggers

DoctorZen.net moved

My home page, DoctorZen.net, has migrated over to a new institutional server. The old site will be up for a while until I get a redirect notice up, but it will eventually close as website support for my previous institution (The University of Texas-Pan American) transitions to my new one (The University of Texas Rio Grande Valley).

If you visit the site by a directly typing in the URL into a browser, you should see no difference.

If you bookmarked the homepage, take a moment to check that it links to the new URL:
http://faculty.utrgv.edu/zen.faulkes

You can let me know if there are any problems by emailing me at zen.faulkes@utrgv.edu.

Okay, SICB students and post-docs, I’m your guy

I knew this was coming, but I just got the official email.

I am writing to appoint you as Chair of the Student & Postdoctoral Affairs Committee within the Society for Integrative and Comparative Biology. Your appointment will be for three years, starting immediately and running until the end of the annual meeting in January of 2019.

I had been approached about this back before the last SICB meeting in Portland. I thought a very, very long time before stepping up and accepting this.

I was extremely hesitant about being another old white guy in a leadership position of a scientific society. This is especially true of a leadership position that is about engagement of young researchers, the place where our diversity in the sciences is the greatest.

I also paused when I considered that I’m at an institution with no doctoral programs or post-docs. Yes, I’m a graduate program coordinator for my department, but it’s a master’s program. Would I be in touch enough with the realities of the more advanced training programs that would make up the bulk of the constituents?

Finally, I had a truly selfish reason: committee work will cut into research time. And the research had been going well, and I don’t want that to stop.

Ultimately, one of the main reasons I agreed to do this was that the hint was dropped that if I didn’t do the student committee, the Executive Committee would keep after me to do something for the society. The judgement had been rendered, and it was all a question of how sentence would be carried out. I picked the devil I knew versus the one I didn’t.