28 December 2018

Crayfish online: The sixth in a trilogy

I’m a little surprised to realize that one of my most recent papers, about the crayfish pet trade, marks almost ten years of “following my nose.” This is a series of little projects that I keep thinking, “This  might be nothing,” But they have not just turned into “something,” but they have been some of my more highly cited papers.

While working on my previous papers on the crayfish pet trade (Faulkes 2013), I noticed that some states and provinces have laws that would make having pet crayfish illegal. But I could still find people placing ads for crayfish on aquarium sites.

I though a lot more about whether legislation had any affect on whether people bought and sold crayfish when looking at sales of crayfish in Ireland (Faulkes 2015, 2017), since I believed at the time (wrongly) that crayfish were illegal there.

While working on those papers about Irish crayfish, I realized that whether laws work was actually something I could test using online ads. Because different jurisdictions had different laws, you had a sort of natural legislative experiment.

But while the expression “laboratories of democracies” is a phrase that is bandied about in US politics, any federal system will do. And, to my surprise, I ended up studying my home: the prairie provinces of Canada.

In looking back at this series of papers, one of the things that I am slightly surprised by, and proud of, is how I was able to improve the techniques. I know that looking at websites isn’t exactly the same as learning how to do some complex lab technique, but still, the potential for how to do some of these things are only obvious in hindsight.

I started off with a survey on my own website, moved to general Google Alerts, then to online auction site ads. The description of the trade in crayfish is more detailed and precise than I started with, and it’s more detailed and precise than I find in similar papers.

Plus, I have finally reached a point where I am using these online monitoring methods to do more than just describe the pet trade of crayfish: I’m using those hand-scraped classified ads data to test hypotheses. It’s the kind of subtlety in methodological refinement that you might not be able to get if you’re just looking at single papers.

I was also pleased the paper found a home in another journal that I had never published in before, Nauplius. I learned about the journal a couple of years ago. I may have read articles from the journal before, but never really clicked in to what the journal was. An well-established, open access society journal with no article processing fees? I’d take twenty, thanks, if I could.

Is this the end of the trilogy of six about the pet trade? I’m not sure. I think I might have an idea for at least one more paper on the pet trade paper. I might have an idea for how to test a question with even more nuance.


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

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

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. https://doi.org/10.1051/kmae/2015016

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

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

Faulkes Z. 2018. Prohibiting pet crayfish does not consistently reduce their availability online. Nauplius 26: e2018023. http://dx.doi.org/10.1590/2358-2936e2018023

27 December 2018

Challenges remain, no matter your career stage

You may know this gentleman pictured at right. It’s Sir Ian McKellen.

This is a person who is pretty good at what he does.

Understatement aside, the word “distinguished” hardly begins to cover his acting career, including that he started to capture public imagination for his performances as Magneto in the X-Men movies and Galdalf in The Lord of the Rings films at a time when many others might be thinking it’s about time to pack it up.

It’s his role of Galdalf that I want to talk about. I was watching the bonus features for The Hobbit: An Unexpected Journey. Because The Hobbit movies were shot in 3-D, the perspective tricks director Peter Jackson and company used to make Gandalf look larger than the hobbits in The Lord of the Rings wouldn’t work any more.

To create the illusion of different sizes, director Peter Jackson and company literally created two linked sets. There was a fully dressed physical set where the actors playing the smaller dwarves and hobbits would act, and a rescaled green screen set that McKellen would act in, responding only to lines he heard the actors in the other set say, using an earpiece to listen in on the other set.

McKellen, literally alone on his set, got frustrated with not being able to have other people to act with. (He later explains that acting with people is the reason he became an actor in the first place.) And he had a moment where those lonely, difficult working conditions broke him. It made him stop, and cry for a little bit.

In retrospect, this shouldn’t be surprising, given how crazily complex and challenging a major movie like The Hobbit must be. But I was still kind of stunned by this moment.

Here is someone who is extremely experienced. Some would say this is someone at the top of his game, but certainly near the top of his profession. And yet he’s faced with a task where he is feeling like a failure, where he’s wondering if someone is going to have to have the awkward conversation with him that it’s time to stop, since he clearly can’t do his work any more.

To his credit as a professional, McKellen did not get angry. He did not throw a tantrum or a fit. He did not lash out at the crew.

The crew, fortunately, being a good crew, took some steps to make McKellen feel better. You can watch the appendices for the whole story. And obviously he carried on and completed filming of all three movies.

And the moral of the story is: No matter how experienced you are, you can run into challenges in your profession that make you feel defeated. That maybe make imposter syndrome flare up. You never stop needing direction, mentoring, and maybe some kindness to get you back on track.

26 December 2018

How wasting time on the internet led to my new authorship disputes paper

My newest paper came about as a direct result of me wasting time on the internet. It’s not the only paper that started out this way, but the pathway here is a little more direct than usual.

This paper started because I was answering questions on Quora like this one: “What should a PhD student do if he finds out that his ex-advisor (for a master's) published his work in a conference paper without adding his name?” Once you answer a particular kind of question on Quora, it shows you more like that one. I started seeing lots of variations on, “I’m being screwed out of credit for authorship. What do I do?”

In retrospect, it’s interesting that I never saw these questions on Twitter or other websites where I hang out with my fellow academics. What you see on one social media site is not what you see on all of them.

I saw this question enough that I thought it was worth writing a blog post here about it. More than any other paper I’ve written, that blog post was the first rough draft of what would become the published paper. Some of the examples were largely unchanged in the progression from blog post through to final published paper.

At a time when lots of blogging veterans are shutting down their blogs (farewell, Scicurious blog, you were fun), I want to hold this out as an example of why academics should keep a blog. Blogging is still the best intellectual sketch board there is. A blog lets you develop half-formed ideas into coherent arguments by writing them out in sentences and paragraphs. For me, a Twitter thread would not have acted as a springboard that could have developed into a proper manuscript.

I first chatted a bit to a couple of anonymous people behind the SmartyPants Science blog (now deleted) to see if they would like to collaborate on it. They apparently had some experience seeing authorship disputes in action, which I never had. That... did not pan out, so I went it alone. I workshopped it with a grad student writing class, who had some good remarks.

I thought this was an article with enough general interest that if I posted it up as a preprint, I might get some useful feedback. That turned out to be... not a straightforward experience. I had my manuscript rejected by the BiorXiv preprint server for capricious reasons, which I wrote about here

The good news about posting the article on the PeerJ preprint server was that I did get people tweeting it, and expressing interest in the topic of the paper. (Indeed, as of this writing, the preprint has a higher almetric score – 29 – than the published paper – 33.) The less good news was that nobody had any specific comments to make.

My reviewers, however, did have comments to make. After some desk rejects from a couple of journals (opinion pieces without data are not the easiest sell), I got some very thorough and encouraging reviews, with comments like, “I thoroughly enjoyed reading this paper” alongside the decision to... reject?! I’ve had accepted papers where the reviewers didn’t say as much positive as in these reviews rejecting the paper.

The reviews were very helpful, too, so I went back and revised and resubmitted it to the same journal. The final paper is so much stronger because of those reviews. The first half is shorter but has more concrete data. The second half has a much sharper focus on dispute resolution, because I realized that there was enough stuff talking about dispute prevention in the literature.

The moral of this part of the story is: Look past the editorial decision itself and pay attention to the tone and substance of the reviews.

And the moral of the whole story is: This paper demonstrates something I often tell people: “Yes, the internet / social media is a waste of time... but it’s not a complete waste of time. The qualifier is important.”

P.S.—I like the picture at the top of this post because these two chess pieces suggest conflict. But if you know how knights move in chess, the reality is that neither can capture the other. In other words, from the point of view of those pieces, it’s a “no win” situation.

I think that represents most authorship disputes pretty well.

Additional, 18 January 2019: Several reviewers argued that journals would never want to get involved in authorship disputes. Turns out the model I proposed is not all that similar from the one describe in this article, which came out shortly after mine was published.

Scientific journals’ creation of dedicated positions for rooting out misconduct before publication comes amid growing awareness of such issues, and stems from a recognition that spot-checking and other ad hoc arrangements were insufficient. ...

Renee Hoch(is)is one of three research integrity team members at PLOS ONE. “We’re not working in a job where people are generally happy to hear from us,” Hoch said. “You need to be a strong communicator, but also a very sensitive communicator.”

Hoch’s team, which was created in January, sees everything from concerns about data, to failure to disclose important conflicts of interest, to authorship disputes, and more. “If you wrote a list of potential ethical issues, we’ve probably seen everything on it,” she said, noting that the largest slices of the pie are image manipulation and data concerns.

Emphasis added.

And the moral of the update is: You will always find helpful articles you wish you could have cited after it’s too late.


Faulkes Z. 2018. Arbitration is needed to resolve scientific authorship disputes. PeerJ Preprints https://peerj.com/preprints/26987/

Faulkes Z. 2018. Resolving authorship disputes by mediation and arbitration. Research Integrity and Peer Review 3: 12. https://doi.org/10.1186/s41073-018-0057-z

Related posts

You think you deserved authorship, but didn’t get it. Now what? 
Does biorXiv have different rules for different scientists?

External links

This blog is dead. Long live the blog.

21 December 2018

Rubber, glass, chainsaw

Being an academic is a juggling act. You’re expected to perform teaching, and do research, and do service. And that’s just the highest level breakdown of your responsibilities.

With so much to juggle, some balls get dropped. It happens.

But one of the things you have to learn is that not all the things you juggle are the same.

Some balls are rubber. You can drop these. They’ll bounce and be okay.

Some balls are glass. You can’t drop these or they crack, break, or shatter.

The trick is knowing which one is which.

A lot of the tasks that administrators give rank and file faculty are rubber balls. Answering every email is a rubber ball.

Teaching, on the other hand, is usually a glass ball. Writing that scheduled exam is a glass ball. Grading final exams so they can go on student transcripts is a glass ball.

And sometimes you’re juggling a flaming chainsaw in the mix, too.

Your research is a chainsaw. Drop it, and it will sputter around wildly and has the potential to really damage you.

External links

Tweet from 4 December

19 December 2018

Writing bad recommendation letters

This finding about recommendations letters shook me:

The commonly used phrase, “If I can provide any additional information, please call…,” was almost uniformly identified as a strong negative comment(.)
Oh crap oh crap oh crap.

How many recommendation letters over the years had I written that had some variation of, “Please contact me”? I was trying to be helpful by letting committees know I was available to them. I though this was positive. And it looks like I inadvertently hurt my students’ chances instead.

I am not the only one who probably hurt peoples’ chances by writing letters that were perceived as weak.

This got me wondering: Why didn’t I know this?

And I realized that nobody ever gave me any guidance for how to write recommendations.

As a student, I am the person requesting recommendations. My training for writing was about how to write papers and grants.

As a post-doc, nobody asked me for recommendations. That was when someone should have warned me.

Become a faculty member, and suddenly you are regularly asked by students to supply recommendation letters. Sometimes there are from students who are one of dozens or hundred in an introductory class who you couldn’t pick out of a line-up. How do you do justice to these students who need recommendations and have few options?

In all my time on university campuses, I never heard any serious discussions about how to compose recommendation letters. Sure, I read recommendations from other faculty members, and saw obvious no-no’s. Some faculty wrote form letters, just swapping out names of students. (That works until someone sees the form letter twice. Then every student after that is harmed.)

Do other faculty ever get guidance from mentors about how to write recommendation letters? I think I’ll be putting that in a Twitter poll. Should we?

I had never seen any “how to” articles in journals about composing recommendations, either. I found this article with a quick search in Google Scholar, but it seems to be a rare specimen of the genre.

And the moral of the story is:

If you are someone who mentors postdocs, talk to them about what you know about recommendation letters. Don’t let them learn it on the fly by trial and error.

Additional, 20 December 2018: Twitter poll results! Small sample, but telling. Nobody was mentored in writing recommendations.


Greenburg AG, Doyle J, McClure DK. 1994. Letters of recommendation for surgical residencies: What they say and what they mean. Journal of Surgical Research 56(2): 192-198. https://doi.org/10.1006/jsre.1994.1031

Moore S, Smith JM. 1986. Writing recommendation letters for students. The Clearing House: A Journal of Educational Strategies, Issues and Ideas 59(8): 375-376. https://doi.org/10.1080/00098655.1986.9955695

External links

How to fix recommendation bias and evaluation inflation
Do professors ever write negative recommendation letters?
Tenure denial, seven years later 

03 December 2018

How to create your academic web presence

You’re an early career academic, and you think, “I should have something more professional than my personal Facebook account.” I’m here to help!

I recommend creating your own academic website at a bare minimum. All you need is a clean website that you are obsessive about keeping up to date. It’s practically a cliché that professor websites are five years out of date, so just a regularly updated website puts you ahead of 90% of the academic pack! Colleagues and prospective students will appreciate it.

Your university’s IT depertment should be able to provide you with server space to host webpages. That’s currently how I host my home page. But Seth Godin has a good idea here: get a simple blog and set up one featured post with your basic contact information. Then you don’t have to worry about someone else hosting your stuff, or your URLs changing because your university’s IT reorganized their directories. Of, for that matter, having to transfer everything if you move from one institution to another.

It’s also helpful to have a website with an easy-to-remember name. My website’s domain name is not provided by the university; the name just redirects to the university location. There are lots of domain name providers. I used to used GoDaddy, but got driven crazy by their wesbite, which has all the restraint of someone competing for “Best Christmas decorations in the city” award. I have been a happy customer of I Want My Name for years. Their interface is clean and simple, and their prices are reasonable. Again, having your own website name makes it less likely to change if IT reorganizes your university website.

I code my own home page using very basic HTML. Basic HTML coding is actually pretty simple. I learned by viewing the code of other people’s websites. You can do this on most browsers by choosing “View source,” although the underlying code of webpages now is so much more complex than it used to be that this might not be a great way to learn. I’ve been able to do a lot without getting into style sheets (CSS) and more recent stuff.

(A side benefit of learning HTML was that it has helped significantly in teaching online. I know how to make my online class material consistent and clean.)

I use HTML-kit (build 292, which is free) as an HTML editor, but there are many more available. I used to use what became SeaMonkey (also free). I recommend against using Microsoft Word. Word adds huge masses of mostly useless code, making pages far bigger than they need to be.

If you don’t want to learn HTML, there are online services that create websites. I used Wix to create a website recently. It looks great, but Wix is very fiddly, and it took a ton of effort to make it look as pretty as it did. You can have Wix websites for free, but then the website runs ads. You can pay to have ads removed. Of course, other services are available.

Moving from a basic website to social media is a big step up, and this is the one most where you are most likely to run into option paralysis. There are so many things you can do, how do you pick one one to do? It’s okay for that answer to be “None.” Pick ones you actually use or enjoy. If you hate Twitter, start a blog. Or get on Instagram if you dig photography.

But there are tricks to streamline some of the work in creating a web presence. For instance, the Better Posters blog has a Twitter account that is completely automated. I set it up through IFTTT (short for "if this, then that").