18 January 2019

Low on “agreeableness”


Grumpy prof is grumpy (low agreeableness score) just because, not because he’s stressed (low negative emotion score).

Test results of the “Big five” personality traits. Take the test here.

Hat tip to Adam Calhoun.

External link

Most personality quizzes are junk science. Take one that isn’t.

14 January 2019

How to fix a lab fail

I did my fair share of physiological experiments with neurons when I was a trainee.

The experiment was an attempt to get a handle on whether a particular pathway between sensory neurons A and interneurons B had few neurons (maybe even only a single connection; monosynaptic) or many neurons (polysynaptic).

One way you can test whether you have few connections or many is by messing with the physiological saline the neurons are sitting in. Physiological saline is a solution that mimics the inside of the animal they are normally found in. Different species have different mixes of salts and other chemicals that keep the neurons alive and firing. There is usually a lot of gold ol’ sodium chloride (table salt), potassium chloride (salt substitute for some people), and so on.

Normally, that physiological saline contains some calcium, because calcium causes neurons to release neurotransmitters. If you change with the amount of calcium in your saline, you make each connection between neurons more and more likely to fail. Using some ions that mimic calcium (like magnesium) make this plan even more effective.

Pathways with single connections between will often keep working with this altered saline: hen you stimulate A neurons, you still see the response in B neurons.

Pathways with many connections usually stop working with this altered saline. When you stimulate A neurons, you are unlikely to see activity in B neurons.

I was doing this experiment, and the results kept being... disappointing. I couldn’t understand the results. And the neurons seemed to keep dying faster than usual. I talked to my supervisor about these experiments. We went back and forth a bit, and at one point, my supervisor asked,

“What did you mix the solution in?”

I replied, “I mixed it in...”

Freeze frame. Record scratch.

It was at that precise, exact instant – after that exact word but before I said the next – that I simultaneously recognized and solved the problem that had been vexing me in the lab. If I was a cartoon, a lightbulb would have clicked on above my head. If I was in a modern movie, I would have had a high speed montage run in front of my eyes showing the key moments I went wrong.

All of this happened in pause that lasted about a second.

But I couldn’t stop myself from finishing the sentence, even though I knew that I was about to reveal myself as having made a dumb, amateur, “I should damn well have known better” mistake.

“...distilled water.”

My supervisor laughed. Not loudly. A chuckle, I think would be the appropriate description. I think the laugh was not only because he knew the solution as soon as I said it, but because he saw the look on my face that revealed I’d experienced “Aha!” and “D’oh!” moments simultaneously.

I’ d put the calcium substitutes in pure water. Not saline with all the other salts that were needed. No wonder the neurons kept dying.

I fixed the saline and went back to trying the experiment. The neurons were much happier, although it turned out the results of the experiment were so muddy and hard to interpret them that we never published that data in a paper. (It appeared on a couple of conference posters.)

And the moral of the story is: Whenever you have a problem in the lab, make sure to tell someone else. Because sometimes, you might just solve your own problem.

P.S.—I told this story on video as part of the SICB lab fail contest in 2018. I did not win. I wonder if the video is kicking around someplace...

P.P.S.—I didn’t know it until years later, but I was using a technique “Rubber duck problem solving.

P.P.P.S.—In the original account, the duck was stuffed (as in, a hunting trophy, not plush fur), not rubber.

P.P.P.P.S.—When I was deep into CCGs like Legend of the Five Rings, I talked a game company staffer who answered the phone. Her name was Mindy. Mindy would get players calling in with rules questions all the time. If you know CCGs at all, you know there are many complex rules questions that arise, because there were a lot of possible interactions between cards. Mindy said she would often get people really wanting to ask detailed questions about the Ninja Shapeshifter or something. But because Mindy was customer service and events, not game design, she didn’t have all the cards memorized. She’d ask the person on the phone to read the card out loud to her.

She said she lost track of the number of times the person would start reading the card to her, pause, and then say, “Oh.”

They answered their own question just by reading the card out loud.

Say stuff out loud, people. I’m telling you. It works.

03 January 2019

When side projects take over

It's probably fair to say that for the last few years in the science community, the thing I’m best known for is the poster blog.

I was on my Google Scholar page a few days ago, and noticed I had a new “most cited” paper: a paper I co-authored on science crowdfunding from the #SciFund days.

Don’t get me wrong, I’m happy with both of those projects and I’m glad they’re successful. But I don't think they are representative of my professional work on brains and crustaceans. And that is a little frustrating.

I suppose that this shouldn’t be a surprise to me. As I tell people, a key part of learning to be an academic is figuring out what you don’t suck at. I realized back in grad school or my post-doc days that other people were much more skilled in the lab than I was. I’m okay in the lab, but I felt writing and communication was where I didn’t suck.

So I had a sense for a while that maybe the place I would make the biggest impact was never going to be at the bench, churning out data, or getting students to churn out data. It’s nice to have that suspicion confirmed. I actually kind of suspected I might get more involved in the editorial side of science, but that hasn’t happened, either.

The papers that I think have the most potential to advance knowledge are a pair of crustacean nociception papers. I wish a lot more people referred to the second paper when the discussion about “Does it hurt lobsters when they go into the pot?” question when it makes the round every eight to ten months or so. Because that’s still the only paper that’s really tested the issue of whether high temperatures are noxious. I don’t think that paper gets as much attention as it should.

So if you would like to make me happy, please have a look at that paper.

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.

References

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.

References

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