Tuesday Crustie: Troglobitic

From a cave in Tennessee. The photographer calls them isopods, although they look a little longer and narrower than many isopods.

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

Tuesday Crustie: Cha-ching!

The ancient so revered crustaceans that they put them on their money! According to the caption:

Coin from the city of Priapos, Mysia, (today Karabiga; Turkey) 1st century B. C.

The page I found this on includes a lengthy discussion of the origin of “lobster” and “crayfish.”

External links

How did lobster mean two different species?

Comments for first half of May 2015

The issue of how science funding should be distributed (To the few, the proud? Or share the wealth?) is brought up at Scientists Sees Squirrel.

Fanboying

Natalie Morales reviewed my itty bitty ebook, Presentation Tips!

Natalie. Effing. Morales!

(And she liked it! Squee!)

Update, 1 August 2017: My little ebook makes a cameo appearance in this new interview with Natalie (my emphasis):

And then there is her Instagram account. “I’ve noticed that all these celebrities were getting a bunch of free shit and sort of faking it on Instagram,” she explains. “I was like, well, why not just, like, blatantly do it? Why not just go, like, ‘Hey, I like free stuff. Don’t send me a shitty thing because I’ll say that it’s shitty, and I’ll post about it.’”

She started the Instagram account @NatalieMoralesLovesFreeStuff, and now she gets free stuff — including a fantasy novel someone has written, a public-speaking manual someone has written, chocolates from a small candy shop, a board game someone developed, and some swag from Dyson.

Tuesday Crustie: Go!

Meet a regular on Teen Titans Go!

Unfortunately, this resident outside Titans Tower seems to have no name.

But he can take comfort.

At least he has his own wiki entry.

And crabs are much cooler than seagulls.

When does authorship stop meaning anything useful?

“My god... it’s full of authors.”

Prof-Like Substance drew my attention to this fruit fly paper, which may be a new record setter. I have never before seen a paper with over one thousand authors. One thousand and fourteen, if my count is correct. (Image at right. Click to enlarge... if you dare. That took some image stitching, let me tell you)

The highest I’d seen before this was a paltry 816.

I was curious what you had to have done to be listed as an author. With that many, it seemed like the criteria for authorship might have been, “Have you ever seen a fruit fly?” I went looking for statement about author contributions, which some journals have. There is not any such declaration in the paper.

The PDF of the paper gives a bit of a clue as to what’s going one. The author list is more modest on the title page, which lists the authors as, “Wilson Leung and Participating Students and Faculty of the Genomics Education Partnership.” So a lot of these authors are students who took a class, and probably completed part of the analysis as a course assignment.

Digging into the acknowledgements, though, suggests that the inclusion for authorship was marginally higher than being an data monkey:

The authors also thank additional students who contributed data analysis to this project, but for various reasons did not participate in reviewing the manuscript.

This suggests that all thousand or so authors at least looked at the paper and signed off on it. But judging from the course listings in the Acknowledgments section, it seems that many of these were undergraduate students, and I wonder whether any of them had any substantive opportunity to have input into the text and interpretations of the paper. And can everyone stand behind, and vouchsafe, the data here? Some guidelines require that of authors, and I think that’s a pretty good guideline.

I am all for engaging students in research, and crediting them. But this is a bad way of doing it.

Papers like this render the concept of “authorship” of a scientific paper meaningless. This feel more like a participation award than authorship. A possible solution, as I’ve suggested before (also here; paywalled), is that we need to give up “authorship” and focus on “credits” that are clearer descriptions of the contribution individuals make. Call the students “contributors” rather than authors. Put it in a supplemental file.

Additional: Okay, this paper has 1,446 authors, and this one has 2,932 authors. (Hat tip to Jens Foell for pointing those out.) Both are particle physics papers, though, a field which has been dealing with large author numbers for a long time. The paper under discussion here, the fruit fly paper, may be a record for biology. Even the draft human genome got ‘er done with “just” 272 authors.

New rule! If the number of authors on your paper can be measured in “kiloauthors,” having your name on the paper will not count for tenure and promotion purposes.

Update, 12 May 2015: The journal’s blog describes how this paper came to have over 1,000 authors, with over 900 of them being undergraduate students.

I will point out that there are guidelines for who gets to be an author. These are not perfect (Drugmonkey hates them), and not often followed in the trenches. But they do represent an attempt to spell out what authorship should mean, by a fairly substantial number of people working in scientific publishing.

I doubt that every undergraduates on this paper truly helped draft or revise the paper (criterion 2) or can be truly accountable for everything related to the paper (criterion 4). To their credit, author number 1,014 says on the blog:

“Actually we got some important comments back from students,” says Elgin.

I’m pleased that some students made important comments, but I have doubts that all the students genuinely met the “draft and revise” criterion. Reading a paper and saying, “Okay,” doesn’t cut it for me.

Update, 13 May 2015: This story has bubbled over to Nature’s website, with some comments from the non-student authors. Warning: contains me.

Update, 21 July 2016: This blog post discusses a highly cited technician (mostly so I can find it again later).

Related posts

Letter in Science

External links

Class projects as publishable research?
Undergrads power genomics research
Who is an author? (ICMJE “Vancouver guidelines”) 
Fruit-fly paper has 1,000 authors

Riding into the sunset: my last class at UTPA

I just taught my last class at The University of Texas-Pan American ever. And, in contemporary fashion, I marked the occasion with a few selfies with my students.

Today is the last day of classes for the spring semester. There are still grades to calculate and such, but there are no more lecture days.

I am not teaching in summer 2015. I desperately need time not teaching to do many, many things. My office is about two years overdue for a purge, I have two manuscripts waiting for my revisions, there’s administrative stuff...

And when Fall 2015 rolls around, I will be teaching at the University of Texas Rio Grande Valley.

When I got here in 2001, the first class I taught was General Biology. And today, the last class I taught was General Biology again. And the students were good sports, so it was a nice class to end my UTPA teaching on.

It’s the end of an era.

Tuesday Crustie: Beautiful

Meet Cherax pulcher. Its last name, “pulcher,” literally translates to “beautiful.”

Unfortunately, the beauty of this species may be its downfall. They are already for sale, and collected in large numbers, in the pet trade. And since the species is new to science, we know almost nothing about its basic biology.

Astacologist Chris Lukhaup mentioned on his Facebook page that he’s spent over a decade working on the description of this gorgeous new species. They aren’t all this pretty; there are a couple of different morphs, and no doubt Chris’s considerable photographic talents are at play in this picture, too.

Update, 13 May 2015: This crayfish is featured in this New Scientist article. Warning: contains me.

Update, 15 May 2015: It’s so nice to see crayfish in the news, and attention being drawn to the potential dangers of exploiting an almost unknown species for the pet trade. This article in the Washington Post says the species looks like a Lisa Frank creation... wait, did they steal Jason Goldman’s joke?

Reference

Lukhaup C. 2015. Cherax (Astaconephrops) pulcher, a new species of freshwater crayfish (Crustacea, Decapoda, Parastacidae) from the Kepala Burung (Vogelkop) Peninsula, Irian Jaya (West Papua), Indonesia. ZooKeys 502: 1-10. http://dx.doi.org/10.3897/zookeys.502.9800

Don’t forget who approves new doctoral programs

The University of Michigan has been hosting a series of talks on the future of graduate and postdoctoral training in biology. There is a comprehensive Storify of tweet here.

American discussions about whether there are too many doctoral students and postdocs appear to be very much driven by federal funding agencies, mainly the National Science Foundation and the National Institutes of Health. Both have an interest because they provide are the source of support (salaries and such) for graduate students and post-docs.

The role of American states in this whole scenario is almost never mentioned.

In Texas, new doctoral programs have to be approved by the Texas Higher Education Coordinating Board. I have not conducted a survey of all the higher education systems in the United States, but I suspect that there are similar boards in other states.

If there is overproduction of doctorates, the states bear some responsibility for creating new doctoral programs.

While I hear from federal agencies on graduate student and post-doc training quite often, I almost never hear what the states think of all this.This mattere, because each state can have its own higher education agenda. And that agenda may not align with the agenda of the federal funding agencies.

The federal agencies get a lot of attention in this regard because they have money. But there should be a lot more attention focused on what the individual states think on the future of graduates and post-doctoral training. The states should not create doctoral programs at whim then leave them to be funded by federal agencies, any more than institutions should recruit grad students, and send their recent graduates off with little more than, “Good luck with that job hunt!” when they’re done.

Epic fail: universities scared of dealing with bad behaviour

If a student called me a “f*cking moron” to my face, do I have the right to fail that student in my class?

Because that happened recently, just not to me. This story broke a few days ago: a Texas A&M professor decided to fail his entire class. The professor involved reported a host of issues with his students, including clear academic misconduct, but it seems that a lot of the problem arose because students were behaving badly. Calling a professor a moron is... not the way to win friends and influence people.

The university, predictably, is responding thus:

Dr. Patrick Louchouarn, the vice president of Academic affairs at the university made it very clear that although they respect Horwtiz, his failing grades won’t stick.

This is a problem, because a professor’s ability to assign grades is usually one of the places were the instructor has a very high degree of autonomy. It is very, very unusual for an administrator to meddle with the grades assigned by a faculty member.

From this article:

Henry Reichman, chairman of the American Association of University Professors’ Committee on Academic Freedom... said faculty members generally do have the right to assign grades, but there are some extreme circumstances under which this may be limited. He said, for example, that if a college found that a professor was failing students for clearly inappropriate reasons, the institution would be correct to intervene. ...

It should be the right of a professor to grade on behavioral issues and not strictly academic ones, whether that means failing a student who engages in academic misconduct or taking off points for people who miss class or turn in work late.

Reichman understandably goes for clear cut cases in his examples. Academic misconduct is an academic issue, not really a behavioural one. There is a well-established tradition and understanding in higher education that late work is penalized, and that also seems to be an academic issue.

What about students lack “honour and maturity”? Or, to use the case I started with, a student says something hateful to a professor? Can a professor fail a student for that?

I have a problem with that approach. I don’t think I have a right to give a student a lower grade because he or she yelled at me. Grade assignment should be related to the content of the work.

That is not to say that I don’t think the student should have no consequences for bad behaviour. Quite the opposite; I want there to be robust ways for me to report and censure such students. But I don’t have a simple toolkit for doing so. Assigning a grade is easy and involves only me. Report a student acting badly, and suddenly there are whole other levels of administrative machinery that kick into gear. I’m guessing three levels of administration (department chair, a dean, maybe a vice-president) and an investigating committee of faculty will be involved, minimum. And it’s not clear that those other levels of the university will support me. Suddenly, you are worried about retaliation, leniency, and more.

I suspect that trying to fail the student is how many, many professors would deal with the problem. They try to turn a behavioural problem into an academic one. It’s just easier.

And it’s not just professors relating to students.

A new professor who is demanding and abusive is more likely to have his or her department try to get rid of them by saying, “You didn’t publish enough papers in the right journals or get enough grants for tenure” rather than saying, “You’re a jerk who is making everyone around you miserable.” The American Association for University Professors specifically recommends that collegiality should not be a criterion for evaluating faculty.

I’ve said this for a long time. Universities are extremely bad at handling behavioural problems head on. The usual approach is to try getting rid of bad players by giving them a rough ride over academic issues, and not addressing the fundamental problem.

Related posts

Their grades were too... high?

External links

Slam flunk
Professor at Texas A&M Galveston fails entire class

Picture by Nicolas Raymond on Flickr; used under a Creative Commone license.

Fix journals you have before you make new ones

In an editorial, Society for Neuroscience president Steve Hyman takes on issues of replication and rigor. Near the end, he writes:

With the launch of eNeuro, SfN aims to alter some of the troubling patterns in publication.

I still don’t see why the society needs a new journal to alter those patterns, when it could just change the editorial policies of the journal it already has.

If you think publishing negative results is important, if you think publishing replications is important, change the editorial policies, priorities, and format of Journal of Neuroscience. Cordoning these results into eNeuro sends a clear signal that replications and negative results are second rate science.

Additional, 6 May 2015: Ivan Oransky notes that the Journal of Neuroscience has some “troubling patterns in publication,” like not explaining editorial decisions on retractions and publication bans.

Comments for second half of April 2015

Dead Sea News has a nice new paper on science outreach. Love that. But confused as to why it’as in a computational biology journal.

DrugMonkey asks why people are scientists.

Tuesday Crustie: Concealment

You may have to look twice for the crustaceans in this picture...

And yes, it’s crustaceans, plural. They are sitting on top of a crinoid.

Picture by Klaus Steifel on Flickr; used under a Creative Commons license.

A new email signals the beginning of the end

Late today, I got notice that it was time to activate my email address for UTRGV.

Done.

It was quick to do, but in many ways, it signaled the end of an era for me.

An institutional email address is central to modern academic life. It is the first point of contact that people look for if they are trying to connect with you. More than office space, building keys, an ID card, or listing on an university website, a .edu email address defines your affiliation with an institution, both to that institution and to the rest of the world.

The UTRGV email drives home for me that UTPA is coming to an end.

Since I practically live online (“Hi, my name is Zen, and I’m a netaholic”), I have made the problem much, much worse for myself. I use my academic email for a lot of online services, and now I will have a long, slow trudge of switching all the profile account information. Updating a single paper in my academic sites took me half a day. I have no idea how long it will be before I swap over all my accounts to my @utrgv.edu email addy.

This is probably a good time to start listing my university affiliation on new manuscripts I submit as “University of Texas Rio Grande Valley,” too.

I have a lot of mixed feelings about this, because I am watching how this institution is developing. And I am not always feeling optimistic about what I see. But maybe that’s another post for another time.

Related posts

Updating, updating. and updating some more

The first registration for UTRGV...

We’ve started registering students for the inaugural fall semester of University of Texas Rio Grand Valley (UTRGV), and it’s kind of a mess.

Student records are not showing up properly in the student record system. Prerequisites are not properly in the system. Classes are disappearing from registration. 

The next few months are going to be extremely interesting.

Tuesday Crustie: Opportunistic

My field work is on a sandy beach, so there are not very many hard surfaces available for organisms to settle on. So I don’t expect to find these crustaceans when I was at the beach on the weekend...

Barnacles! Some variety of gooseneck barnacle, I reckon, growing on some sort of floating seed (I think). I love that they would just keep extending their feeding legs (cirri, pretty calmly, even though I was holding them out of the water.

Comments for first half of April 2015

Awesome discussion over at Small Pond Science about the disparities in the National Science Foundations graduate research fellowship program (GRFP). It looks like institutional prestige is a great big trump card in competitions, again.

The discussion about GRFPs continues at Savage Minds.

Neuroskeptic wonders what you need to make a perfect brain scanner.

At Mistress of the Animals blog, Potnia Theron looks at why we do what science we do. (Spoiler alert: money can have a bloody awful lot to do with it.)

Pondering Blather examines a forthcoming article on papers that don’t get many citations.

Mark worries about “self-funded” doctoral degrees. Is this exploitation? Maybe, but I’m curious about where the line is drawn. Should we be drawing lines in the sand over “self-funded” master’s degrees, particularly with thesis? Undergraduate degrees that are research intensive?

Tuesday Crustie: Skeletons in your closet

I’m not terribly familiar with these skeleton shrimp. When I saw the picture, I had to go look them up on Wikipedia, just like everyone else.

So many crustaceans, so little time...


Picture by Klaus Steifl on Flickr.

Nature wants to eat you

I’m trying to work out which is the more terrifying image.

This:

Or this:

The lion’s face is perhaps the purest expression of fury I have ever seen. The penguin picture is shocking because it is completely unexpected. It’s also a vivid reminder that birds are the direct descendents of meat-eating dinosaurs.

Why can’t I cite Mythbusters?

I’m sorry, Adam and Jamie. I tried.

In our most recent paper on nociception, one of the major points is that not all animals react to potentially nasty stimuli the same way. And it turns out that there’s a very nice demonstration of that idea on Mythbusters. In the 2008 Shark Week “Jawsome Special,” the Mythbusters did a segment called “Spicy Salsa Shark Shield.”

They showed that sharks were not deterred by the presence of capsaicin-laden material.

I included this in the references as:

Dallow, A. and Lentle, T. (2008). Mythbusters: Shark Week Special 2, Episode 102. Discovery Channel, USA: Beyond Entertainment Limited.

The journal copy editors wrote:

Only peer-reviewed references are permitted in the reference list.

This policy is nowhere to be found in the journal’s instructions to authors.

I took it out, because there were other references that made the point about how responses to noxious stimuli varied from species to species. It wasn’t worth fighting over, and I think I’d have lost.

Regardless of the esteem you hold for the work done by Mythbusters, the journal’s citation policing raises bigger issues. A current trend in academic publishing is to broaden the kinds of research products that people can get academic credit for. Why should only publications “count,” and not sharing a database, or writing useful code?

Consider figshare, the cloud storage data archiving service. One of their big selling points as a data repository is that they generate digital object identifiers (DOI) for stuff submitted there. The DOI itself is not the selling point, but they strongly imply that this makes whatever is archived on Figshare citable in scholarly publications. Here’s the top from their “about” page: making things citable is the first thing the list. (my emphasis):

figshare is a repository where users can make all of their research outputs available in a citable, shareable and discoverable manner.

But all those hopes can be dashed by a single sentence from a journal. “Nope, we only take peer reviewed papers.”

Interestingly, the journal let us keep in a couple of conference abstracts. The abstracts were in published in a peer-reviewed society journal, but the abstracts themselves were not peer-reviewed.

I’ve noted before that some journals have had a tradition of allowing people to cite “grey literature,” like conference abstracts, newspaper articles, web pages, or tweets. I think that is a positive thing. I worry that this sort of “journals citing (and therefore promoting) journals” policy might become more common as journals compete for scientific products. Such policies could hamper the development of academic publishing innovations.

Even worse, a “journal only” policy has the potential to force authors into intellectual dishonesty. “We got this idea from another lab’s data on figshare, but we can’t say that in the paper, so we’ll just have to say something else.”

Authors and possibly reviewers should be determining what is a legitimate citation on a case by case basis, rather than a journal setting a blanket policy favourable to itself.