27 January 2015

I’m a People of Canada!

I’ve taken over the @PeopleOfCanada Twitter account for the week!

I’ll be tweeting about maintaining a Canadian identity while living out of the country, a little science, and a maybe little more personal stuff than I normally get to at my usual Twitter account.

Join me for the week!

External links

Week 126: Expat Zen in Texas, USA

26 January 2015

Maybe the UTRGV mascot should be the zombie, because the debate won’t die

Just when thought we had finished with the whole Vaqueros controversy, it’s back in the news. Texas lawmaker Terry Canales has made good on his threat.... er, promise... to introduce legislation that would almost certainly get rid of the “Vaquero” as mascot.

The bill, from my point of view, is... problematic. It reads:

The university shall include on the ballot:
  1. the “Broncs”;
  2. the “Ocelots”; and
  3. any other options the university chooses, including nicknames nominated by students and approved by the university.

This is a rigged ballot for a single outcome: to get the Bronc back. It was clear in the discussion leading up to this that people affiliated with UTPA students favoured the Bronc, and everyone not affiliated with UTPA were “Anything but the Bronc.” Nobody was strongly arguing for the Ocelots.

There is no doubt that if there was a student vote held now, UTPA students would overwhelmingly vote for the Bronc.

I get that “majority rules” is very popular option... when you’re in the majority. It completely sucks to be given a message that what you have to say is not even worth listening to when you’re in the minority.

Let me give you a little “Zen predicts” on this bill: it will never come up for a vote, for two reasons.

First, legislators from the rest of the Texas will not see the value in interfering with a decision that was done above board and according to Hoyle. It was always Guy Bailey’s decision, and while his decision was unpopular, it was his to make.

Second, the UT System, and other Valley legislators from outside the Edinburg area, will lobby against this bill and stop it before it hits the legislative floor for a vote. The representatives of the UT System will resent what they see as political second-guessing and micromanagement. Other legislators will resent that the bill silences their constituents.

Additional, 27 January 2015: What also bugs me about the wording of this bill is that it removes the voice of any stakeholders other than current students. I’m faculty member, and I have a stake in this institution and am affected by mascot decisions (as much a students, at least). Why would I not get a say under HB901?

Maybe if the wording of the bill was “Vaqueros, yes or no?” I could get behind this bill, as it would address legitimate concerns about that particular mascot; that is, issues around cultural sensitivity, inclusion of men and women, and so on. But the point of this bill is to not to get passed. The point of this bill is for Representative Canales to be seen to be doing something.

External links

Bill seeks election for UT-RGV nickname
Proposed bill to leave UTRGV nickname up to students

22 January 2015

A step back for UTRGV grad programs

Well, this is frustrating.

Currently, both The University of Texas-Pan American and University of Texas Brownsville handle graduate applications using a externally provided specialty system called Embark. Having used it for a few years, I can say it works well.

I learned yesterday that the new University of Texas Rio Grande Valley will use a completely new system for processing student applications to graduate programs. Actually, it’s already in place. It’s called ApplyTexas. It was intended to let students apply to any public university in Texas. Its sounds like a nice, simple idea: one system for students to deal with instead of many.

So, existing system that universities already have replaces subscription service, money saved, what’s the problem?

The problem is that ApplyTexas was designed to handle undergraduate admissions. It does not support attachments like personal statements or recommendation letters. To deal with this, it looks like applicants will have to go to ApplyTexas to enter their demographic data, then go to another website to upload documents, and then a third website to deal with recommendations. So instead of one common site, grad applicants will actually be interacting with three. The, they are “hoping” that all of the documents generated in these three systems can be combined into a single document.

And this decision was made after some UTRGV graduate programs had already started taking applicants.

It’s a mess.

Who decided this? The University of Texas System. Thanks a bunch, people.

20 January 2015

Who paid for my open access articles?

A recurring concern from some researchers about open access is the cost to authors. This is an area of persistent misconceptions and a lot of fear. It’s a legitimate question of whether article processing charges create a Matthew effect, with labs with grants gaining an unfair advantage over those without grants. Or, worse, shutting out contributors entirely.

This interests me, because by most standards, I am a scientific “have not.” And yet, I’ve published many of my articles open access for some years now. I did not have stand alone research grants in that time. How did I do it?

It’s a mix.

The most common situation was that the journal did not levy an article processing charge. In other words, these papers were free to me. (In fairness, one – Aquatic Biosystems – was a limited time “free to publish” offer; they normally do charge a fee.)

While I personally did not have grant support, our institution has had undergraduate training grants (notably HHMI). Those external grants picked up the tabs for a couple of papers with undergraduate co-authors:

Lately, I’ve been fortunate to have my chair agree to support article processing charges of a couple of some papers from departmental funds.

  • Carreon N, Faulkes Z. 2014. Position of larval tapeworms, Polypocephalus sp., in the ganglia of shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 54(2): 143-148. http://dx.doi.org/10.1093/icb/icu043
  • 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. http://dx.doi.org/10.3391/mbi.2015.6.1.09
  • 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

I paid the costs of a couple of few papers out of my own pocket. The two PeerJ papers were covered by a single lifetime membership, which was $99 at the time.

  • 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. http://dx.doi.org/10.3391/ai.2010.5.4.16
  • Feria TP, Faulkes Z. 2011. Forecasting the distribution of Marmorkrebs, a parthenogenetic crayfish with high invasive potential, in Madagascar, Europe, and North America. Aquatic Invasions 6(1): 55-67. http://dx.doi.org/10.3391/ai.2011.6.1.07
  • Faulkes Z. 2015. Motor neurons in the escape response circuit of white shrimp (Litopenaeus setiferus). PeerJ 3: e1112. http://dx.doi.org/10.7717/peerj.1112
  • Faulkes Z. 2017. Filtering out parasites: Sand crabs (Lepidopa benedicti) are infected by more parasites than sympatric mole crabs (Emerita benedicti). PeerJ 5: e3852. https://doi.org/10.7717/peerj.3852

I paid the costs for two using indirect costs recovered from an external undergraduate training grant that I was awarded.

Update, 29 September 2019: One paper was paid for mostly by the indirect costs mentioned above, with my department kicking in the remainder.

  • DeLeon H III, Garcia J Jr., Silva DC, Quintanilla O, Faulkes Z, Thomas JM III. Culturing embryonic cells from the parthenogenetic clonal marble crayfish Marmorkrebs Procambarus virginalis Lyko, 2017 (Decapoda: Astacidea: Cambaridae). Journal of Crustacean Biology: in press. https://doi.org/10.1093/jcbiol/ruz063

Finally, I don’t know how the article processing fee my most recent paper was the papers below were paid for by my co-authors.

Looking at this list, I’m willing to bet that some researchers will say, “But Zen, even if you didn’t have traditional research grants to pick up the tab, you’ve still had a lot of support to pay for open access.” True. It’s hard to say if the number of open access papers would have been much different if, say, my department declined to pay for papers. I might have tried other journals, might have dipped into my pocket again, might have tried to find other pots of money.

From this perspective, the issue that might stop some researchers (retirees and amateurs, say) from publishing open access would not be “lack of grants,” but being disconnected from larger institutions. Being part of an institution brings a lot of infrastructure, and diverse resources that go way beyond who has external grants.

All of that said, several of my articles in “traditional” subscription-based journals also had page charges (one journal asked me for $320 for its 2.75 year publication process). It’s interesting to me that people don’t very often bring up those page charges as barriers to publication.

Additional, 17 March 2015: Updated list.

Additional, 2 August 2015: I added two new papers to the main list: one had no publication fees, the other was modest (PeerJ) and paid for out of pocket.

Additional, 18 November 2015: Added newest paper to list (reasonably low fees that I will pay for out of pocket).

Additional, 20 January 2016: Updated the list. One paper that I thought might cost me something ended up costing nothing. I also completed some citations.

Additional, 7 February 2017: Updated the list. Second time I dipped into some funds I have from indirect costs.

Additional, 10 June 2018: Updated the list, adding two more papers. And here’s a graph!

Additional, 18 June 2018: Updated the list, with one more paper. Graph above not updated yet.

Additional, 24 September 2018: While tweeting out this link again, I am reminded that I need to add Hilda Bastian’s important blog post about open access fees.

(N)ot having an APC doesn’t mean the journal is accessible to everybody. It has to accept work from your field. You have to be eligible to publish in it – an APC is not the only possible access issue. You have to write in its language of publication. And you want it to be accessible to people in your field. In mine, that means you really want it to be indexed in PubMed. And having DOIs is critical for citations to be counted by key systems.

Hilda does a little analysis to show that this winnows out to a small number of journals for most people.

Additional, 9 November 2018: Updated the list, with one more paper. Graph updated!

Additional, 29 September 2019: Updated the list, with one more paper.

Related posts

Waiving publication fees
The journal ecosystem

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

Tuesday crustie: Buy garlic

“Those aren’t fangs...

“They’re claws!”

Geosesarma hagen is a new species dubbed a “vampire crab” in a new paper by Ng and colleagues (2015), and you can see why.

This interesting paper has details even more new and very colourful crab species. Another one is cream and bright violet. Several of these species were showing up in the pet trade well before this paper appeared, with completely unknown provenance. It’s a little scary to see how often collectors start pushing things into the pet trade even before we have a decent species description.

Another notable thing in the species names is that the crab Geosesarma dennerle, which the authors write:

The new species is named after the German company Dennerle, who kindly supported the third author’s study in Java.

It’s sort of weird, because first, it’s an aquarium company. This would seem to be a potential conflict of interest, which isn’t declared. Second, this funding source isn’t acknowledged anywhere in the acknowledgements at the end, which is the normal place you’d look for something like this.

Related posts

Tuesday crustie: I vant a cape!


Ng PKL, Schubart CD & Lukhaup C. 2015. New species of “vampire crabs” (Geosesarma De Man, 1892) from central Java, Indonesia, and the identity of Sesarma (Geosesarma) nodulifera De Man, 1892 (Crustacea, Brachyura, Thoracotremata, Sesarmidae). Raffles Bulletin of Zoology 63: 3-13. http://zoobank.org/urn:lsid:zoobank.org:pub:9F76CF88-A3DD-4F0E-B348-EEB9558DBBC4

13 January 2015

Tuesday Crustie: Now, a little to the left...

I’m working up a storm to get a crayfish paper done before classes start next week, so I wanted to feature crayfish in this spot today. And I like this combination of critter and camera.

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

09 January 2015

New rule for medical research headlines

Dear science journalists—

I propose this simple rule for all headlines about medical research:

All headlines must include the species the research was carried out in.

I’ve suggested this a few times here and there on social media, but the latest case was the title of this Telegraph article:

Has Stanford University found a cure for Alzheimer’s disease?

My reaction might be summed up thus:

The problem is so obvious it doesn’t need a spoiler alert. The study was done in mice. Yeah. There have been a lot of studies on lab mice that suggested a cure for something or other was on the horizon. They often vanish without a trace.

Even after animal studies suggest that a treatment will be safe and effective, more than 80% of potential therapeutics fail when tested in people.

While “But if you read the rest of the article...” is a handy out for science writers, it doesn’t change that headlines are 90% of communication effort. If we’re going to improve science communication, headlines would be the place to start.

Imagine the difference in people’s response between the headline that was used and this:

Has Stanford University found a cure for Alzheimer’s disease in mice?

This provides people with a much more realistic idea of how far along the research is in that “bench to bedside” pathway.

External links

Betteridge’s Law

07 January 2015

A cog in a teaching machine

In the Chronicle of Higher Education, Leonard Cassuto asked:

That phrase – “my own work” – has bugged me for my entire career. It’s always used to distinguish research from teaching, but how does teaching not qualify as “my own work”?

Teaching qualifies less as “my own work” because institutions clearly signal that I am a replaceable cog in their teaching mission.

Take introductory biology, for example. There are a bunch of textbooks out there. They all follow the same topics in the same order: Organic chemistry, macromolecules, cell structure, cellular respiration, photosynthesis, cell division, Mendelian genetics, DNA structure, replication, and protein synthesis.

My job in teaching is not to set the curriculum. Other people have done that. There is a very standardized introductory curriculum across North America, partly homogenized by the efforts of textbook publishers and the efforts of lawmakers. My job is to get up there and talk about the content that other people have decided I should teach.

Further, in my institution, there are multiple sections of introductory biology, each taught by different instructor. Since this is nominally the same class, the sections I teach must be broadly comparable in content, and to some degree delivery.

There are many lab sections, scheduled by a single lab coordinator, with topics selected to align with the expected lectures.

It should be no surprise that I don’t feel like teaching is “my” work, particularly at the introductory levels. I did not have much creative input into the content of the class, and I am very constrained in how I teach it.

If you want more evidence that institutions consider the real life instructor almost superfluous, have a look at this story of a class where one professor, the instructor of record, is acting as a commentator to a series of video recordings. A similar thread runs through all the interest with MOOCs and the Khan Academy: the face-to-face interaction with a human instructor is downplayed.

At higher level courses, things can be a little different. I have greater freedom in deciding what content to teach. But even then, there are few cases where I think that what I have to offer in a class is unique. I teach a neurobiology class where I had complete creative control. That’s great. But at the end of the day, there are neurobiology and neuroscience classes all over the country, and “I took neurobiology at university X with instructor Y” is not that indicative of a unique experience.

But research? There are not other people doing the studies I do. There are not other people writing the papers I write. My research remains hand crafted, not mass produced. Research is entirely my own work in a way that teaching rarely is.

Additional, 8 January 2015: Siobhan O'Dwyer riffs off this post: "Artisanal academia."

External links

Teach while you’re at it
When a flipped-classroom pioneer hands off his video lectures, this is what happens

06 January 2015

South Padre Island winter seminar series kicks off this week!

Writing and data analysis is going very well for me right now (one manuscript revisions submitted, two manuscripts developing at a nice clip), but I wanted to stick my head up long enough to say that I’m kicking off the UTPA Coastal Study Lab’s winter seminar series this Saturday! (Click to enlarge the schedule.)

I’m giving a talk about my sand crabs, summarizing what I’ve learned over the last half a decade. (Wow, has it been that long?) I will have a lot of new stuff, including stuff I’m analyzing right now. I’m excited about it!

And 1,000 style points for those who recognize the musical reference in the talk title.

Tuesday Crustie: I like spikes!

This amphipod is probably Acanthogammarus victorii. It’s about 70 millimetres long, and found in Lake Baikal in Russia.

Photo by Olga Kamenskaya, from here. Hat tip to Rob Camp and Miss Mola Mola.

01 January 2015

2014: fruitful and frustrating in equal measure

I worried that I would never had a professional year as productive as 2011. I had six papers that year. I'm super pleased I matched my 2011 record this year, with six papers out again, four of which were data-driven papers.

The year started crazy, with the parasite symposium I co-organized with Kelly Weinersmith being a big success at the Society for Integrative and Comparative Biology meeting. What I thought would result in one paper turned into three. And a few other manuscripts deadlines on top of those meant that I had my door closed a lot of the first part of the year.

I had two papers that, according to their altmetric scores, were more widely seen and discussed (post-publication peer review and crowdfunding) than anything I've ever written.

But I was also frustrated. For one, I could have broken that 2011 record by a couple of papers.

One paper, whose publication seemed to occur in geological time, came out this year... but it has a 2013 publication date on the article, because it was supposed to come out at the end of last year. So it doesn't add to annual tally in my CV.

Then, I had a paper that could have been out in November. But it didn't make it out because my institution couldn't pay the publication fees on time. It's now scheduled for March.

My frustration was compounded by my apparently inability to get manuscripts off my desk and into the hands of editors in the latter part of the year. In this quiet week between Christmas and New Year's, I made good progress on revising one long-suffering manuscript. Now if I just can get a couple of other manuscripts started, which have data in the can and ready to write up... maybe I'll start feeling more productive.

Personally, it was a year of many unbloggable changes.

I am hoping that a habit of a productive person is to think about not just what you have done, but what you could have done better. And there was a lot I could have done better.

The big news on the horizon for 2015 for me is easy to pick. My current institution, The University of Texas-Pan American, is abolished and we will see the start of University of Texas Rio Grande Valley. I expect all manner of craziness to ensue as part of the creation of the new university. We have less than a year to go, and there are huge amounts of things that haven't even been close to being decided.

Related posts

All downhill from here?
In the hands of editors now

Comments for second half of December, 2014

Terry McGlynn makes the case that professors shouldn’t be sharing student gaffes.