25 July 2014

Where’s the site for the parasite?

I’ve had the good fortune to have a glut of papers appear, thanks in part to the publication of symposium proceedings I helped organized with Kelly Weisnersmith. One of the papers in the symposium proceedings is the follow-up to Carreon and colleagues (2011), which I described here. (My goodness, was that three years ago already?)

In our previous paper, we showed that living inside the neural tissue of shrimp were these little baby tapeworms:



After Nadia Carreon (pictured) finished her bachelor’s degree, she volunteered to stay and try to push the project forward a little further before she went off to graduate school.  (Nadia will will soon be finishing a master’s degree at University of Texas Brownsville.)

We decided to have a first pass at trying to answer the question of where the parasites were located in the shrimp nervous system. I knew the basic landmarks of the crustacean nervous system, and the general function of different parts of the nervous system. If parasites were infecting one region but not another, we would have a reasonable first explanation for why.

We did this work a couple of years back, so why is it only being published now? For two reasons. First, projects often sit waiting for a student to pick them up. I don’t have the sort of research lab doctoral students, post-docs, or technicians, so progress comes in fits and starts.

Second, and more importantly, there things that I hoped to add to this paper to make it a richer and deeper story. (This is a recurring theme in my writing. It happened with another recent paper, too. Note to self: don’t let the perfect be the enemy of the good.)

First, I wanted to analyze the position of parasites in the brain, not just the abdominal ganglia. There are fewer parasites in the brain, though, so it would take longer to build up a coherent picture, which is why we started where we did. Checking the position in the brain will have to wait for another paper.

Second, I wanted to section the nervous tissue, and look at those at higher power; under an electron microscope, say. This would help us to see where the larval tapeworms are sitting in three dimensions, not just two. The higher magnification might also help us get a better sense of how the neurons are displaced around the tapeworms, and whether the tapeworms were damaging the tissue.

One reviewer said it would be nice to have these sections. I agreed, but Nadia had left, no other student had picked up the project, I don’t have sectioning skills, and we have no histology core with technicians who might help with something like that. There was no telling how long it might be before I could get sections, so this paper went forward without them. that will be in a later paper (I hope!)

Speaking of which, one reviewer suggested something very helpful. We show in this paper that there are more tapeworms in the ganglia than the nerve cord between them. We show that in the first figure.

The reviewer suggested correcting for the number of parasites by the volume of tissues. Doing this required a quick couple of measurements from photographs I already had, and some quick back of the envelope calculations. And it made the difference in infection even more striking: more parasites in the ganglia than the nerve cord, even though the ganglia are smaller than the cord!

Although I describe it in the text, I could have shown this figure in the paper, which would have emphasized the differences all the more:
Even when you are happy about a paper coming out, you will always know there are things that could have made it better. At least I share the better graph here.

Coda

Nadia and I dedicated this paper to the late Luis Colom. I am glad we we able to give some personal recognition to Dr. Colom. Dr. Colom’s influence on UTB (and, eventually, UTRGV) looks like it be a lastng one, judging from this picture Nadia shared yesterday:




Related posts

823 days: a tale of parasite publication
Luis Colom, the peer I never met

Reference

Carreon N, Faulkes Z, Fredensborg BL. 2011. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology 97(5): 755-759. http://dx.doi.org/10.1645/GE-2749.1

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

24 July 2014

In search of an identity for UTRGV, or: why Bucky must go

To the right, we have the new University of Dayton logo (hat tip to Matthew Hartings):

It looks like the initials, “VD,” which, for many people, still conjures up the phrase “venereal disease.” It’s astonishingly bad. It’s going to be the start of jokes for years.

The reminder of how tricky university team names and logos are is on my mind a lot, because we are going through the process of branding The University of Texas Rio Grande Valley. Yesterday, an important decision was made, as our incoming president, Guy Bailey, emailed his decision on the new university logos.



I like these. The custom swish of the R makes it distinctive and a touch graceful, without being distracting.

The logos are not quite finalized, yet. The colours may change, because we are still selecting a new mascot and team name for University of Texas Rio Grande Valley. There was an initial meeting here at UTPA last week, which I attended, and another at UT Brownsville, which I followed on Twitter.

What was striking, per maybe predictable, was that many in the UTPA crowd wanted to keep the current UTPA team name (Broncs) and mascot (Bucky). A #KeepBucky hashtag often crops up on Twitter during these discussions.

On the other hand, the UTB crowd was completely and utterly opposed to keeping Bucky.

I side with the Brownsville people on this one. Bucky must go!

It’s interesting to me to compare the current Bronc / Bucky fan cry of “Why does it have to change?” It sounds so much like the sort of “nerd rage” that you see when the announcement comes that Thor will be a woman, or that Daniel Craig will be James Bond. (“Bond not blonde!”) People freak out, then come around when they see the final thing (assuming the end result is good, of course). But even if it isn’t, Sean Connery fans will always have his performance in From Russia With Love regardless of Craig’s turn in Casino Royale.

Bronc fans, a new mascot will not take away your memories of the old mascot. It does not remove history. You will always have the great memories of Bronc events with Bucky.

But the bottom line for me is this.

The University of Texas Rio Grande Valley is a new university, the first new American research university of the twenty-first century. It needs a new team name, a new mascot, and new colours. UTRGV can’t be stuck in the past.

Here are three suggestions that I happen to like, particularly the first two.

The Green Jays



The green jay is a charismatic local bird that sports both green (a colour associated with UTPA) and blue (a colour associated with UTB). The bird is only found in southern Texas in the United States. A few other US universities use blue jays as mascots, but nobody else uses the green jay. And the green could look good with UT System orange. (Picture from here.)

Rockets


 

Texas is known for its NASA facilities and the role they played in the American space program. This tradition looks set to continue with the likely creation of a SpaceX launch facility in south Texas. Only one other US university has that as its team name. Plus, it’s forward looking. And you could have the repeated “R” in the name, the Rio Rockets.

Armadillos



Another common species in Texas, although not as much as the birds mentioned above. They’re quick and tough and recognizable. And great stuffed toy potential. Currently, no university team uses this name. (One San Antonio university used to as a nickname, but they’re officially the Saints.) And the “RGV Armadillos” has some nice repeating “ar” sounds.

Chachalacas



Another prominent, distinctive bird that is found only in the region within the U.S. While it’s not as striking a bird as the green jay, it would have one big advantage: it would be fun to say! Come on, say “Chachalaca!” out loud! It’s practically it’s own battle cry! (Picture from here.)

Names we probably shouldn’t use:


Vipers: If it weren’t already the name of a local basketball team, it would be perfect! We do have a lot of snakes in the region. The name has the repeated “V” with the “Valley Vipers.”

Bees: Also taken, this time by a local hockey team. I liked this one because of the repeated long “e” in RGV Bees.

Monarchs: As in, butterflies. Not terrible, but used by several other universities. Also, monarch butterflies are so wide ranging that they’re not terribly distinctive to the region.

Hawks: This one got suggested at one of the town hall meetings. Hawks are common and visible here, and fine looking birds. My only concern is that a lot of universities already use this name.

Mustangs: I thought about this one a lot. With so many of the UTPA community wanting to keep the Bronc, I thought maybe you could keep the horse motif going. Ultimately, though, I don’t think it separates itself far enough from the Bronc to establish a new identity for UTRGV. Any horse-related name or mascot is going to cause hard feelings and resentment, which we absolutely do not need in trying to create this new institution. It already has enough challenges.

Colts: All the same problems as Mustangs, plus... colts are male horses. It would be weird to have our female athletes having a male team name. And it would be even dumber if they tried to make it okay by feminizing the women’s team name to “Coltettes” or something.

Toros: Spanish for “bull.” There was an impressive marquette shown at the UTPA meeting of a bull, but see my notes on “Colts” above: do we really want the name of a male animal for women’s teams? Also, another university already has this one.

Vaqueros: Spanish for “cowboy.” It has a regional flavour, but I worry about this being slightly too esoteric for a name. But I could be wrong; I was surprised to learn that this one is already used by another university.

Hurricanes: I know other sports teams have been named after natural disasters, I have a problem with naming teams after an event that causes so much damage and suffering. Plus, this one is taken by a couple of other teams.

External links

Broncs buck identity change as UT-RGV plans for new, merged identity in Edinburg and Brownsville

23 July 2014

Way down south: stumbling across a sand crab (Lepidopa websteri)

“Hey Meera, check this out.”

Not as powerful or concise as Archimedes’s “Eureka!”, but that was what I said at the moment of discovery – exactly two years ago today! – that led to my newest paper.

I have been making regular trips to collect sand crabs on South Padre Island for a few years now (e.g., Murph and Faulkes 2013). A couple of years back, I had a summer intern, Meera (pictured), who was working on the parasites of the local species, Lepidopa benedicti (just out; Joseph and Faulkes 2014). I thought it was important that she see the animals in their native habitat, so she came out to the beach with me to collect.

Somewhere along the way, I turned over a shovel of sand, as I do, and I saw antennae sticking out of the sand.

Even as I reached down, I recognized instantly that this was something unusual. The antennae were way longer than usual. I had it in my hands, and that was when I said, “Hey Meera, check this out.”

I jotted it down in my notebook with three little words: “Super long antennae.”

 
I’d forgotten until I did this post that this animal was the last one of the day before we packed it up and drove back to the main UTPA campus.

We took it back to the lab, and it was getting late in the afternoon. It wasn’t until the next morning that I sat down with a dissecting microscope and looked at the definitive guide to sand crabs, Chris Boyko’s magnificent monograph (Boyko 2002). (In retrospect,this was dumb, because the animal could have died overnight.)

Meera and another student, Karina, were in the lab, and I turned around and announced to them, “New species.”

It wasn’t a species new to science; it was Lepidopa websteri, described in 1903. But it was a new species for the region. I had made a lot of maps of the distribution of sand crabs species in the Gulf of Mexico, and I knew that Lepidopa websteri had never been found this far south.

Then I started taking a lot of pictures. It is hard to get good pictures of the entire animal, because the antennae are so long. I’m still not happy with the pictures I got, but they are better than most depictions of this species (more on this in a moment).

Because I knew this species was rarely collected (noted in the Boyko monograph, which I quote in the paper), and I am in a department with several ecologists, I knew that range extensions could be published. The advice I got was that Crustaceana was the logical choice, because they have a history of publishing notes on range extensions.

Given that I found this animal two years ago, why did it take so long for this paper to appear? Unlike another recent sand crab paper of mine (don’t get me started), the time spent getting this one out had nothing to do with the publisher.

I spent a lot of time trying to “add value” to this paper. I was confident that it could be published as a note, but I do like to have something more substantial when possible. I spent months with students and colleagues trying to include two other things in this paper. One addition kept having technical failures, and the data were never clean enough to publish. The second addition was completed, but none of the reviewers liked it. I took that out, turned the longer paper back into a note, and will try to find a home for that in another journal.

Funny story.

Before the paper came out, I did have a chance to talk about this. Back in January 2013, I gave a public talk at the World Birding Center on South Padre Island. I talked about sand crabs in general, and how I found Lepidopa websteri, which had never been recorded on South Padre Island before.

After my talk, I walked around the inside of the Birding Center. I’d visited the Birding Center before, but had mostly walked around outside. Imagine my surprise when I found this on display:



Here I was saying, “Nobody’s found Lepidopa websteri here on South Padre Island before!” and there’s this picture, which must have been there for years. Good to be proven right for a change, given that the last time I’d seen sand crabs on a sign, I pointed out so many errors that it was taken down soon afterwards. I can overlook that these animals don’t build burrows, and there is no solid evidence their antennae act as straws.

I am betting that the artist was working from a preserved specimen, though (click to enlarge)...


When I mentioned on Twitter that this paper was out, someone noted that the paper was paywalled within minutes. True, but I’m pleased that Brill has a much more reasonable publishing and copyright agreement than many other publishers:

The Author may post the post-print version of the Contribution on his/her own personal website free of charge with the appropriate acknowledgment and link to the Brill website. This means the Contribution may be shown exactly as it appears in print.

This means that if you want a PDF of this paper, you can find it at DoctorZen.net!

This paper reminds me of the value of just looking. You never know what you’ll find.

Related posts

Building or beast?
Public talk at World Birding Center next week! 
Tuesday Crustie: Oh no it isn’t

References

Faulkes Z. 2014. A new southern record for a sand crab, Lepidopa websteri Benedict, 1903 (Decapoda, Albuneidae). Crustaceana: 87(7): 881-885. http://dx.doi.org/10.1163/15685403-00003326

Joseph M, Faulkes Z. 2014. Nematodes infect, but do not manipulate digging by, sand crabs, Lepidopa benedicti. Integrative and Comparative Biology 54(2): 101-107. http://dx.doi.org/10.1093/icb/icu064

Murph JH, Faulkes Z. 2013. Abundance and size of sand crabs, Lepidopa benedicti (Decapoda: Albuneidae), in South Texas. The Southwestern Naturalist 58(4): 431-434. http://dx.doi.org/10.1894/0038-4909-58.4.431  

22 July 2014

Updating, updating, and updating some more

I’ve had four papers published in the last seven days.

I’m pretty sure this is a record for me. Three came out as part of the Society for Integrative and Comparative Biology symposium collection I co-organized with Kelly Weisnersmith (two papers open access), and the fourth is a short note about a crab that has been seen further south than ever before (full paper on DoctorZen.net!).

The publication of that last paper, however, robbed me of about half a day. Of course, I tweeted and posted about it. Until it came out yesterday, I did not know the publication details, like the volume, page numbers, and DOI. I started updating my information. That meant typing in information for...

  1. My CV.
  2. My own website, DoctorZen.net.
  3. ImpactStory.
  4. ORCID.
  5. Academia.edu
  6. ResearchGate.
  7. Mendeley.
  8. My institution’s “digital measures” website.
  9. Update: Doh! I forgot Google Scholar!

ImpactStory had far and away the simplest process: paste in a DOI. This, to me, is exactly how is should be. Because it is a unique identifier, a DOI should be everything needed to get information about a paper, like authors, the journal it was published in, etc.

I also learned that ImpactStory will automatically import projects listed in ORCID. Meanwhile, many publishers will be collecting ORCID information as part of the submission and publication process, presumably allowing profiles to be updated automatically when new papers come out.

The remaining websites all had many boxes and somewhat clunky interfaces. Academia.edu and ResearchGate require you to enter data over multiple screens.

By far the worst was – perhaps not surprisingly – my institution’s digital measures website. These sorts of “enterprise” software packages always seem to end up being barely functional, butt ugly to look at, and a pain in the butt to use. Instead of a single field (DOI), it has about 24 separate data fields. The exact number depends on how many authors you have to enter (click to enlarge). This makes me glad I don’t publish in large groups where the number of authors can run into double digits.

It asks for a lot of strange information, like institutional “themes” and “city of journal / publisher.”

And this one screen is only for publications! There are similar screens for our presentations, committee work, teaching, and so on. I have no doubt they are probably as complicated, if not more so.

Despite my whinging about the amount of duplication, I don’t think I can just walk away from these sorts of sites. I know I get people who find my stuff from those sites, so I think it is useful to have a presence on them.

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

Tuesday Crustie: Conversely


Spotted on a car outside my apartment.

18 July 2014

Where are they now? (Veterinary edition)

Back in 2006, I wrote:

In another one of those still-not-quite-sure-how-this happened events of the summer, I spent this afternoon meeting with various people about a summer internship program with high school students. I’ll have a student, Amanda, working with me for six weeks starting next Monday. Not quite sure what I'll have her do yet. Will have to spend some time sorting out project ideas next week.

What happened after that? I came up with a project, Amanda rocked it for six weeks, got data way more interesting than I expected, and we published a paper from it (Flores and Faulkes 2008). It was very cool to have a paper with a co-author who was in high school at the time.

Amanda went off and did one degree at Texas A & M University. She told me that having a publication from her internship was helpful, because it always gave her something that set her apart from the crowd. She stayed at A&M for another degree, and today posted this:


From ascidian intern to practicing vet! Sniff. They grow up so fast... Anyone in the region who needs animal care, please visit Dr. Flores, and tell them Zen sent you.

Related posts

In turn...
Best of times, worst of times, best of times
Personal review of 2008

Reference

Flores AR, Faulkes Z. 2008. Texture preferences of ascidian tadpole larvae during settlement. Marine and Freshwater Behaviour and Physiology 41(3): 155-159. http://dx.doi.org/10.1080/10236240802360914

17 July 2014

Zombie symposium outbreak

The latest issue of Integrative and Comparative Biology is now out! And the cover story comes from one of the papers from the parasite symposium I co-organized with Kelly Weinersmith! It’s been three years in the making, and I want to tell you how it all happened.

It all started with #SciFund.

I sometimes tell students, “You never know who’s going to walk through your door,” as a way of saying that research and career opportunities and plans are often completely unpredictable. Someone you never heard of before walks through your door, and boom! You’re off on a new adventure.

Kelly Weinersmith walked through my door (figuratively) in the first round of #SciFund. We both had projects in round one, and got to know each other a bit through that. She invited me to be a guest on The Weekly Weinersmith podcast, which I was happy to do. We talked about zombie shrimp, because I had just published my first parasite paper (Carreon et al. 2011).

Shortly after this, around the end of 2011, I suggested to Kelly that we should do a symposium about parasite manipulation. The idea of parasites as “natural neuroscientists” had been used by a few people. It seemed to me that Kelly and I had a good combination of skills to sell that idea as a symposium (parasitology and neurobiology, respectively) .

I did not suggest we do this for Society for Integrative and Comparative Biology (SICB), where it ended up. No, I suggested writing a proposal for a different, and much larger conference.

It was rejected. But... the reviews were actually encouraging. The program committee had suggested we submit it again next year.

Before the 2012 deadline for Big Conference rolled around, the deadline for for SICB came up. The SICB meeting for 2014 was in Austin. Living in far south Texas, a major conference in my field happening close enough to drive to is so rare that when it happens, I go.

It also seemed to me that SICB might also be a good fit, if not a better fit, than the Big Conference would have been. So we dusted off the proposal, rewrote it, and it was approved by the program committee.

The moral of that story is: Never throw away any of your writing.

From there, it was a matter of looking for external funding. SICB requires symposium organizers seek external funding. Kelly and I wanted to try a crowdfunding campaign, as between us we had a few successful crowdfunding campaigns under out belts. The SICB leadership, however, didn’t like the idea and told us not to. They were worried it would interfere with other SICB fundraising efforts. This baffled me, and is still rather a sore point.

Kelly and I wrote a grant for the National Science Foundation, which I had to submit because I had the faculty gig. And we got it.

The symposium came, and then we had to hunker down and get papers out to the journal Integrative and Comparative Biology (another requirement of the symposium).

I expected to submit one paper, based on data I presented at the symposium. I was caught off guard when the editor contacted Kelly and I to ask us for another paper, to introduce the symposium.

We wrote it, but it did make the early part of this year a bit frantic. I was in the middle of submitting a bunch of other manuscripts. Kelly was just about to deliver her first child. And yes, that Kelly was about to deliver her baby was the inspiration for this post.

I am pleased that our paper together is dedicated to the young Weinersmith, Ada Marie, shown at right.

But writing an introductory paper was not the first surprise I received from the journal editor. But that’s another story for another day.

Related posts

832 days: a tale of parasite publication
Zombie (scientific paper) outbreak!
Science babies

References

Carreon N, Faulkes Z, Fredensborg BL. 2011. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology 97: 755-759. http://dx.doi.org/10.1645/GE-2749.1

Weinersmith K, Faulkes Z. 2014. Parasitic manipulation of hosts’ phenotype, or how to make a zombie—an introduction to the symposium. Integrative and Comparative Biology 54(2): 93-100. http://dx.doi.org/10.1093/icb/icu028

16 July 2014

Make believe rich people


One of my undergraduate mentors told me, “Academics are make believe rich people.”

Academics don’t get the actual money, but they get some of the same perks that rich people get. Some of the examples he used were maybe more relevant to some universities than others (access to faculty clubs, campus golfing, and so on), but others, like being able to travel regularly (thank you, conferences) are true of most academics.

Likewise, the ability to say what you want is easier if you’re either rich, or working in an institution that embraces academic freedom. Some of the eccentricities that professors are allowed are also reminiscent of what you can get away with if you’re wealthy. Of course, the dark side of this is that both the wealthy and the professoriate have power that they use to abuse others.

Academics a “make believe rich people” my professor argued, had a historical basis. It’s certainly true that historically, scientists were well off. They had to be, since research wasn’t really a substantial professional until the twentieth century. There was also the belief that financial independence helped to ensure objectivity.

Additional, 17 July 2014: Of course, the day after I post this, I find this flagrant and unthinking display of wealth from a university provost.

My wife and I gave our daughter a choice for her sixteenth birthday. If she wanted, she could have a party or we could go on a family cruise. ... She would like her birthday cruise to be the same islands cruise we took as a family six years ago.

A vacation cruise may not be something that many people would be able to suggest as a teenager’s birthday present. And two vacation cruises in six years is probably not within the range of most rank and file faculty at universities, and particularly contingent faculty.

Needless to say, when I wrote the post, I was not thinking about upper echelons of university administration. I was thinking about the most regular, non-administrative faculty.

Related posts

Gentlemen scientists

Comments for first half of July 2014

Anna Sharman asks why authors publish in small, paywalled journals, using my story as an example. I try to answer.

Lenny Teytelman notes that retractions don’t seem to hurt journals very much. Brands can survive mistakes, which may be a good thing.