Showing posts with label stories behind the papers. Show all posts
Showing posts with label stories behind the papers. Show all posts

29 July 2014

Tracking tiny worms

Continuing the series of “behind the scenes” stories around papers in the new issue of Intergrative and Comparative Biology issue...

Brian Fredensborg and I had successfully collaborated on a project looking at parasites in the shrimp nervous system. Along the way, I bugged him about the possibility of doing another project on the local sand crabs, Lepidopa benedicti. I’d decided that there was so little known about that family, that anything we discovered about their basic biology would be new and publishable. And part of the basic biology of any species is the parasites.

I remember Brian mentioning to me after some of the first sand crab dissections that he saw some worms “But,” he said, with a slightly far-away look, “they’re tiny.”


But we knew there was something there to look at, which just meant that we needed a student to pick up the project.

As it happened, two years ago, in 2012, I got roped into having a summer high school intern, Meera Joseph:


I’d had a summer high school student back in 2006, and the experience was positive all around. But I didn’t want to take on more high school students for a long time. I just wanted a break.

Part of the reason I was persuaded to take on another high school student was I had an undergrad in the lab, Karina, who was very gung ho to mentor other students. I relented, and Meera got put on the sand crab parasite project. We knew there was something to look for, so this made it a project that would almost certainly give us some data in the time frame of the internship.

Brian showed her how to do the dissections and look for the parasites. I helped her set up the video recordings for the behaviour. Everything went well, and Meera finished her internship with a poster presentation and a very nice data set.


There was only one reason we didn’t write it up at the end of her internship.

We couldn’t identify the nematodes.

This seemed to both Brian and me to be kind of important. We hoped we could get down to something more specific than the phylum. It would be like identifying the sand crabs the worms were living in as “arthropods.” You could never do that for the crabs, so it seemed wrong to have no better identification for the parasite.

We made a little headway on the worm identification. But before we could get the level of clarity we wanted, it was time for the SICB parasite symposium in Austin, which I’d co-organized with Kelly Weisnersmith. Because Meera had already done a poster, I suggested she give a talk at this meeting, which she did.

Two things happened then.

First, I met and talked to actual parasitologists in this field at SICB, who sort of gave me their blessing. They told me that for this kind of work, saying “Species A, Species B, Species C” in a paper was okay. Suddenly, a gap that seemed insurmountable was now potentially navigable.

Second, the editor of Integrative and Comparative Biology surprised Kelly and me again. We thought we only had to deal with papers by speakers at our symposium. The editor said, “Why don’t you ask people who presented in the complementary sessions if they’d like to publish in the same issue?”

Well, gee, we’d just made all the graphs for Meera’s SICB talk. The text was written, submitted, reviewed, and I’m very happy.

I’m particularly pleased that because Meera was supported by our institution’s HHMI grant, they agreed to pay the fees so that Meera’s paper is open access, and free for all to read!

Additional, 1 August 2014: Bethany Brookshire (a.k.a. Scicurious) has written a nice article about Meera’s research!

Reference

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

Related posts

823 days: a tale of parasite publication

External links

Crabby project inspires young scientist

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.

By the way, thanks to the support of my department, this paper is open access and free for all to read!

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

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  

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

04 June 2014

1,017 days: when publishing the paper takes longer than the project

At. Last.

Long ago, in a distant land, I, Zen, a sand crab biologist, unleashed an NSF grant for undergraduate research upon my department. And students applied to this.

In the third REU cohort, Jessica Murph (pictured) ended up working with me. Jessica was looking for a project that involved field work. She asked just at the right time, because I’d been digging up the local sand crab species (Lepidopa benedicti) for a while. I realized how little we knew about the basic biology. People would ask me things like, “How long to they live? What do they eat?” And I’d say, “No idea.”

Because I wasn’t trained as an ecologist, I couldn’t quite figure out how to go about studying the basics of a little animal that was completely concealed in the sand. Ultimately, my former colleague Anita Davelos Baines gave me the idea of digging transects. As long as we did it consistently, we might be able to get some meaningful information.

I asked Jessica to start collecting sand crabs for her REU project. She did, and between her efforts and mine, we got a year’s worth of data, which took her out to the end of her time with the REU program.

I compiled all her data, and was getting ready to write it up and submit it... but I balked. It’s that gut instinct you have to develop as a researcher about whether your own papers are ready. I knew that if I was reviewing this paper, I would say, “One year of data is not enough.” So I continued making monthly trips and collecting sand crabs myself for another year.

Then, I submitted the manuscript to what I thought would be an appropriate journal. This was regional natural history kind of stuff, and fortunately, there is exactly a regional journal dedicated to just such research: The Southwestern Naturalist.

When I mentioned this to one of my colleagues, he groaned a little and said, “They take forever.” I sort of shrugged and said, “I’m not in a hurry.” It’s not as though I am worried about getting scooped on this project: ecology of an obscure species of digging crustacean? Not exactly a “hot” research field. But in retrospect, I wish I had checked the “submitted” and “accepted” dates in a recent issue more closely.

I submitted the paper on 22 August 2011. No, that is not a typo.

When I finally got the page proofs, it chafed my chaps to see the “submitted” date at the end of the paper: “26 September 2011.” Apparently, nobody even looked at this manuscript for over a month.

I got my reviews back on 24 May 2012. That’s nine months there. I sent back the revision one week later, and I hadn’t though the revisions were that major.

Time passes. Sound of crickets chirping.

My patience ran out around the ten month mark (we’re at February 2013 now). I emailed the associate editor about the status of my manuscript. He emailed me back to say:

I am no longer an editor for the Southwestern Naturalist.

I was gobsmacked. It seemed to me that a logical thing to do when an editor leaves would be to email the authors for correspondence to say, “This person is leaving; please direct your inquiries on your manuscript to this editor.”

I finally heard back that the article has been recommended for publication, and should appear in the December 2013 issue of the journal. This made me happy, because I thought it would be out by the end of the year, and I hadn’t had a lot of papers out in 2013.

In early November, I get an email that I should get page proofs for my article in January... which is already after December, dashing that hope that the article would be out before the end of the year.

With all that’s happened so far, I suppose I should not have been surprised that, having been told to expect proofs in January, I actually get them mid March. I sent them back quickly, in hope that the December, 2013 issue might be out around the end of March, 2014.

In the waiting time between when the paper was supposed to be published and when it actually was published alone, I submitted articles to three other journals, had them accepted, and proofed. I’m not trying to boast here, just contrasting my experience with this journal with others.

The paper has finally seen the light, and it has taken substantially longer to get this article through the editorial and production process (2.75 years) than it did to collect the data and write the paper (two years). I should have seen this coming, because the journal does list the initial submission and acceptance dates. But even those dates underestimate the publication time. My “received” date was a month after I submitted, and the publication date on the cover of the issue, December 2013, was months before the issue actually hit the web.

And, by the way, did I mention that there was a $320 page charge for all of this? And it’s a paywalled subscription journal, with no open access options?

Speaking of costs, I got an email on 19 May 2014 allowing me to order reprints. The paper still wasn’t available on the journal website, but I thought it was at least a promising sign that it hadn’t been forgotten. I clicked on the link, and was stunned to see this part of the ordering form:


They wanted $69.68 from me so that I could have a PDF of my own paper. I had never had a journal want to charge me for a PDF before.

I was also stunned to see that a copy on CD would be more than another $10, when the cost of a blank CD from Staples can be as little as 18 cents. It feels like a money grab. And I can’t remember the last PDF I needed or wanted in CD format. And why would you need a DVD (another $13) for a single journal article PDF?

The paper was finally available online on 4 June 2014. That’s 1,017 days – or two years, nine months, and thirteen days from submission to publication.

This whole process has soured me on submitting to some of these niche journals. That is a shame.

I submitted this article to The Southwestern Naturalist because it seemed to be the most appropriate journal for the paper. I see value in topical journals; it makes things easier to find. I think many researchers have certain journals they check regularly. But after this experience, I think I would have been much better off submitting this paper to PLOS ONE or PeerJ or a similar venue.

Except... wait, PeerJ didn’t exist when I submitted this paper. With publications like PeerJ, journals like The Southwestern Naturalist are going to be in trouble soon.

I feel bad for the staff at The Southwestern Naturalist. They clearly don’t have enough resources. I don’t know whether they don’t have enough people, enough pages, or something else, but these time frames are not signs of a healthy scientific journal. And, as I said, I do think journals like this can serve an important purpose! I want to support the journal. I do.

I’m pleased that the paper is out. Because of this paper, my co-author, Jessica, is more excited and positive looking back on her research experience now than she was when she was doing the work, I think. It gaves me a chance to add another UTPA success story to the REU Bio website. And it is the first to provide any sort of basic ecology for any species in this family. It’s a cute little paper. I love it for what it is: a little natural history on organisms that only a few people in the world care about.

But it’ll be a long time before I think more about the science in the paper than the frustrations and delays in publishing the paper.

Additional, 11 June 2014: The printed copy of the journal arrived today, which is reasonably quickly following the online publication.

Reference

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

(And yes, I’m annoyed to have to put that 2013 date in the citation when we’re months into 2014.)

External links

Never go against your gut
Some Things Last A Long Time

16 April 2014

Kabuki theatre versus the mosh pit: notes from my Neuron article on post-publication peer review


I have a new article in Neuron! This is a pleasant surprise to me, because I never thought I would ever get anything in that journal.

One of the Neuron editors emailed me out of the blue in December, asking if I would be interested in doing an opinion piece for them about social media. (In this journal, opinion pieces are called “NeuronView.”) After a follow-up phone call, it became clear that she was interested not just in social media, but particularly how people are using it for post-publication peer review.

I wanted to do it, because it’s nice to be asked. As I said... Neuron!? Neuron! Being asked to write this article is an example of what is one of the most important points in it:

One of the most profound things about social media is that it has lowered the barrier to creating and spreading conversations.

Without social media, I don’t think someone like me would have had a shot at being asked to write a feature like this. There would be too many obstacles for me to start conversations: there are geographic barriers (physical isolation), disciplinary barriers (I’d never published in Neuron), and so on.

Even so, I was initially a little reluctant. I was in the middle of writing my Manuscript of Desperation (more on that one later). I was in the thick of prepping for the parasite symposium I was co-organizing with Kelly Weinersmith, and I knew manuscripts from that would be due early in the new year. I asked when it would be due. “End of February.” I decided I could probably make that happen.

I managed to get the article submitted a little early and exactly on length. From there, the editorial and proofing process was very fast and completed in early April.

My last task was to create an image for the Neuron home page (shown above). The production team decided they didn’t want to use an image with the Creative Commons credit text on it, but used it as a template to create a new image:


The problem with writing an article like this is that no matter how fast you write it, and how quickly it’s published, there will be things coming out after you sent in the article that you wish you could have talked about.

For instance, the day after I sent back the checked page proofs, I read this article about how blogging about a research paper leads to increased corrections.

I thought of adding in at the eleventh hour was a mention of the current STAP stem cell kerfuffle. When I submitted the article, this story hadn’t really taken off, but during the intervening time of reviewing, production, and proofreading, it just got bigger by the day. Bigger by the hour, almost. But I decided that the STAP case didn’t yet have any clear lessons for post-publication peer review that wasn’t shown by examples already in the paper.

Then, I learned of this story by Haier and colleagues concerning the editorial process at Neuron, the journal I had just written for (my piece was in press by then). The short version is that authors had been asked to write a preview piece. Haier and company submitted a critical article, and the journal pulled the plug on it. Commentary on the Neuroskeptic blog ensues (Haier et al. link to the blog, but not the specific article, which is here), which includes remarks from someone who had knowledge of the typically anonymous review process.

This is an excellent example of one of the issues I talk about in my Neuron article: the difficulty of getting critical commentary published. Haier and colleagues started this process in the second half of 2012, and only more a year later, in April 2014, are they able to detail their concerns about the editorial process.

I could have talked about the importance of sites like ScienceSeeker, Faculty of 1000, and Researchblogging in providing portals for post-publication peer review. ResearchBlogging was certainly critical to my own development as a science blogger.

But despite all that, I’m pretty happy about this piece. Sometimes, when you keep having to re-read something you wrote, you get a little sick of it. I’ve had to re-read this one quite a lot, and there are some turns of phrase in it that I still quite like.

Now, I’m looking forward to the post-publication peer review of my own paper! Whether you think I had anything interesting to say or whether you think I was wrong, wrong, wrongity wrong, please comment here on the blog, tweet your thoughts to me (@DoctorZen), write your own blog post, or whatever form of social media turns your crank.

Meanwhile, I’m going to enjoy seeing this on the home page of Neuron for the next two weeks:



Additional: The cycle begins... my article gets post-publication peer review on PubPeer. And thanks to those who have tweeted so far!

Update, 17 April 2014:  My article is open access at the Neuron home page here, but, weirdly, paywalled at Science Direct.

After a little after one day, I’m also very happy to see this article’s Altmetric score:

(T)his article has done particularly well and is in the 98th percentile: it’s in the top 5% of all articles ever tracked by Altmetric.

It is not surprising that an article about social media does particularly well on social media. But, as I said, it is nice nevertheless.

I’ve also created a Storify of some of the responses so far.

Reference

Faulkes Z. 2014.The vacuum shouts back: post-publication peer-review on social media. Neuron 82(2): 258-260. http://dx.doi.org/10.1016/j.neuron.2014.03.032

External links

The new dilemma of online peer review: too many places to post?
Online exposure ‘leads to higher research paper correction rate’
What can we do about junk science?
How intelligent is IQ?
Stick to Your Ribs: The Problems With Calling Comments “Post-Publication Peer-Review”
A guide to post publication peer review

11 March 2013

How much is that crayfish in the window?

I could not have written my latest paper without Google Alerts.

I can’t remember when I set up Google Alerts for “Marmorkrebs” and “marbled crayfish,” but it goes back to at least 2008. Given that I set up the Marmorkrebs home page in late 2007, that was pretty clever of me, though I say it myself.

In 2009, I set up a survey on the Marmorkrebs home page that ran throughout the year (I blogged about this process here). I was very familiar with a the problems of surveys. I learned a lot about them during my undergraduate degree, where I majored in psychology. People have to be willing to come to you, and those people, being volunteers, are not necessarily representative of the general population.

Now, with so many ideas, it’s difficult to pinpoint or remember the origin of the idea. But late in 2009, a paper was published in Nature that you could predict flu outbreaks fairly well by tracking things like how often “flu symptoms” was typed into Google. (This led to this online resource.) I think the led me to the idea of using the information being delivered through the alerts to keep track of the locations where people were keeping Marmorkrebs as pets.

This project changed a lot as it went along. Initially, almost all I was concerned about was the locations where people were keeping Marmorkrebs. I had the date, the city, the American state or Canadian province.

As the project went on, and I kept collecting data, I kept expanding what I was recording. What were people calling these crayfish? (This may have been prompted by seeing made up species names.) What were people doing with them? Are the same people cropping up over and over again? And how much is a crayfish worth on the open market?

The problem was, when I went back... there was a lot of link rot. Craigslist entries came down fast, and I often couldn’t find them. It was only late in the day that I started the practice of turning every web page I could into a PDF so I could archive the entry. In retrospect, I could have done all this so much better.

Creating this paper was a little bit like making repairs on a plane while it was still in flight.

That makes the other thing I’m trying with this paper a little nerve-wracking. I decided to put the entire spreadsheet (slightly cleaned) I used in this paper up on figshare. Now, for reasons I have just described, this is not the cleanest data set out there. All the more reason to be transparent about how the set was put together, and make it available to check. I’m also happy to share PDFs of particular entries in the spreadsheet, as I expect link rot will continue to take its toll on the entries in the list.

I did some more analysis for when I presented this work at the Society for Integrative and Comparative Biology meeting in January, and I found a few more interesting things that were too late for the paper, and are probably not substantive enough for the next pet paper I’m working on. To continue the metaphor above, I am still not sure the plane has landed, and I’m still trying to fix it.

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. http://dx.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. http://dx.doi.org/10.5869/fc.2013.v19.039

Faulkes Z. 2013. Online monitoring of Marmorkrebs in the North American pet trade: figshare. http://dx.doi.org/10.6084/m9.figshare.645344

Ginsberg J, Mohebbi MH, Patel RS, Brammer L, Smolinski MS, Brilliant L. 2009. Detecting influenza epidemics using search engine query data. Nature 457(7232): 1012-1014. http://dx.doi.org/10.1038/nature07634

Related posts

Tracking Crayfish Zero: the threat of pet crayfish

07 September 2012

Why I published a paper on my blog instead of a journal

TL;DR: I had a research project that has been sitting for more than a decade without finding a home in a scientific journal, so I decided to post it on my blog instead as an experiment.

Yesterday, I posted an original scientific paper here on my blog. The obvious question is, “Why is it on the blog instead of in a peer-reviewed journal?”

This project goes way back to the last century. I was doing my first post-doc, and I applied for an NSERC post-doctoral fellowship. I proposed a project that came out of my Ph.D. research. I had been studying leg motor neurons in crustaceans (published in Faulkes and Paul 1997). There was this one paper about spiny lobsters that just did not jive with everything else I had found. In my fellowship application, I proposed to try to resolve those questions by re-examining spiny lobsters’ neurons – in other words, the project that I posted yesterday.

To my surprise, I got the fellowship. I used it to move to Australia and do a post-doc with David Macmillan. It was a wonderful experience. But what happened to the proposed project was... normal research happened.

David Macmillan asked me to pick up another project in addition to the leg motor neuron one (Faulkes and Macmillan 2002), and help mentor an Honors student (Patullo et al. 2001).

I had setbacks in getting animals. Spiny lobsters were too hard to work with. Suppliers for slipper lobsters didn’t come through, and I thought I was sunk until I finally stumbled on seafood place down the road that had live slipper lobsters. All hail the Queen Victoria Market!

Then, once I had the slipper lobsters, I made serendipitous discoveries that I just had to pursue. Discoveries like that slipper lobsters didn’t have giant neurons needed for escape behaviour (Faulkes 2004) and that they were diggers (Faulkes 2006a). And the seafood supplier came through again, with live spanner crabs, which I’d been dying to look at since my thesis on sand crabs (Faulkes 2006b).

I did the leg motor neuron project around all of those others during that post-doc. Clearly, I had lots to show for my time in Australia regardless. But that was a post-doc project, and I’m a tenured associate professor now, so... you can do the math. This has been sitting around, waiting, for over a decade, to see the light of day.

I haven’t even presented this research at a conference. I should have.

All that time, it’s been gnawing at me.

It’s been gnawing at me that I had this project done, but that it wasn’t out yet. Especially because this was the project that I had gone to Australia to do in the first place.

And it’s not been for lack of trying. I’ve submitted this paper, in one form or anther, to about three different journals over the years. It was rejected every time. I may post the reviews later in a separate post. In a nutshell, one of the major issue that the reviewers had was that the data just weren’t conclusive enough. And honestly, I think they’re right. It drives me nuts that I wasn’t able to pin down what was happening with those two medial cell bodies. Reviewers of a different paper that used the same techniques called the methods, “old fashioned.” If they were old fashioned before, they’d probably be criticized as ancient or obsolete today (even though they let me answer the questions).

What could I do? I’m not in Australia, so I couldn’t get more Ibacus. There are no slipper lobsters around the South Texas coastline that I know of. There was no way that I can get any more slipper lobster data.

For a long time, I thought I would try to do the anatomy of the leg motor neurons from another unstudied crustaceans, like a shrimp. It would turn it into a broader comparative paper with more data. But... that wouldn’t shore up the weaknesses in the slipper lobster data. Plus, even if I did get more data from another species, that would take even more time – time spent when I have enough other irons in the fire. How long would it take before this project would be out? Another decade?

I still considered submitting the manuscript, more or less in the form I posted, to yet another journal and trying my luck. But I couldn’t figure out what was an appropriate one. Journals that used to publish crustacean locomotion stuff don’t do much of that now, mainly because the number of researchers in the field has contracted. I was considering submitting it to the forthcoming PeerJ when it opened, for instance. Even then, that I agreed with the limitations that the reviewers pointed out to me meant that I didn’t fancy my odds. Nevertheless, I’m confident enough in what I wrote that I bet that if I keep at it, sooner or later I could find a home for the paper. But do I want to put it out in the Chinese Journal of Irreproducible Crap? Is that any better than burying it in my back yard (if I had a back yard)?

Those, if you like, are the negative reasons to publish the slipper lobster paper on my blog: because it sucks so much that it couldn’t get past the gate at a real journal.

But there are positive reasons to publish it on my blog, too.

Because I am tenured, I have the good fortune to be free to experiment a little. I’ve been productive enough the last few years that whether this slipper lobster paper gets out or not is not going to affect my promotion prospects, any grant applications, my career advancement, etc. Having tenure is supposed to be a way for people to try risky things.

I thought, “Let’s try something new.”

Regular readers will notice that over the last year or so, I’ve been experimenting with different ways of doing my science. I’ve written about independent science. I’ve participated in #SciFund in addition to writing regular grant proposals. I self-published my Presentation Tips ebook on Amazon. Publish some original science on my blog? Well, why not?

As I wrote back at the start of the second round of #SciFund (new emphasis):

(S)o many scientists are still in the place artists were. We’re waiting to be chosen. Waiting to be given permission. Working and working and working in the hope of being given a shot at the big time by someone else with more money, power, and influence. ...

It doesn’t always have to be that way now.

After all, in the last year we’ve seen Rosie Redfield live-blogging her research on arsenic life, even before depositing a complete pre-print in arXiv. And all of that was okay with Science magazine, who published the final version. The rules for biological publishing are not as rigid as they were. Putting manuscripts out on the Internet for people to see is not the absolute kiss of death for publication in a journal that it used to be. I’m thinking my blog post is functionally equivalent to a pre-print on arXiv. Maybe at some point, I can still get this into a real journal. (Hope springs eternal.)

I’ve also been paying attention to the people who say that scientific publishing is broken, and we should blow it up and start over. Lot of those people are basically advocating what I just did yesterday: “just blog the paper.” (The list of influences here is long and varied, and I can’t pull up all the relevant names, posts, ideas and such right at this moment.)

Could blogging research work? We won’t know until there are a few people crazy enough to try. It’s not without precedent. Bora Zivcovic had a blog post of original research that eventually was cited in a paper in a peer-reviewed journal. (Also crustaceans, coincidentally!) [Correction: I got this exactly wrong. Bora was making the point that his post was not cited. Redfaced that I didn’t re-read his post entirely.]

This paper was a good one to try for the experiment. As a scientist, you have to develop a gut instinct for evaluating your own work. Is this publishable? If I was reviewing this, what would I want to see? My instincts told me this paper was stuck in an uncomfortable zone between “publishable” and “shouldn’t see the light of day.” There’s enough good about it that I want to share it, but there’s enough shortcomings with it that I know it would be a continuing struggle to go through traditional scientific publishing.

I do not plan on doing this routinely. It was this very particular set of circumstances with this particular project that led me to try blogging it.

The problems I’ve had getting my slipper lobster paper published are far from unique. People talk about the “file drawer” problem: projects that were never published because they were negative results, or weren’t significantly novel, weren’t published fast enough to avoid getting scooped, or any number of other reasons. There might be a single experiment that that the reviewers think is inconclusive, so you take that out of the final manuscript, even though it might be a clue to other researchers. What do you do with all that data?

Figshare is partly a reaction to, and solution for, problems like this. It allows people to put up datasets and figures and such that wouldn’t going to make it into a paper on their own. (The two key data figures in yesterday’s post are on Figshare and have DOIs, making them citable on their own.)

But I wanted to do more than share the figures. I wanted to tell the scientific story. I wanted to give context to those figures. So, I’m trying this with a blog post.

Do I have concerns? Hell, yes. Another thing I’ve written routinely about on this blog are problems of archiving.

While I was converting the manuscript to blog format yesterday (almost as intense as if I were getting ready to submit it to a journal), I was updating the references. I was pleasantly surprised; almost amazed, honestly. Almost every paper was online, with a DOI, and a PDF. The exceptions were book chapters and a couple of now defunct journals. A lot of them did not used to be online; I know, because I’d checked. The commercial publishers have done a fine job in digitizing those back issues, and making a lot of that old literature more readily available than ever before.

I am worried about that blog post being ephemeral. I do plan to put up a PDF on my home page, and will probably deposit copies to my university library, too. Any other suggestions would be welcome.

Ultimately, I published the paper on my blog because it wasn’t doing anyone any good sitting on my hard drive. It may still not do anyone any good (it is pretty darned specialized, and there are not as many crustacean neurobiologists as there once were), but at least now the chance is more than zero.

Okay, everyone. Fire away. I know people are going to have opinions on this. Indeed, I bet that this will be like the situation where the DVD bonus features are more interesting than the actual movie: more people will care that I posted a paper on my blog than about crustacean motor neurons. And that is just one more positive reason to do it: publishing a paper on a blog is still unusual enough to be worth talking about. Another paper in a niche journal isn’t. Conversation starter, publicity stunt, call it what you will: I plead guilty.

Did I give up on trying for a peer-reviewed journal too easily? Am I showing the way for how science publishing will be done in the future? Am I crazy, or just completely crazy?

Related posts

The distal leg motor neurons of slipper lobsters, Ibacus spp. (Decapoda, Scyllaridae)

Abandonment issues by Al Dove (the homeless paper I mention in the postscipt was the one I posted yesterday)

External links

Why or why not cite blog posts in scientific papers?


Circadian Rhythm of Aggression in Crayfish

References

Faulkes Z. 2004. Loss of escape responses and giant neurons in the tailflipping circuits of slipper lobsters, Ibacus spp. (Decapoda, Palinura, Scyllaridae). Arthropod Structure & Development 33(2): 113-123. http://dx.doi.org/10.1016/j.asd.2003.12.003

Faulkes Z. 2006a. Digging mechanisms and substrate preferences of shovel nosed lobsters, Ibacus peronii (Decapoda: Scyllaridae). Journal of Crustacean Biology 26(1): 69-72. http://dx.doi.org/10.1651/C-2628.1

Faulkes Z. 2006b. The locomotor toolbox of spanner crabs, Ranina ranina (brachyura, Raninidae). Crustaceana 79(2): 143-155. http://dx.doi.org/10.1163/156854006776952874

Faulkes Z, Macmillan DL. 2002. Effects of removal of muscle receptor organ input on the temporal structure of non-giant swimming cycles in the crayfish, Cherax destructor. Marine and Freshwater Behaviour and Physiology 35(3): 149-155. http://dx.doi.org/10.1080/1023624021000014734

Faulkes Z, Paul DH. 1997. A map of the distal leg motor neurons in the thoracic ganglia of four decapod crustacean species. Brain, Behavior and Evolution 49(3): 162-178. http://dx.doi.org/10.1159/000112990 [Note: Yesterday’s post will make a lot more sense if you look at this paper.]

Patullo BP, Faulkes Z, Macmillan DL. 2001. Muscle receptor organs do not mediate load compensation during body roll and defense response extensions in the crayfish Cherax destructor. The Journal of Experimental Zoology 290(7): 783-790. http://dx.doi.org/10.1002/jez.1129

Photographs by David Paul.

28 June 2012

Big in Japan

This is not a paper I wanted to write.

I didn’t want to write it – not because I was coerced, or because I don’t think it’s valuable – but because I would rather have had one paper rather than two.

Early in 2011, I co-authored a modeling paper on Marmorkrebs with my colleague down the hall, Paty Feria. We had tried to figure out the risk of Marmorkrebs invading in places where they had been documented as being released, or were available in the pet trade. Despite rumours, there was nothing confirmed about Marmorkrebs in any location in Asia at the time.

But papers take time to write. The manuscript was already done and had been submitted to journals by late summer 2010.

In early fall 2010 that I’d learned of an older report of Marmorkrebs being found in Japan at the Sapporo Salmon Museum (pictured above) in 2006. It had been reported in a book, and one written in Japanese, so it not the easiest piece of information to come across using my usual Internet search strategies. I dutifully reported on the Marmorkrebs blog.

We thought out paper was based on a complete set of records of where Marmorkrebs had been found... and then we discover, not just another record, but one in a whole new continent. This fact was probably influencing my SciAM Guest Blog post (later included in Open Lab):

Scientists like to think of themselves as being ahead of the curve. In the case of Marmorkrebs, we’ve consistently been about a few years behind events on the ground. Pet owners in Germany report the crayfish to scientists — paper comes out three years later. Marmorkrebs show up in market in Madagascar — paper comes out four years later. This isn’t anyone’s fault; it’s an indication both of how long careful science takes and how rapidly events are unfolding.

If anything, though, finding of the Marmorkrebs in Japan probably pushed us to get the first paper out, feeling that it could be useful in helping policy and planners.

That left us with a new paper to write. We had one individual Marmorkrebs in the Japanese ecosystem, so the threat was real. There were interesting conservation and economic impact angles here, too.

We did end up pushing things further in this paper in terms of the models, and gained a new collaborator in the process. Based on some of the feedback we got, we did not just run the same models as in the 2011 paper. Now, there are five models in the new paper. Paty and I were able to run... four of them. One of the models kept refusing to render, for reasons that were were never able to determine. It was maddening. Paty reached out to her colleague overseas, Jesús Muñoz, who agreed to help us. He helped not only to fix the problem, but also helped us do more types of analyses than we initially set out to do.

That Jesús was not at the same campus as us overseas made for some interesting collaborative issues, primarily getting files from point A to point B. Some of the files generated in modeling are huge, and even my trusty Dropbox folder was spitting the dummy. We went though many rounds of trying to figure out how to get the files from on computer to another. But that was eventually solved.

Something of an offhand comment by another colleague, Kristi Lowe, led to the choice of journal. She mentioned that she had just published a paper in Aquatic Biosystems. To be honest, I hadn’t heard of the journal before, but she had been very happy with the editorial process. She’s also told me that the journal had changed from Saline Systems and broadened its scope to include freshwater systems.

And they were having a sale.

Aquatic Biosystems, like many other open access journals, has a publication fee. But they were waiving the fee until the start of June as part of a promotion.
My current projects are being funded by things like my #SciFund donors (♥ you guys), and publication fees are often almost as much as entire projects cost. While I have no problems asking for a waiver, it was a good deal. I was a sucker for a bargain and decided to go for it.

I’m very happy about much of this paper: new co-author, new journal, open access, relevant to policy.

But in my perfect world, this paper wouldn’t exist. I admire papers that are comprehensive. I would have much preferred had the 2011 and 2012 papers all in one bigger, more substantive paper. But I was overtaken by events. This has happened to me a couple of times now, which is disconcerting.

But better to be overtaken by events than be stagnant.

Related posts

Potential invasions anew new horisons
How my ethics of brain scanning paper was overtaken by events

References

Faulkes Z, Feria TP, Muñoz J. 2012. Do Marmorkrebs, Procambarus fallax f. virginalis, threaten freshwater Japanese ecosystems? Aquatic Biosystems 8: 13. http://dx.doi.org/10.1186/2046-9063-8-13

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


02 December 2011

Science after a storm

My newest paper kind of got started because of an act of God.

Hurricanes are still considered “acts of God” in insurance policies, right?

You see, my grad student at the time, Sandra, was continuing work on spiny lobster that she had started as an undergraduate (Espinoza et al. 2006). We were gung ho to continue that work to see if we could figure out if there were behavioural differences that were related to spiny lobsters’ loss of escape neurons.

But a problem emerged. Spiny lobsters show up around South Padre Island once in a while, but they are rare. So we had gotten all our lobsters from Florida, from the Keys Marine Lab.

And Keys got smushed by Hurricane Wilma in October 2005.

And there went our supplier for spiny lobsters.

Now, we might have been able to find another supplier, but we decided to press on ahead with some crayfish experiments. We originally planned to do experiments with spiny lobsters that paralleled the crayfish experiments in this new paper. We were going to do experiments immobilizing the spiny lobsters’ antennae, blindfolding them, and so on.

But the logistic problems of getting spiny lobsters continued to plague us. We eventually abandoned those experiments.

As it happened, Sandra had a baby girl very soon after her thesis defense. She was more occupied with a child than writing up some of her thesis research. And I wasn’t quite sure what to do with these experiments. We had presented the research at conferences, and gotten reasonably good feedback. But I wasn’t sure what would be an appropriate home for the manuscript.

The paper – I suppose it was still better described as a thesis chapter at this point – sat.

Last summer, I attended the International Association of Astacology meeting in Missouri (which I blogged extensively about on the Marmorkrebs blog). During the meeting, there was considerable chat about the society’s journal, Freshwater Crayfish. I liked what the editors were trying to do: get it out more regularly, and make it more clear that it was a journal, not conference proceedings. The production values of the journal were always very good.

It dawned on me that this was probably a good home for this project. That there were some known limitations to publishing in Freshwater Crayfish – like the long time between issues – were not a big deal for this project. After all, the research had already kind of sat, waiting for me to do something, for a couple of years.

I am so pleased that it is out. Sandra is now one of the few master’s students in our departments to have two peer reviewed papers arising from her master’s degree.

And the moral of the story is: Don’t abandon hope of publishing your projects because it’s “been too long.” Patience makes many things possible.

Reference

Espinoza SY, Faulkes Z. 2011. Escaping while defenseless or blind: effects of sensory input on tailflipping in crayfish, Procambarus clarkii (Girard, 1852). Freshwater Crayfish 18(1): 13-17.
http://iz.carnegiemnh.org/crayfish/IAA/members/fc/abstracts.asp?uid=guest&pubid=287

Espinoza SY, Breen L, Varghese N, Faulkes Z. 2006. Loss of escape-related giant neurons in a spiny lobster, Panulirus argus. The Biological Bulletin 211(3): 223-231. http://www.biolbull.org/cgi/content/abstract/211/3/223

05 October 2011

823 days: A tale of parasite publication

It’s unusual that I can pick exactly how long a project took from beginning to end. This time, I can: 823 days.

Day 1: 4 July 2009


Since 2006, I’d been examining the nervous system of shrimp (for a project that is still ongoing – sigh). When I looked at the nerve cords under the microscope, I kept seeing odd little bits that I thought were caused by some problem with the fixation or clearing process. I realized that was wrong when on 4 July 2009, I took this video:



Okay, those slight odd looking bits in the nerve cord didn’t have anything to do with staining. They were moving. They were something alive inside the nerve cord.

Well. That was unexpected. Also, slightly freaky.

Here’s my notebook entry for the day:


(And yes, I am well aware of my terrible handwriting and other problems, thank you very much.)

Soon after, I went down the hall and showed this stuff to the man on the right in the photo below.


This is my co-author Brian Fredensborg, who is a real parasitologist. He had joined our department a couple of years previously. I showed him what I had. He didn’t immediately say, “Oh, yes, that’s a [name], and it’s well known that they live in the nervous systems of crustaceans. Not very interesting at all.” This was a good sign. We were both interested, for different reasons, in what the heck was going on here.

Day 4: 7 July 2009


Brian gives me a tentative ID of the beasts we’re dealing with: larval tapeworms. I record in my notebooks, “Possibly PROCHRISTIANELLA PENAEI or PARACHRISTIANELLA or POLYPOCEPHALUS.” Brian seeks out some help in narrowing down the possibilities from a colleague, and he hears from one of his colleagues that the last guess is the right one.

But the project had to wait. Neither of us had the time to follow it up immediately, and all our students at the time were already deep in working on projects of their own.

Enter the woman on the left.

Day 59: 31 August 2009


The last day of August in 2009 is the first day of class for the Fall semester. I am teaching my neurobiology class, and though I didn’t know it at the time, one of the students registered for the class is Nadia Carreon. We had some good conversations in that semester. This good relationship in class helps paves the way...

Day 200-317: Spring 2010


After the semester is over and neurobiology is done, Nadia comes into my office and asks about the possibility of doing a research project before she graduates. We sit down in my office, and I throw out a whole whack of half-baked ideas that could be turned into research projects, including the mystery shrimp parasites. Nadia thinks the parasite project is cool, so we walk down to Brian’s office and I introduce them to each other.

Everything looks good, so we start to plan a project that Nadia can complete over the summer that will, we hope, be publishable.

Days 318-422: Summer, 2010


And we are go for data collection! We plot, we plan, and we set up a way to gather data at the Coastal Studies Lab. We fiddle with webcams. We figure out ways to tag the animals so we can track them individually. I pull out a big honkin’ heavy mechanical cell counter – made of metal and that makes a very satisfying click every time you press one of the keys – to aid in the counting of all those parasites.

(For the record, I wish to apologize to Nadia publicly: I had no idea just how many parasites were going to be in those shrimp. I never expected that one shrimp alone might have 500 parasites infecting it.)

Proving the old adage, “If it weren’t for the last minute, nothing would get done,” much of the planning takes place in May and June, while a lot of the actual data collection happens late in August.

Day 451: 27 September 2010


We do get a first pass at data gathered over the summer, and get it together in time for a poster at the HESTEC science symposium. The poster wins third place in the undergraduate poster competition.

The analysis and writing continues at a slow but steady pace through the fall semester.

One moment I particularly liked was when I finally got the big, massive spreadsheet of all the behavioural data. For whatever reason, in my research, there are very few “Aha!” moments. There’s a lot more sneaking suspicions followed by a long period of trying to convince myself that what I think I’m seeing is actually what I’m seeing.

As it happened, we had a little bit of data destruction problem. Some of the last video shot was unusable. Brian and Nadia and I had talked about whether we might need to run some more behavioural tests on shrimp, but we still had a decent sized number of animals. We decided that if we didn’t see significant differences, we might run some more. But if it was significant, but it saw significant differences with the smaller sample, we could start writing up in earnest.

There was so much data here, there was no way to get a sense of whether there were going to be any trends associated with infection rates. So I was quite excited to run the first analysis, because I had no idea how it was going to turn out. ... and see significant differences in behaviour!

Day 533: 18 December 2010


Nadia graduates with her bachelor’s degree in biology!

Brian and I are committed to writing and finishing this manuscript before the year is out. The main reason is that Brian is expecting to become a father for the first time in very early January. This gave us very strong incentive to finish, because, as I said to several people, “I don’t know of anyone who has ever said, ‘Yes, we just had a baby. And my productivity has gone through the roof!’”

Day 545: 30 December 2010


Manuscript submitted! Happy New Year!

Day 609: 4 March 2011



Nadia gives the first presentation of this story to the larger scientific community at the Texas Academy of Science meeting. This poster later appears on the Better Posters blog.

Day 633: 28 March 2011


The manuscript is accepted. On the first submission, without any revisions. This has never happened to me before. Holy cow. And the pre-print goes up the same day!

Day 704: 7 June 2011


I present an updated version of the Texas Academy of Science poster at The Crustacean Society meeting in Honolulu. The new data makes this poster 33% bigger than its predecessor.

Day 823: 4 October 2011


The paper finally moves from “pre-print” to published status! And now, I have a paper in a parasitology journal, which was never something I expected to happen. Hooray for collaboration and academic freedom.

Day 824: 5 October 2011


“And on the eight-hundredth and twenty-fourth day, he blogged.”

But wait! We’re not quite done yet! Nadia continued working on this project a bit on a volunteer basis through 2011 after she graduated. We have more data, that we hope will eventually become part of the first follow-up paper.

Day 864: 14 November 2011


Come meet Nadia and myself at the poster session for the Faculty for Undergraduate Neuroscience at the Neuroscience meeting! 6:45-8:45 pm in the Grand Ballroom Central and North in the Renaissance Hotel.

There you have it. The long, winding road from an initial observation to a final, pretty, published article, with brushes along the way of both the thrill of victory (“No revisions?!”) and the agony of defeat (“The video’s gone?!”). It’s also fairly typical of research at undergraduate universities, I think, in that things can wait for a long time because you’re just waiting for a student to pick up the project. And I was surprised in writing up this retrospective to be reminded that stuff gathered even early in the project can be useful:

I took the picture in Figure 1a on Day 1.

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. DOI: 10.1645/GE-2749.1

Faulkes Z. 2007. Motor neurons involved in escape responses in white shrimp, Litopenaeus setiferus. Integrative and Comparative Biology 47(Supplement 1): e178. DOI: 10.1093/icb/icm105

03 June 2011

In memory of Charley Lambert

I’m sad to report that Charley Lambert has died suddenly from a stroke.

I co-authored a paper with Charley, and his wife, Gretchen, after a busy weekend of data collection at South Padre Island. I was lucky enough that they were able to fit in a stop in Texas to travel plans as they were on their way to Florida, if I remember right. They got their before me, and I met Charley and Gretchen on a dock where they had just pulled up a rope loaded with tunicates and were busily photographing it.

I remember Charley saying that weekend that you should never throw away any writing. He said he had one paper where he wanted to speculate on the ascidians that might have been attached to the hull of the early explorers. One editor hated it and made him take it out. But he kept it, and got it into another paper later.

I met him once more at the Tunicate meeting in Santa Barbara in 2005 (group photo at right; I think Charley is two down from me, on a 4 o’clock diagonal), and I remember him making the entire room laugh during his presentation. I wish I could remember the joke exactly, but the gist of it was that he had reached a point of not worrying too much about what other people thought.

He might not have cared that I thought it, but I thought Charley was a lovely guy, active and full of a sense of humour.

Additional: Finally found a much better picture of Charley that I’d taken during their visit here in August 2004. A photo gallery of Charley is here.



Reference

Lambert G, Faulkes Z, Lambert CC, Scofield VL. 2005. Ascidians of South Padre Island, Texas, with a key to species. The Texas Journal of Science 57(3): 251-262.