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


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


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.

15 July 2014

Tuesday Crustie: iSopod, the original iPod?

But wait! You can do this!

From here. Hat tip to Jarrett Byrnes.

04 July 2014

One tiny step for credibility of a new journal

After over a year of existence, the journal DeNovo has still not published a second article. Its single article remains a paper on sasquatch DNA (Ketchum et al. 2013) that has not convinced the scientific community. However, DeNovo can now claim at least one small step towards something resembling credibility.

It’s been cited.

It’s in a new paper by Sykes and colleagues (2014) about DNA claimed to be from sasquatch, yeti, and other unknown species. However, it’s not a positive citation. Sykes and colleagues find no evidence consistent with the claim by Ketchum and colleagues (2013), which proposed sasquatch was a hybrid of different hominin species. More bluntly, Sykes and company find no evidence for anything unknown. Samples all track back to known, familiar species like bears.

(Sykes and company gets the title of the the DeNovo paper wrong, too.)

More on the new paper by Sykes and company by Grrl Scientist here.

No word on whether any of the samples came from the pictured Xcel Sports Nutrition bottle.


Ketchum MS., Wojtkiewicz PW, Watts AB, Spence DW, Holzenburg AK, Toler DG, Prychitko TM, Zhang F, Shoulders R, Smith R. 2013. Novel North American Hominins, Next Generation Sequencing of Three Whole Genomes and Associated Studies. DeNovo 1: 1–15.

Sykes BC, Mullis RA, Hagenmuller C, Melton TW, Sartori M. 2014. Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates. Proceedings of the Royal Society B: Biological Sciences 281: in press. doi: 10.1098/rspb.2014.0161

Related posts

Sasquatch DNA: new journal or vanity press?
How is De Novo doing?

External links

DNA analysis indicates Bigfoot may be a big fake

03 July 2014

Taking responsibility for peer review, STAP edition

I have both hearts and darts for Nature in the wake of its retraction of two stem cell papers from earlier this year, now known as the “STAP” (stimulus-triggered acquisition of pluripotency) papers.

I have many more darts for Nature than hearts, particularly for this astonishing statement:

We have concluded that we and the referees could not have detected the problems that fatally undermined the papers.

Then what is the point of peer review? Sure, I accept that detecting problems may be difficult in practice, but I would feel a lot better if Nature at least acknowledged that it was at least possible that they could have caught the mistakes. It seems strange to claim that nobody could have done better after reviewing this timeline from the PubPeer blog:

(L)ess than a week after publication, an anonymous comment on PubPeer pointed out that a gel showed signs of having a lane spliced in (http://imgur.com/1nBfKTr). ... (A)n unannounced splice was potentially deceptive and probably caused people to examine the papers with a more critical eye. Over the following weeks, quite a number of comments highlighting small (inconsistent scale bars) and potentially serious (possible figure duplications) problems were posted.

Nature barely mentions the role post-publication peer review played in this story in either its editorial (noted by Retraction Watch and Paul Knoepfler), although its news piece on research integrity links out to PubPeer.

This is another example of a journal seemingly trying to absolve itself when peer review fails. Come on, Nature. Why not just say you made a mistake?

On to hearts.

Earlier this year, in an article on post-publication peer review, I wrote that when faced with criticism through post-publication peer viewer, about the tendency of journals to “cheerlead for (pre-publication) peer review.”

Even when faced with cases in which peer review failed to detect a highly problematic paper, editors rarely change their journal’s policies to improve the peer review process.

Consequently, I want to congratulate Nature for trying to improve their review processes.

(O)ur approach to policing (image manipulation) was never to do more than to check a small proportion of accepted papers. We are now reviewing our practices to increase such checking greatly, and we will announce our policies when the review is completed.

We will see if this change alone is enough, or whether journals need to go further in upadting peer review. Publishing peer reviews is mentioned in the news article, and that might be a good step to consider.

Related posts

Sharing responsibility for bad papers

External links

STAP retracted
STAP stem cell papers officially retracted as Nature argues peer review couldn’t have detected fatal problems
Science self-corrects – instantly
The rise and fall of STAP
Interview with Nature on their editorial process in wake of STAP 

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

01 July 2014

Tuesday Crustie: Beasts of burden

I’ve always thought that the potential of lobsters as draught animals was under appreciated.

Hat tip to Retronaut. This was part of a larger poster series. Sadly, the other posters in the series are crustacean free...

Comments for second half of June 2014

Complex Roots hates manuscript submission systems. I put in my vote for one of the better ones out there.

DrugMoneky is eagerly awaiting online collaborations to start bearing fruit.