02 September 2017

Thank you, New Hampshire


It’s been a week since Harvey changed everything for Houston, Texas.

And since then, I’ve been waiting. After Katrina hit new Orleans, my university (then The University of Texas Pan American) offered enrollment to students affected by the hurricane. Since Harvey was hitting Texas, I expected that and more.

I emailed our president’s office, reminding them of what happened back in 2005. I got an email back from our Office of Emergency Preparedness, saying:

(UTRGV) has been in communication with University of Texas System... since last week. There are system-wide plans in place in the event student relocation becomes necessary.

I waited to hear what those system-wide plans were. I waited all week. All that happened at my institution was that the Atheletics department teamed with a Texas grocery store to fundraise. Hardly an institution wide response or plan.

Finally, University of Texas System Chancellor William McRaven writes this, titled, “Texans stop for no storm.”

This annoys me to no end. It feels like McRaven is taking this moment to do say, “Look how tough we are,” posturing instead of actually offering concrete plans for help.

On Twitter, the UT System account tweeted a Storyify about how institutions were helping people affected by Harvey. And this is nice, but it’s things like student organizations doing fundraising, universities offering counseling services, not institutions offering anything like what a New Hampshire university has done.

Franklin Pierce University will provide free tuition, room and board to up to 20 students for the fall semester.

That’s what I was expecting UTRGV and other UT System universities to do. But no.

Thank you, Franklin Pierce University, for doing for Texas students what Texas universities didn’t.

Related posts

Credit where it’s due

External links

New Hampshire university to take in students after Harvey
Texans stop for no storm

Picture from here.

29 August 2017

Why a proposed UTRGV doctoral program will probably struggle

When I took my current job, one of the things that attracted me was that I was told the department would probably have a Ph.D. program, maybe in about five years. It’s been a lot more than five years, but a biology related Ph.D. is finally on the horizon for my university. This should make me happy. It does not.

Last week, the UT System tweeted:

.@utrgv Pres Bailey looks to create PhD in Cellular, Molecular & Biomedical Sciences and Doctor of Physical Therapy programs. #UTRegentsMeet

And yesterday, it was confirmed that the university has the go ahead for preliminary planning for this proposed doctoral degree.

I want to go on record as to why I think this is not a good idea. (You get tenure in part so you can make these kinds of analyses.) For context, I have been the graduate program coordinator for biology at this institution for over a decade. So yeah, I know the backstory here.

First and foremost, the primary issue I have with the proposal for this degree is that it is being driven by institutional wants. Not to meet clear needs in the community. Not students’ interests. Not faculty research strengths. The university is trying to get to ten doctoral programs as fast as it possibly can, so it can meet the criteria for an “emerging research university.” Getting to that number of Ph.D. by any means they can is more important than coming up with a program that has faculty support and that will ultimately serve the students.

Second, the proposed program – “Cellular, molecular, and biomedical sciences” – might as well say, “and the kitchen sink.” There is no theme or connection there. There is no department of “cell, molecular, and biomedical sciences.” It seems like the plan is to conscript any faculty member in any department that knows how to use a PCR machine. With no single department to house the program, there will be tremendous problems of organization and cohesion. It will be difficult to instill that intangible but critical sense of community.

Third, there are already four cell and molecular biology doctoral programs in Texas (not to mention broader general biology programs). They are at University of North Texas, UT Austin, UT Dallas, and one of our closest neighbours, UT San Antonio. There is an case to be made that the proposed degree would unnecessarily duplicate existing programs, which the Texas Higher Education Coordinating Board warns against.

Lastly, the graph that no administrator has an answer for is this one (from here):


The article has UTRGV president Guy Bailey talking about job growth projections from the Bureau of Labor Statistics. But knowing demand don’t tell you much unless you know the supply. Administrators will ignore the existing backlog in students being trained, and the growth of programs training them.

The Bureau of Labour Statistics lists one biology related occupation that requires a doctoral degree: “Biological science teachers, postsecondary” (i.e., professors). They project a total of 21,200 job openings from 2012-2022. Using 2011 data on doctoral production, the projected 10 year need can be met in less than three years at recent rates of doctorate creation at the national level.

The only other biology related occupation listed by the Bureau of Labor Statistics that requires a doctoral degree is animal scientists (1,200 job openings, 8.8% growth). Again, this need can be met by current levels of doctorate attainment in the United States.

There are not clear projections for how much demand there will be for biology doctoral recipients outside academia, because the Bureau of Labor Statistics does not separate “Life sciences” jobs on whether they require a B.S., M.S., or Ph.D.

I think the students and the region deserve a good doctoral program they can be proud of. Instead, we’re likely to get a rushed, rudderless, “me too” doctoral program that nobody asked for and nobody wanted.

External links

UTRGV gets green light to seek two new doctorate degrees

28 August 2017

A sense of community


Last week, Stephen Heard wrote a post about being paid for peer review that generated a lot of discussion on Twitter. A fair number of people were quite emphatic that they were not being paid, and a few seemed very grumpy about that.

Earlier in my career, I remember people complaining about the individual reviews they got, or how long reviews took. But I don’t remember people grumbling over doing reviews, or not being compensated for them. And I never heard complaints from editors about how many people were refusing to do reviews.

Now, I suspect part of this is just a shift in perspective. I hear more voices via social media than I did before, and hear more perspectives. I know people who are on editorial board on Twitter, which I didn’t before. Still, from my perspective, it feels like grumpiness over having to do peer review is a relatively recent thing.

It seemed to me that annoyance about doing reviews might be symptomatic of researchers having a degraded sense of community.

When you feel like you belong to a community, you just pitch in. You help. Not because you are paid to do so, but because it’s friends and neighbours and it’s just what you do to make your community a nice place to be.

I think people are refusing to do reviews in part because they don’t feel connected to the academic community. And I get why that would be: it’s a rough, competitive market for ideas now. The shortages in funds and jobs and everything else feels like it’s forcing people into a “me first, me only” mindset to try to survive.

People will complain about journals more when they don’t feel they those journals are part of their scientific community. Maybe this is why many academics have continued to support society journals, even as more and more of them get run by one of the big main “for profit” publishers.

I have been thinking a lot about community, too, because of things like university administration. This tweet went out last week, reading in part:

@utrgv President Bailey looks to create PhD in Cellular, Molecular & Biomedical Sciences.

Yeah, neither faculty nor students asked for that program. It certainly doesn’t make me feel part of a community in my own institution.

Same with graduate programs. I’ve seen some research that one of the biggest predictors of successful programs is that graduate students feel a sense of belonging. That is, of community. And while I tried to create that feeling in our graduate program, I have come to the conclusion I have failed.

This is one reason why science Twitter and the science online community has been important to me: because it truly does seem like a community. People offer ideas and support, for no reason, just because. Someone came up with the term “pocket friends,” which I think is a good phrasing. I’ve said to a lot of people that online conversations are real conversations. And online friends are real friends.

Update, 29 August 2017: This post was featured in today’s Daily Briefing in the Chronicle of Higher Education. Thanks to them!

Update, 30 August 2017
: Mike Taylor has a response.

External links

Can we stop saying reviewers are unpaid?

Picture from here.

25 August 2017

Big bad Harvey

I’m probably going to be mostly unaffected by Hurricane Harvey. The University of Texas Rio Grande Valley campuses are closed today and tomorrow. Currently, the forecast is for a few inches of rain and possible power outages.

But the rest of Texas isn’t going to fare so well.

Harvey’s going to be very, very bad.

It’s hard to believe that on Monday, nature was treating millions to probably her most beautiful sight – a total solar eclipse. And here we are on Friday, same week, with millions of people dreading one of her most deadly events.

I hope my friends and colleagues elsewhere in Texas and Louisiana stay safe.

Update, 27 August 2017: Houston this morning. Pic from here.


This is after one day, and there’s more days to come yet.

This tweet shows water flooding into a news building after it rose a foot in 15 minutes. Terrifying.

External links

Hell and high water (From 2016, on why Houston did not get more prepared for a hurricane like Harvey after Ike in 2008)
Hurricane Harvey aims for the Texas fracking boom’s favorite port

21 August 2017

Eclipse 2017

It’s eclipse day, 2017!


Here in South Texas, we only got a partial eclipse. I’ve seen a total solar eclipse (in 1979, the last one over North American before today). and a partial one pales in comparison. Seriously, if you ever get a chance to see a total solar eclipse, go. It’s stunning.

Today, the main thing I did was play around with making a pinhole with my hands. I was surprised at how easy it was to see the crescent of the sun, with a distinct “bite” take out of it. Here’s the image with a bit of processing:


And close-up, looking more like the moon at night than the sun in day.



Related posts

A gift

10 August 2017

Me, 2017



My selfie game is not strong. And I generally feel super scruffy when I am out at the beach collecting. But I like how this pic of me in the field Tuesday came out.

I was scruffy, but the day was gorgeous. I was very lucky to be out on the beach that morning.

But this is a good opportunity to draw your attention  to Paige Jarreau’s project on scientist selfies. There is an Instagram account of other scientist selfies here, a Flickr collection; a Twitter hashtag, #ScientistsWhoSelfie (of which the picture above is one). And you can support her project on Experiment!

External links

04 August 2017

The Journal Loyalty Index

Happy coincidences make good prompts for blog posts. Earlier this week, I returned a review of a manuscript for a journal. It was one I had never reviewed for before, so I added it to a list of reviews I keep in my CV. It was the thirty-ninth  journal I had reviewed a paper for.

I was curious if this was a particularly high number. People often complain talk about how many reviews they do (or are asked to do), but not how many different journals are asking. I asked on Twitter. 39 different journals does seems to be on the high end:



Coincidentally, Stephen Heard published this post about how many journals he had published in, which he, following the example of twitchers, called a “life list.” This interested me, because I deliberately try to publish in as many different journals as possible. It’s a science macho thing: I want to see how many different editors I can fool convince.

As with reviewing, I knew about how many papers I had published, but not the journal distribution. Stephen had proposed the Journal Diversity Index (JDI) the number of journals divided by number of papers. Everyone has a JDI of 1.0 when they publish first paper, and it only declines from there.

My JDI is higher than Stephen’s, but several commenters in his post beat us both.

But this got me thinking about the two things together. What’s the relationship between the journals we publish in, and the journals we review for? I expected there to be substantial overlap:


After all. the whole reason you submit to a journal and review for a journal are the same: you have expertise in that. Moreover, editors look at their lists of authors when looking for reviewers, which I would expect would lead to greater overlap in the journals you publish in and the journals your review for.

I mean, it would be weird if there was almost no connection between your papers and your reviews, right?



But when I crunched the numbers, I was a bit surprised. The sets were almost equal.




There were 18 journals I have published in, but have never reviewed for.

There were 15 journals for which I have both published and reviewed papers. What I was expecting to be the biggest category turned out to be the smallest category.

There are 24 journals I have reviewed papers for, but never published in. That the “review only” part of the Venn diagram is bigger than the “publish only” part of the diagram doesn’t surprise me, because my online friends on editorial boards are constantly talking about how hard it is to find reviewers for manuscripts.

Like Stephen, we can make a simple index. The number of journals you have both published a paper in (B), divided by the total number of journals you have interacted with editors (E). We’ll call it the Journal Loyalty Index (JLI).

I have 15 papers I have both published and reviewed for, out of 57 journals I have interacted with. Making my JLI (15/57) is a mere 0.26.

I of course curious how loyal other researchers are to their journals.

Related posts

Peer review pariah, update

External links

My journal life list
Journal life list

26 July 2017

World’s worst... scientific papers


I have a new project to share! Just for fun, I spent the last few days making another little ebook, similar to what I did with Presentation Tips.

Stinging the Predators is a collection of deliberately horrible papers that were created to punk predatory journals. There have been six such pranks in the last two years. The most recent, which sort of triggered this project, was on Neuroskeptic’s blog last Saturday. Thinking about all the “sting” papers I’d seen over the years, it occurred to me that fake papers were practically their own emerging genre. And what better way to draw attention to a genre than with a curated anthology?

I collected all the sting papers I knew about. There turned out to be thirteen, and collecting them convinced me that it was useful to have all these examples in one place. Each paper has a short new introduction, and links to articles about it. I rounded off the collection with some short essays, some of which appeared here on the blog before, and a couple of which were new.

Once I got started with this project, I couldn’t let it go. I promised myself I would only let myself work on it for a few days, and then get back to work on writing that could be published by other people.

The ebook is available on figshare and on DoctorZen.net.

Update, 28 July 2017: After I posted the first version, I was reminded of another sting paper on Google Plus (see? It’s not a ghost town). I found another abstract after that. I decided to make a quick turnaround from version 1 to 2. There are now fifteen entries in this anthology.

The easy to remember link is http://bit.ly/StingPred. (Capitalization matters! “stingpred” will not work.)

Update, 31 July 2017: I know, two revisions in less than a week? I learned of another sting paper, and another conference abstract, bringing the total number of entries to 169 pages of mostly rubbish. (Some will probably say all is rubbish.)

Update, 7 August 2017: This little project is featured in Times Higher Education today and the Improbable Research blog!

External links

Stinging the Predators on Figshare
Predatory Journals Hit By ‘Star Wars’ Sting
Worst ever research papers revealed
“All these papers were deliberately bad”

18 July 2017

Rough rides at tenure time


Yesterday, I wrote about Dr. Becca’s tumultuous ride through her tenure process. (And thank you to all who read, like, tweeted, shared, and commented!) Becca has done many early career scientists a favour by documenting this difficult process.

I’ve talked from time to time about how important it is to share our failures. But we particularly don’t like to draw attention to issues that came up at tenure time. I wrote about my problems with tenure after I squeaked through the process. I was not writing a pseudonym, and I didn’t blog about the process much while I was going through it. I was very mad about it then. I don’t get visibly upset talking about like I used to, but I can’t say I’ve made peace with it. With the better part of a decade between then and now, I can see why I got a hard time at tenure, but I still feel I was not treated well.

Terry McGlynn had an even rougher time. He was denied tenure, which he wrote about extensively in the Chronicle of Higher Education.

But what I haven’t done specifically is to talk about what came afterwards for me. A lot of people think that after academics get tenure, they drop off and take it easy.

I got better.


After tenure, I finally had everything in place. The gears were turning, and I started to get the researcher coming out much more consistently, with more original data driven papers. And I had seen the adage, “Don’t let the perfect be the enemy of the good.” I lowered my standards and stopped waiting for projects to get that one last bit of data. And stuff started to happen for me. I became one of the most published faculty in the department.

I am not trying to brag here. I know many people would look at my research track record and deem it second rate (at best). “Sand crabs, Zen? Nobody cares about your sand crabs.”

The moral of the story? It’s to remind people that trouble, even at this critical point in an academic career, does not have to cripple the rest of your career.

And that publishing well is the best revenge.

Related posts

Now part of the problem
Low points
Nevertheless, she persisted

External links

Coming out of the closet, tenure denial edition

17 July 2017

Nevertheless, she persisted

Sometimes, you get to watch a friend win one. And that win is practically as sweet as one of your own.

Friend of the blog Dr. Becca has been getting a rough ride at tenure time. Until today:

THE PROVOST REVERSED HIS DECISION AND IS RECOMMENDING ME FOR TENURE

First things first: Congratulations, Becca! I am so happy for you! Wooo!

Other things: Becca’s win is important beyond just the obvious significance for her and her students and collaborators. It needs to be seen and discussed widely for two reasons.

First, her case needs to be talked about because the grief she was getting was all about one thing: money. Scratch that: it was because she didn’t get the right kind of money. Her job was being threatened because she hadn’t brought in a stand alone research grant from the National Institutes of Health (an NIH R01, to use the jargon).

Becca’s situation is the nightmare scenario that many early career scientists are staring down. The NIH budget is flat, applications are up, and most recognize that the success rate in applying for NIH grants is now so low that many perfectly good projects go unfunded.

In other words, getting a grant has a healthy dose of luck to it and no amount of granting savvy can ensure you will pull down any particular grant. Lack of a grant does not mean your colleagues don’t think you’re doing crummy science.

Becca’s situation shows how dire and destructive this habit of “outsourcing” tenure decisions to granting agencies has become. Professors and administrators need to talk about this and adjust their expectations to line up with reality, and not expect the stone to give blood if you “incentivize” the stone enough.

This is something that has been buzzing in the background for a long time, but the situation has worsened in the last 6-7 years. Academics are used to stability at much longer time scales and aren’t prepare to adjust to the ground shifting underfoot in the time it takes to hire a professor to her tenure review.

Second, Becca’s case matters more generally than her alone because, as Neil Gaiman (channeling G.K. Chesterton) says:

Fairy tales are more than true: not because they tell us that dragons exist, but because they tell us that dragons can be beaten.

Becca shows that you can fight the dragons of university administration, and you can win. And a lot of early career academics need to know that. Because dragons are big and scary and it is easy to give up and concede the battle.

Becca was confronted with career dragons.

Nevertheless, she persisted.

Related posts

The secret life of a banner
The secret life of a banner, part 2

16 July 2017

The future is female

This year has seen something special. There’s been a hunger for new heroes. You can see it in these projects.


Hidden Figures. It challenged the pop culture juggernaut Star Wars at the box office, and got Oscar nominations, too.


Wonder Woman. The biggest hit of the summer, still going strong.

And now... the thirteenth Doctor.


It’s going to be fantastic.

Congratulations, Jodie Whitaker! I look forward to seeing you pilot the TARDIS and fight the monsters!

Added: Reaction to the latter.

13 July 2017

Five years for seven points of data

I was very excited yesterday. I got to add another data point to this graph:


It’s taken me five years to get those seven data points. Five. Years.

It’s not for lack of trying. Each data point depends on me catching a rare event. There’s a limited amount I can do to try to catch those rare events, so this graph is building up slowly. It’s not quite a pitch-drop experiment, but I am seriously wondering if I am ever going to have enough data that I will feel confident about publishing it.

I share this because there are a lot of people fretting about the speed of science these days. People want want fast review, and fast publication. Some are turning to pre-prints for greater speed. But sometimes, try as we might like, some questions force you to take a long, slow slog to get to the answer.

12 July 2017

The bat signal: Can cricket ears hear their predators?

(This was originally published here in 2005.)

Few events in animal behaviour evoke an observer’s visceral response as interactions between predators and prey, leading to poetic metaphors like, “nature red in tooth and claw.” The mechanisms through which prey avoid being caught and eaten provide some of the best examples of behaviours whose neural basis is reasonably well understood. For example, in fish, the Mauthner cells are key players in generating C-start escape responses (Korn and Faber 2005); in crayfish, the lateral and medial giant interneurons generate escape tailflips (Edwards et al. 1999). Surprisingly, however, our knowledge of when these well studied circuits are triggered by actual predators in the wild is rather limited, though those gaps are beginning to close (Herberholz et al. 2004).

Crickets have neurons that trigger escape responses, named AN2 (also referred to as Int-1). Unlike fishes’ Mauther neurons or crayfish’s giant interneurons, which can be triggered by a wide range of sudden stimuli, AN2 neurons appear to serve as detectors for one particular type of predator, namely echolocating bats (Nolen and Hoy 1984, 1987). While AN2 neurons respond to a wide range of sound frequencies, they are particularly sensitive to ultrasound, that is, sound frequencies that are too high for human ears to hear (Nolen and Hoy 1987). This is the approximately the same range of sound frequencies that echolocating bats use when foraging. But, as a recent paper by Fullard and colleagues (Fullard et al. 2005) notes, the key word is “approximately.” There are many species of bats, which differ in their foraging tactics, and emit a wide range of sounds as they do so. Most lab studies, for understandable reasons of simplicity and convenience, have used pure tones generated by computers to trigger crickets’ auditory neurons.

Fullard and colleagues studied Teleogryllus oceanicus, a cricket species found across much of the western Pacific. They recorded the calls of a half-dozen species of bats that share habitat with this cricket, then recorded AN2 neurons as they played back the bat calls at different sound intensities.

The crickets’ AN2 neurons responded to calls from all six bat species, if the sound intensity was 80 decibels sound pressure level (dB SPL) or more, although they did not react equally to all bat search calls.

Simply firing the AN2 neuron, however, does not determine if the cricket can avoid a foraging bat, because a single spike of AN2 is not sufficient to trigger an escape response (Nolen and Hoy 1984). By examining the pattern of firing in more detail, the authors were able to estimate how far away a bat call might trigger an escape response. Only calls by three of the bat species fired AN2 neurons strongly enough to generate escape responses before the bat would be aware of the cricket's echo.

If the AN2 is indeed a “bat detector,” it is reasonable to hypothesize that it has been shaped by natural selection to detect bat species living in the same habitat. All bat calls tested were from species that live in the same regions as T. oceanicus (i.e., sympatric species), but one might reasonably predict that AN2 should be less responsive to calls of bats that do not live in the same regions (i.e., allopatric species). That T. oceanicus has such a wide distribution, however, might mean that its auditory system has remained a bat “generalist.” Another prediction of the “bat detector” hypothesis would be that the bats that AN2 detects best would be those of species that are the most successful predators of crickets. In this case, the bat species Tadarida australis generated the greatest AN2 responses, raising the question of what the natural ecological interactions are between the cricket and the bat.

The bat species that is arguably the least conspicuous to crickets demonstrates the importance of understanding natural ecology in interpreting patterns of neural activity. Of the six species of bat whose calls were tested, the least conspicuous to crickets was Nyctophilus geoffroyi, because the echolocating calls of this species are too short and too high frequency for the crickets’ ears to detect reliably. The simple hypothesis might be that this bat species is a mammalian “stealth bomber:” by using echolocation calls that are almost undetectable by crickets, the bat would seem to be well equipped to pluck crickets from the air at will. Instead, N. geoffroyi seems to forage primarily by “gleaning,” i.e., locating insects by the sounds they emit and picking them off the ground (Bailey and Haythornthwaite 1998), a tactic that circumvents crickets’ tuned AN2 “bat detector” almost entirely.

References

Bailey WJ & Haythornthwaite S. 1998. Risks of calling by the field cricket Teleogryllus oceanicus; potential predation by Australian long-eared bats. 513. Journal of Zoology 244(4): 505-513

Edwards DH, Heitler WJ, & Krasne FB. 1999. Fifty years of a command neuron: the neurobiology of escape behavior in the crayfish. Trends in Neurosciences 22(4): 153-160.


Herberholz J, Sen MM, & Edwards DH. 2004. Escape behavior and escape circuit activation in juvenile crayfish during prey-predator interactions. The Journal of Experimental Biology 207(11): 1855-1863.


Nolen TG & Hoy RR. 1984. Initiation of behavior by single neurons: The role of behavioral context. Science 226(4677): 992-994.

10 July 2017

Goodhart’s Law



When a measure becomes a target, it ceases to be a good measure. - Goodhart’s Law

The longer I’m in academia, the more I appreciate the wisdom of this statement.

07 July 2017

Why I stopped writing grants

A couple of threads on Twitter recently reminded me of something. This from Liang Gao (my emphasis):

Just visited a new PI. He showed me beautiful research, top publications , and thousands pages of unfunded proposals. What the hell is going on?

Then there was Prof-like Substance:

Remember that when applying to NSF, this is what you’re up against. ~6% success from the process. Which is why I tell people over and over and over that if you don't diversify, you will get eaten alive. You. Can. Not. Go up against 6% success for a decade and think everything will be fine. It won’t.

Then there was this charming reminder from Jacquelyn Gill that in addition to dealing with biases about sex, race, and “academic pedigree,” you have to deal with biases about geography:

An equipment grant I'm a co-PI on is #NSFunded! I'm grateful for the chance to do some fun new research. But two reviewers mentioned how small UMaine is. One said it “only has 13,000 students.” Another said there’s “not much up there but moose.”

A lot of people are reaching the point I got to maybe four of five years ago, when I wrote:

Personally, if you’d asked me when I started this job if I thought that I’d be able to get grants for my research, I’d have said, “I think it’ll take me a few tries, but I think I can do it.” Well, that hasn’t happened. So I’ve had to re-invent myself, my expectations, everything, from almost the ground up. It’s been a decade-long battle to redefine myself as a scientist. I’m still not done.
 
I realized that producing thousands of pages of grant proposals was not satisfying for me, either personally or professionally. The odds were long and not improving. People probably think there’s less in South Texas than there is in Maine.

I also realized that managing those grants I did get were not satisfying for me. I’ve complained for a long time that trying to spend a dollar from a grant requires a bottle of aspirin, because it’s an instant headache.

So I mostly quit writing grants. I’m still writing some pre-proposals for NSF, but none have gotten an invitation for a full proposal.

Instead, I have focused on the bit that I find most satisfying for me: writing papers. I have focused on creating “$5 projects” that can go forward, grant or not. My research doesn’t run on money. It runs on willpower.

And I just submitted a manuscript to a journal today, thank you, that was generated with no grant support at all.

03 July 2017

American Society of Parasitologists, Day 5

For the last day at the Parasitologists conference, I mostly sat in on taxonomy talks. Now, I love taxonomists and admire the work that they do to no end, but I think it’s fair to say that their talks do not always have the most compelling narratives. So most of my notes for talks I saw were very short.

Sara Brandt: Schistosome taxonomy. Thinks snail ecology plays the biggest role in determining the schistosome relationships.

Santos Portugal (@jsportugal3): Tick phylogeny.

Tim Ruhnke: Cestode tapeworm phylogeny.

Veronica Mantovani Bueno: More cestode tapeworm phylogeny. The revision the taxonomy of host skates and rays led to big changes in interpretation of the taxonomy and ecology of their cestode parasites. There seems to be very relaxed associations between host and parasite. Some of the cestodes she studies have very similar DNA sequences, but dramatically different morphology.

Anna Phillips: new medicinal leech. #CollectionsAreEssential

Carlos Ruiz: I came in late and missed the start of this talk, but it involved possible new copepod species.

Jackson Roberts: Turtle blood flukes, of which he described one new species. A bunch of stuff is coming about flukes in South American turtles.

Bret Warren: Looking at flukes in sturgeon. I learned that Lake Winnebago has a sturgeon fishery, which is spearfishing in winter, through holes in ice. That alone was worth the price of admission. Here’s a video of this great tradition:


Carlos Ruiz again (this was sprung on him about 10 minutes before the talk): Myxozoans are parasitic jellyfish. In this case, they cause “whirling disease” in fish. Very tough to get rid of. Started with reports from anglers noticing strange fish. State natural resources came on board to get samples.

After the contributed talks, the moment I had been waiting for: poster session! I had a poster that I was very happy with. I’ll show it on the Better Posters blog after the paper is published. (I’m writing it now!)


I was also super pleased to be reunited with my SICB symposium partner in crime, Kelly Weinersmith, who had new progeny with her.


Because the diversity of parasite research is so wide, it can be hard to detect commonalities across a conference (which I saw less than half of, at best). But there were a recurring theme from this meeting.

Parasitology, like much of biology, has been transformed by molecular biology. The techniques are making it possible to answer questions that would have been very difficult to answer without them. For instance, “Is this species of parasite in this intermediate host the same species in this definitive host?”

But parasitologists emphatically do not want molecular biology to take over their field.

Several speakers referenced the #CollectionsAreEssential hashtag on Twitter, which was prompted by the possible loss of NSF funding supporting museum collections. Museum collections are constantly under threat, and constantly proving useful to current science.

Several people noted that DNA sequence data needs to be connected to “ground truths”: you have to be able to see the organism whose DNA you are sequencing.

The recurring theme of this meeting was that for parasitology to remain a viable field, never mind a vibrant one, organismal biology has to remain strong. This is going to be a challenge, because many people find the “Sequence it all and let algorithms sort it out” approach enticing and alluring.

One last note that is tangential to the conference, but relevant to a recent post on publishing costsThe Journal of Parasitology has very competitive article processing charges, particularly for open access. Even nonmembers can publish open access for $1,000, about the same as PeerJ, which is one of the most cost effective open access megajournals.

Related posts

American Society of Parasitologists, Day 1 and 2
American Society of Parasitologists, Day 3
American Society of Parasitologists, Day 4

01 July 2017

American Society of Parasitologists, Day 4

These are my notes from talks I saw on Friday's sessions!

R Grunberg gave a very nice talk about whether parasite abundance (density) scales with body size (Damuth’s Law). Her data suggests not. But host body size comes into play: if you do that, the parasites follow Damuth's Law. How you feed and disperse tweaks the effect a little.

Janine Caira: This project started with a donation of a huge, awesome army ant collection. Over 500 species were associated with just one species of army ant – guests associated with the army. Lots of ectoparasites live on specific parts of specific species. This prompted a lot of outreach at her campus, around the tag line, “Be our guest.” Antu.uconn.edu

Jessica Light: surveyed parasites on property in South Texas, supported by East Foundation. Not many mammals in museum collections are from South Texas. #collectionsareessential Found 19 mammal species, about 70% parasitized. Tick borne diseases are particularly interesting.

Niyomi Wijerardena: pika parasites! Pikas have five very distinct lineages, but the endoparasites don’t track those lineages. What about the ectoparasites? Fleas don’t track those lineages either, suggesting ancient contact between pika populations that are not recorded in DNA.

Lijun Lu is doing transcriptome work on what makes snail resistant to infection by schistomes.

Lauren Bassett
was looking at the genetics of a microsporidium that is a potential biocontrol for red invasive fire ants.

Maria Castillo is also studying protein expression related to schistosomiasis infection of the snails. Thioester containing proteins seem to be related to resistance to various kinds of infection.

Presidential lecture by Gerald (Jerry) Esch. Described three stories, each of decades long and filled with obstacles from fights, fallacies, and waiting for blind luck, to emphasize the long road that research faces. He ended saying, “What does the future hold? I don’t know. But neither did the researchers who founded the field of parasitology 150 years ago.”

Michael Zimmerman
starts describing the mating system of bluegill sunfish, which has dominant alpha males and beta males, which perform “drive by insemination.” Parasites may contribute to the maintenance of these two forms. The alpha males had higher diversity and abundance of parasites than beta males or females.

Nicci Carpenter
: Helminths reduce fitness in mosquito fish (Gambusia affinis, also known as the plague fish)mosquito fish. The nematodes reduce brood size, and parasite diversity reduces embryo size.

Victor Vidal Martinez: healthy ecosystems have more parasites. Studying parasites on the fish on the Mexican portion of the Gulf of Mexico, which are subject to pollutants. Saw a higher diversity of parasites off the Yucatan Peninsula, which is good! It indicates a a healthier ecosystem than in the rest of the Mexican region of the Gulf.

Isabel Caballero: Although the cestode species she studies are definitely inbred, they show no strong evidence of inbreeding depression.

Stephen Greiman
(@sgreimanbio): what drives species interactions now and in the past? He points out that when you look at just the top ten museum for mammal species, there are literally millions of samples in just those ten institutions. Using next generation sequencing, he was able to use next generation DNA sequencing to identify known parasites in shrews. Different sequences were slightly better at resolving some groups than others.

Seth Bromage: Bluegill and pumpkinseed sunfish are about the same size, but very different parasite infection patterns. The same species, U. dispar, is bigger on bluegill. Seth filled his talk with speculation, because “It’s fun for me.”

P Robison: For fish, salinity is a major environmental factor that limits distribution. Guppies will tolerate salty water in an aquarium, but you never find them in any salty water in the wild. Metacercaria are very high near the range limit, but rare near the center of the distribution (further from ocean). Exposure to brackish water killed more fish, and resulted in a higher parasite load, for the guppies.

John Shea: How do horsehair worms find each other to reproduce in hosts? Blood borne parasites can potentially have miles of blood vessels to search. It looks like in aquariums, there is substantial luck involved. But it looks a little better in lower water depth, with more evidence of successful mate detection.

Justin Wilcox
: Most parasitologists think most animals are parasites, but that is just a hunch. He tested the hypothesis that parasite diversity will be comparable to free living microbial communities, using  parasites in macaques and next generation sequencing. Diversity of parasites and free living species is comparable. And there is a lot of diversity in these macaques.

Matt Bolek
: presenting work of master’s student Chelsie Pierce. How do amphibian tadpoles differ from the adults in their parasites? Tadpoles are herbivores, e.g., and adults are carnivores: very different parasite habitats. Tadpole size, just like adults, affects parasite communities. Difficult to compare species, because the tadpoles’ basic natural history is so different. But parasite life cycle strategies were major factors in determining community structure.

Charles Criscione: The goal is to try to work out mating systems in parasite systems in the wild, and the particular focus here is on inbreeding. We know little about the ecological drivers of parasite mating systems. Looking at gecko tapeworms, which probably have high inbreeding. But, as mentioned in Isabel’s talk, not evidence of inbreeding depression.

The day ended with a student/faculty mixer, which the organizers called “The Vortex.” It was a good  idea, although it might have done with a little more room.

30 June 2017

American Society of Parasitologists, Day 3

I brought my iPad, with one of those nice little keyboards, and all the keys were working except the space bar. Great. That rather slowed my plans for tweeting, blogging, and so on.

The day started with the presidential research symposium on parasite ecology, given by Celia Holland on Ascaris. She is talking about how parasites tend to aggregate:  the variance to mean ratio is almost always greater than one (higher numbers mean more aggregation). Ascaris infection is a very bad, neglected tropical disease – maybe one of the worst in terms on number of people infected world wide. A big chunk of her talk was about trying to develop a model for Ascaris infection. The only animal that Ascaris will go through its entire life cycle are pigs. Well, pigs are big, expensive, and tricky to house. So, can we do it in a mouse? Well, sort of. The Ascaris will do some of their life cycle in mice, and some mouse strains are better hosts than others.

Kim Jacobson talked about using parasites as tags for fisheries management. Artificial tags are often too big for commercially important fish, like anchovies. Parasites can tell you were fish have been, since they can only get infected in the parasite’s endemic range. They used parasites to try to figure out the migration of sardines.

Derek Zelmer (who apparently is the punchline for many jokes at ASP) talked about the synchrony of parasite populations in sunfish. Variance to mean ration of 1 is random, variance to mean ratio less than one is even. Over and over, he saw more synchrony between sites that were further away from each other. This can allow for “rescue effects”: if one population drops, another can replace it.

Notes from some of the regular contributed talks I saw:

Rachel Paseka showed carbon,nitrogen,and phosphorus ratios vary across species. This is mostly related to body size; growth needs phosphorus.

Sarah Bush gave one of my favourite talks so far. It was like the classic peppered moth story in evolution, except with lice and bird feathers instead of moths on blackened tree trunks. Feather lice are under strong selection pressure from host preening, and they evolve cryptic colouration to match feather colour quite quickly.

Martina Laidemitt: amplification or dilution effects. Coolest part of this talk was discussion of how one trematodes species can completely take over a host from competitor species.

Tim Anderson more snail parasites. Schistosomes parasites vary in Ho the time in when their cercaria are shed. Some species synchronize their release. In one case, the same species releases at different times depending on what host they have infected. Does this have a genetic bases? Oh yes. And they have tracked it down to chromosome 1, which affects lots of cercaria release traits.

Laura Eliuk: trematodes life cycles often have a three host life cycle. Not much research on mollusk (first intermediate) hosts. Parasites may alter mucus composition of first intermediate host, to make them more attractive to the second host. The moral of her talk was never trust sweet smelling snail snot (my summary, not hers).

Alyssa Gleischner: does parasite competition influence virulence? Related parasites should have reduced virulence, as per kin selection theory, since if host dies, it takes all kin with it. But if parasites are not related, there is direct competition, so you care less if competitors die. She tried answering this in schistosomes. Results were sometimes supportive of kin selection, sometimes not, depending on what you measure. Low virulence for intermediate hosts, high for definitive hosts. Stage in life cycle may also matter.

Frederick Chevalier: schistosomes were transported from Africa to South America. How are they adapting to new habitat? Quite well.

Erika Ebbs was supposed to be speaker, but Sara Brant ended up giving it instead. Watch the fun when a supervisor has to take over a student's talk. Duck ecology shapes influence microevolutionary changes of parasites. I think at one point she mentioned that one of her duck species was infected 98% of the time, and she couldn't remember seeing prevalence that high before. Heh. I got something that ties that; come to my poster tomorrow!

The afternoon ended with a student session about funding. People discussed NIH, NSF, and small society grants. I took over the session for a minute or two to talk about crowdfunding.

Then, I walked around. San Antonio is a very walkable city.

29 June 2017

American Society of Parasitologists, Day 1 and 2

I missed Day 1 entirely. Nothing to report. Sorry.

I drove up to San Antonio on Wednesday afternoon. During the four hour drive, I reflected on how I chose this meeting to come to this summer instead of many of the others that interest me because it was “close.” Ah, Texas, where a four hour drive is “close.”

I got there too late to get my name tag. But when I walked up to the social without the name tag, the man at the door gave me two drink tickets, unprompted.

I guess I looked scruffy enough that I couldn’t be anything but a biologist.

27 June 2017

Being scared: academics getting death threats for having an opinion

Kate Clancy is someone who I admire. She is someone who says stuff the needed saying. Like pointing out the high incidence of sexual harassment in field work.

For the second time today, I am compiling a Twitter thread about something important. Lightly edited.

My local paper, the News-Gazette, ran an editorial yesterday. That editorial, written by their staff, was half about me. I am the “ideologue” who got a James Watson talk cancelled. The thing is, date hadn’t been set yet, and Watson has a history of being implored to give science-focused talks then just saying racist shit. Perhaps I was the only one who publicly denounced the Woese Institute for Genomic Biology talk. But I wasn’t the only one who spoke against it.

Here’s what happened next: Julie Wurth of the News-Gazette called and asked to interview me about my tweets, and I said yes. So the News-Gazette was the first, and for a while only, story about the Watson cancellation. After that, the story got picked up by conservative websites and blogs. This is when I started getting hate mail. It turns out the smartest thing most conservative trolls can zing at me is that I’m a “fucking cunt.”

Unfortunately days went by and the story didn’t go away. For this reason, I eventually started getting more serious hate mail, threats. I involved campus police. One officer has been sympathetic. But the most I got was a form to fill out for a domestic violence safety plan.

So far, neither the University of Illinois nor Institute for Genomic Biology have corrected the record on my being the sole person against the Watson talk. Nor have they done anything to defend my academic freedom, nor support my personal safety. I’m 36 weeks pregnant by the way.

Today, the day after that editorial, I found a sticky note on the front door of my home asking me to check my email.

I want to say, very clearly, that I hold News-Gazette, the University of Illinois, and the Woese Institute for Genomic Biology responsible for this loss of my personal safety.

In response to another thread about science blogging and activism, Kate wrote:

Honestly, with the experience I’ve recently had and how the conservative trolls are getting worse, I’d advocate against speaking up.

This is how a lot of people lose. Kate loses, for obvious reasons. Academics lose, because they see someone who was a strong voice saying that it’s a mistake to be outspoken. News organizations and universities lose, because people lose trust in those institutions.

Intimidation is how fascism wins.

Update: Kate has asked for the following:

For those of you offering to help: first steps are to write News-Gazette and Institute for Genomic Biology for their lack of control/protection. Contact info for News-Gazette: http://www.news-gazette.com/contact. For head of Institute for Genomic Biology: generobi@illinois.edu.