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:


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.


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.

The problem is scientists, not publishers

Because I hate people who just retweet something interesting and say, “Thread,” I’m compiling Jason Hoyt’s series of tweets about the state of scientific publishing into a blog post. Jason’s thread was initiated by this article in The Guardian, “Is the staggeringly profitable business of scientific publishing bad for science?”

For context, Jason is founder and CEO of PeerJ, which I have published in, and will do so again. I have lightly edited the tweets for clarity and emphasis.

This will be controversial, but the problem is scientists, not publishers. While the article may get the history of the problem accurate, it is going to perpetuate several myths about the current root of the issue. Scientists continuing to blame publishers, rather than the root, is pretty damn unscientific.

Plenty of cheap or even free publishing solutions exist. PeerJ even provides lifetime publishing open access for almost nothing, but very few scientists care about price when deciding where to publish. Scientists care about impressing grant and tenure and hiring committees, made up by other scientists, and the committees care about Impact Factor as a vanity metric for quality. It is the tenure/hiring, NIH, NSF, grant committees, not publishers, that are the ones in power and need to make the changes. Demanding publishers do so will do little.

So why aren’t the pitchforks out against the committees? There is only one group that can lead that charge, and it isn’t the publishers. Why aren’t committees looking at the merits of the article rather than the journal it is published in? Why aren’t committees more proactive in saying publish in cheaper open access alternatives like PeerJ?

PeerJ started out at $99 for lifetime publishing. That would have saved governments and funders $9 billion a year. Yet zero funders and committees have yet to approach PeerJ since it was launched five years ago with any support, acknowledgement or promotion. Instead, Nobel laureates and funders launch an elitist journal (I believe Jason is referring to eLife. - ZF), perpetuate the Impact Factor, whilst hypocritically blaming Cell, Nature, and Science journals. Instead, they fund elitist “non-profit” journals that charge $2,000 an article yet still only cover half their costs. This makes no sense.

Then scientists wonder why PeerJ had the gall to raise lifetime open access publishing from $99 to $399. The world doesn’t want nice things.

One of the myths is that academics do all the work. And daily I see an academic complain about journals and propose starting their own. Well – I am one of those academics who started their own. And let me say a peer-reviewed journal does not run itself. At best you’d get a few pubs out per year with only volunteers. And the quality would be shite.

For starters – authors demand peer review to be timely. Counter to that, the reviewers don’t want to be rushed and get angry. Without anyone chasing reviewers, the world would never see reviews hit the light of day. That’s fine then, the world doesn’t need millions of papers, just the ones people want to actually review without chasing. The problem with that is the literature is full of papers now highly cited that were rejected many times. So who is going to chase the reviewers for a million manuscripts? Volunteers? Nope. You have paid staff. So how do you pay the staff? Either through grants, subscriptions, or open access fees. So now the journal you started in protest of commercial publishers is in the same boat.

“But certainly you could do it cheaper!” you say. Cheaper than $99 for lifetime publishing like PeerJ? Don’t forget long-term archiving storage, a stupid typeset PDF, because that’s what readers demand, etcetera, etcetera.

“Well, screw it,” they say. “We’ll do preprints and have ‘overlay’ journals for post-pub peer review.” Except preprints aren’t free either. Arxiv costs more than $1 million a year to operate as a non-profit. And again, who is going to chase the reviewers for the preprint post-pub reviews? Volunteers? Volunteers for over 1 million preprints?

So again, when I see people complain about high cost of publishing, I have to laugh. More like cry. We have the solutions already, but little uptake. Who is to blame then? When I read tweets from academics that they won’t bother reading low Impact Factor journals, who is to blame? (By the way, how unscientific is skipping a literature review just because the journal has a lower Impact Factor, for fuck’s sake?)

The world doesn’t want nice things. We built a quid pro quo system of cheap open access with PeerJ. We asked $99 lifetime members, if invited, to do a peer review to support the community. People complained about the quid pro quo. The world could still have cheap publishing – if it is willing.

Elsevier and others are more than happy to keep taking the blame for the system. It’s a misdirection. As long as scientists don’t start protesting tenure and hiring committees, then Elsevier’s profit margins are safe. Every time there is a new Elsevier boycott, it lasts a week, and then everyone forgets. They know this. And they’re just cogs in the system like everyone else.

Update: Shortly after I published this, this appeared in my Twitter timeline, which is in line with many of Jason’s points. Butch Brodie promoted Evolution Letters by saying it was open access, had low publication costs for Society for the Study of Evolution members, and those costs go back to society initiatives.

The article processing fees for Evolution Letters is $1,800 if you’re a member of the Society for the Study of Evolution. If you’re not, it’ll cost you $2,500. And you know that not all of that fee will go directly back to the society. Some of it is going to the publisher.

PeerJ is also open access and is cheaper: $1,095. You pay a 64% premium to have your article in a society journal.

I suggest publishing in PeerJ, donating a few hundred bucks to your scientific society directly, and leaving yourself a few bucks for dinner and a movie.

External links

How much does it cost to run a small scholarly publisher?
On pastrami and the business of PLOS
An efficient journal

Related posts

The cages we scientists make for ourselves

24 June 2017

Texas losing academic opportunities from its dicriminatory agenda

Yesterday, I learned that the Society for the Study of Evolution will not hold meetings in Texas for the foreseeable future. And they were in Austin just last year.

Yesterday, I learned that public employees of California cannot come to Texas using state funds. This includes professors from the University of California system and the California State University system, such as Janet Stemwedel, who visited our campus back when it was UTPA.

The reason is that Texas is one of several states that has been actively pushing legislation that allows for discrimination against LGBTQI individuals (e.g., with so called “bathroom bills”) and against certain religious views.

I doubt that these will be the last academic and scientific organizations that will be taking public stands against Texas and other states with this agenda. I’m deeply disappointed that these actions should be necessary, but they are. These are the right decisions on the part of those organizations. Sadly, I doubt legislators will pay attention. But one can hope.

19 June 2017

Beware simple narratives in academic publishing

NeuroLogica blog has an article examining the loss of Jeffrey Beall’s list of dubious publishers. This post presents a nice, clean narrative: a good guys versus bad guys story. Jeffrey Beall is the good guy and predatory publishers are the bad guys. You can practically here the movie trailer voiceover. “In a world where lawless predatory journals abound, one librarian has the courage to name and shame them. Fighting strongarm tactics from the publishers and spineless university administration, he fights to save the world from ever more dodgy science.”

But the reality is more complicated, I’ll argue.

The NeuroLogica post says:

Traditional journals earn their money from subscriptions and advertising.

This suggests that libraries – the main customers for traditional commercial publishers – are going in and making journal subscription decisions on a case by case basis (like you would with magazine subscriptions). But many libraries don’t have that option. Instead, most libraries get journals through “big deals” from publishers, where large numbers of journals bundled together in a single indivisible package. These “big deals” don’t have a standard price (plotted graphically here) and librarians are bound by confidentiality agreements not to discuss them.

Subscription publishers have incentives to create more journals to justify increasing the price tag on their “big deals.” It’s not clear that incentives to create more journals has substantially different results than incentives to accept more papers.

Many journals do not run ads at all. Some do, but don’t run many.

And, as one commenter noted, this description overlooks page charges entirely.

NeuroLogica continues:

In 2013 Science magazine published the results of a sting in which a fake and terrible paper was submitted to over 300 open access journals. Sixty percent of the journals published the bogus paper, which should not have made it past even the flimsiest peer-review.

The implication here is that zero percent of subscription journals would have accepted the fake paper. But we don’t know, because no subscription journals were sent the fake paper. But some of the journals that accepted the fake paper were listed in Web of Science, which is supposed to be a vetted database of “best of the best” scientific journals. This suggests more subscription journals might have fallen for this fake paper than we would like to think.

The game of “How did this get published?” is one that scientists played long before the phrase “open access” was coined.

Predatory journal contribute to a blurring of the lines between science and pseudoscience, essentially flooding the world with low quality and bogus studies and promoting the borderline academics who produce them.

One of the biggest academic publishers in the world, Elsevier, publishes a subscription journal called Homeopathy. It doesn’t get much more pseudoscientific than that.

Beall was providing an invaluable service by pointing out practices among some journals that violated the spirit and the process of quality control in science.

Granted, but we should not overlook that “Beall’s list” was written and maintained by one person. His decisions were based on criteria that were not objective or transparent. For example, Beall once included then new publisher Hindawi on his list of predatory publishers, then later removed it for no readily apparent reasons.

This seems like an opportune moment to note that there is a new service from a Texas company called Cabell’s that will attempt to provide both a journal blacklist and a journal whitelist. This is an established company (founded 1978), but their lists are new. I think this is a very interesting development worth watching.

External links

Open Access Predatory Journals

Cabell’s: ‘Our journal Blacklist differs from Jeffrey Beall’s’

Related posts
Open access of vanity press, the Science “sting” edition
How much harm is done by predatory journals? 
Time for a new list of junk journals

12 June 2017

First in the family

I was the first in my family to go to university. My mom finished high school. My dad didn’t get that far. (People attended university less often then.)

What strikes me now is that I don’t know how that affected me.

In my institution, much is made that most of our students are “first generation” students. There’s a lot of talk about how hard it can be for them to transition to university, how they don’t know how to navigate university systems, and that we should try to provide more support mechanisms for them.

I don’t know if that was even a conversation faculty at my undergraduate university were having at the time. In any case, I never felt like I needed any of that.

Maybe it was because I was graduating high school from a small town with no university that I had no idea which adults had university degrees and which didn’t. It seemed to me that the cohort of students from my high school were all just in the same boat. I never felt like people from families with university experience had any sort of “inside information” coming from their parents.

Maybe it was because I was a white middle class guy. I wasn’t faced with some of the socio-economic hurdles that are often associated with “first generation” students in some places. Particularly here.

Maybe it was because I was academically inclined, and a nerd, and universities were just a good fit for me that I didn’t feel the culture shock that others felt. After all, I liked universities so much that I’ve basically spent my entire adult life in them.

But I think this is something I need to mention to my students more often. It might help some of them see that university degrees are not inherited feudal titles. And maybe it can help my “first in family” students see the possibilities for themselves. “You can’t be it if you can’t see it,” as the saying goes.

Just because you are the first to travel a pathway in your family doesn’t mean you’re the first ever.

Hat tip to TatooedDevil on Twitter for the hashtag, #FollowFirstGenerationAcademics.

10 June 2017

A blog quinceaƱera

I’ve been very excited by the way this graph has been coming along:

You don’t get many graphs like that in my business where the difference between the groups is so clear!

I get one, maybe two, points on that graph most weekdays, so that’s a few months of steady work there.

I’ve been so distracted by the awesome data above that I neglected to mention that this blog clocked past the 15 year mark. Fifteen years is one of those anniversary years that feels... almost not worth celebrating. But I was reminded because I was tweeting about what I do as part of the #NDTMeetScienceTwitter hashtag, and I mentioned the blog’s age.

It’s now been so long that sometimes even I forget how long this project has been running. I recently re-read a forthcoming piece I wrote about blogging, where I said I started this blog in 2003, not 2002. Whoops. That’s going to drive me crazy if I see that in print now.

While much of science online has moved to other media platforms (and to some degree, I have followed that trend), the longer I have done this, the more the value of this blog has risen for me. “Tweetstorms” and Twitter threads are okay, but I still like sentences and paragraphs for some things. Blog posts are easier for me to find. I refer back to old posts constantly for one reason or another. Lots of topics are practically evergreen in science and academia, so a blog post can have a very long tail.

01 June 2017

New snail species is hard to find, in more ways than one

Last year, I tweeted:

One of today's highlights: helping a colleague photograph the holotype of an undescribed species!

I’m pleased that this species description is now out. The species in question was a little snail, now named Praticolella salina! The discovery is highlighted on the university’s home page! But the university’s article doesn’t tell you where to find the paper. Putting the name into Google Scholar didn’t help either. I finally found it because someone posted a shot of the article on Instagram:

Once I knew the journal, I went looking for its home page. I found it is still a print-only affair, with PDFs of the journal lagging three years behind the publication date.

Just remember that the next time anyone says of scientific publishing, “Everything is all online now.” No. No it is not.

External links

UTRGV professor and student researchers discover, name new species of South Texas snail
The Nautilus (journal)

29 May 2017

Ireland vs. the pet trade

My newest paper is part of my own Pirates of the Caribbean franchise. It’s the fifth in a series, “pet crayfish on the internet.” 

The first (Faulkes 2010) used surveys; the second, Google alerts (Faulkes 2013); the third, online auctions, and (Faulkes 2015a); the fourth (Faulkes 2015b), classified ads. The fourth one was short, but I pushed it out because I thought documenting the illegal sale of marbled crayfish in Ireland would be useful for policy makers.

But there was an obvious question: if I blundered across ads for illegal crayfish in Ireland without looking, how many illegal crayfish would I find if I went looking?

While doing this paper, I was reminded was how useful it is to start writing the paper as soon as possible. This paper has a year of data from the Republic of Ireland, but only about half a year of data from the UK. Thats because I started writing the manuscript halfway through the year. I thought, “Hey, I’ve got half the data, I know what this paper is going to look like in broad strokes, so I can start putting this together.”

As soon as I started writing, I started thinking, “Uh oh.” I realized that there were gaps in what I was collecting (sigh), but that I might still have time to address (whew!). Writing forced me to articulate what I was doing, and I started imagining what the reviewers might say if I didn’t have certain things.

An advantage of having a scientific franchise is that some things get easier. I learned that it was useful to have a project run one calendar year. It’s a time frame that people get, and is manageable. You have a clearly defined end date, so you know how far along you are at all times. Data collection finished 1 January, 2016. Because I had done quite a bit of the leg work up front, I was able to finish writing and submit the paper less than two weeks later.

Where to submit the paper was tricky. Some articles have obvious homes, but there wasn’t for this one. There is no Journal of Pet Trade Studies. I looked at a lot of journals before settling on Biology and Environment. I had never published there before, but I couldn’t get a better fit than a regional Irish journal with a broad editorial mandate.

There was a cost to that good fit, though. The journal had no open access options. I’ve been trying to publish my papers open access when possible, and this is one of the first papers in a while (besides book contributions) that isn’t. In this case, I thought the fit was so good, this journal was the best chance for my paper to find its target audience, and that was worth the sacrifice.

Once the paper was submitted, I waited. I sent an email after two months, asking if I could post a pre-print while waiting for a decision. I was politely asked not to, so I didn’t. I waited some more. And waited. After six months, I sent an email making sure nobody had forgotten my manuscript. (Because that’s happened to me before.) I was assured it hadn’t been. I waited some more.

I checked in again around the nine month mark to make sure the manuscript was still a live concern for the journal. The editors really wanted a particular person to review this paper, and was just waiting on the one review to come in. So, yes, this is one of those frustrating cases where the editorial decision making was slowed by reviewers not promptly returning reviews. I was a bit miffed, since the paper was neither long nor complex, and I didn’t think it needed the many months it took to review. But I was pleased that I had learned to be more persistent in checking with the journal.

That said, once the reviews were back, I was pleased with the rest of the journal’s service. The typesetting and copy editing process was thorough and responsive, and it felt like they genuinely wanted to get everything right.

It’s funny to think that when I started my academic career as an undergraduate, I didn’t have an email address. The Internet existed, but practically nobody knew about it. The web was about a decade away. And now, I can publish papers about Ireland from my desk in Texas just by watching what people do the Internet.

Like any good franchise, I am already working on the sequel.

Update, 1 June 2017: I received a hard copy of the journal in the post today (cover above). It’s been a while since that happened! And I must say, the production is top notch. The colour pictures look bright and beautiful. The paper feels good in your hands. And there is an editor’s introduction to each article. The one to mine reads, in part:

Ain’t no barricade high (or wide) enough

Enforcing any restriction on the movement of goods or organisms is beset by problems even when physical barriers are used. We have been lucky in Ireland that the movement of many unwanted organisms has been prevented because we are separated from both the UK and continental Europe by natural water barriers. Whilst natural barriers are important these can still be circumvented often through trade-related, human assisted transportation. ...

Perhaps there is a message here–that the implementation of any barrier to the movement of an unwanted species is always likely to be too later–and that such a move has to be combined with an appropriate follow-up management plan?

This relates to a point I made on Twitter last week. It’s not fair to compare the delay in posting a pre-print to the delay in publication in a journal, as Leslie Vosshall did.

I say that knowing that I myself have complained about editors have never helped papers become more readable. But I think that was a little unfair. For one, I’m a native English speaker, and though I say it myself, a pretty good writer. My writing probably doesn’t need dramatic revision to be readable.

Since I wrote that blog post, I’ve worked with more journals. Several of them actively made my paper better after acceptance. Like this one, the improvement came in the copy editing and proofing stages. Lots of little details got detected and corrected before the final version was produced that would appear in the journal, and be the version of public record. I greatly appreciated that intense, detailed, checking of the text. That care showed up in the production of figures and tables, too.

Sometimes, it seems that some scientists are so confident of their abilities that they think their uncorrected, unreviewed manuscript cannot possibly be improved. Reviewing and editing are just unnecessary delays in getting their brilliant science out to the world .

I think that such manuscripts are extraordinarily rare.

Related posts

Can civil servants defuse a bomb? An Irish crayfish problem
Academic publishers need better defenders
The editor’s influence


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. 2015a. Marmorkrebs (Procambarus fallax f. virginalis) are the most popular crayfish in the North American pet trade. Knowledge and Management of Aquatic Ecosystems 416: 20. http://dx.doi.org/10.1051/kmae/2015016

Faulkes Z. 2015b. A bomb set to drop: parthenogenetic Marmorkrebs for sale in Ireland, a European location without non-indigenous crayfish. Management of Biological Invasions 6(1): 111-114. http://dx.doi.org/10.3391/mbi.2015.6.1.09

Faulkes Z. 2017. Slipping past the barricades: the illegal trade of pet crayfish in Ireland. Biology and Environment: Proceedings of the Royal Irish Academy 117(1): 15-23. http://dx.doi.org/10.3318/BIOE.2017.02 

25 May 2017

Incoming: ReSearch: A Career Guide for Scientists

I just signed an author’s agreement for ReSearch: A Career Guide for Scientists. It’s been a while since I’d thought about this project.

I didn’t write it, or even a chapter. Back in 2015, one of the co-authors, Nathan Vanderford, cold emailed me asking if I would be willing to write something about “personal branding.” I said, “Sure!” So I wrote a little sidebar as a case study.

The book is slated for release next month. I’m curious to see how my little contribution is woven into the text.

External links

Publisher’s website
Amazon page