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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

I thought, “Let’s try something new.”

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Related posts

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

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

External links

Why or why not cite blog posts in scientific papers?

Circadian Rhythm of Aggression in Crayfish

References

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

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

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

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

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

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

Photographs by David Paul.

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

Zen Faulkes
Department of Zoology, University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia

Current address: Department of Biology, The University of Texas-Pan American, 1201 W. University Drive, Edinburg, Texas, 78539, U.S.A. Email: zfaulkes@utpa.edu

Ibacus peronii (left) and Ibacus alticrenatus (right). Photographs by David Paul.

Abstract. To test whether palinurans share a common ground plan of distal leg motor neurons with other decapod crustaceans, I examined the distal leg motor neurons in the scyllarid species Ibacus peronii and Ibacus alticrenatus. By backfilling the distal leg nerves individually, a total of about sixteen cells fill are seen, distributed in three clusters in the ganglia: an anterior cluster of about twelve, a posterior cluster of three, and a single medial cell. Although one medial cell fills when distal leg nerves are filled separately, two cells that are similar to two medial inhibitory cells in non-palinurans are visible in more proximal fills. The neural map is similar to those described for other species, suggesting that the distal leg motor neuron grand plan is conserved across reptantian decapod taxa.

Key words: decapod crustaceans, evolution, neuroanatomy, pereopods, walking legs

Tuesday Crustie: Baby pictures

If you look at someone’s baby pictures, you might have a hard time matching them to photos of that person as an adult. Recognize this person?

Or this one?

And you have it easy with humans. Humans don’t undergo metamorphosis or anything. Unlike this wee beastie:

This crustacean baby was described from the stomach of a dolphin way back in 1828. Just for perspective, Charles Darwin was still in university at the time, and his voyage on the H.M.S. Beagle was still a few years in the future. Because this species had these big horns and elaborately armoured exoskeleton, it was named Cerataspis monstrosa. You can probably recognize the second half of its name means “monster.”

At the time, it wasn’t clear that this was a larva, which obviously hindered a more definitive identification. But there was a bigger problem: it was just rare. So even as new genetic techniques were developed, Cerataspis monstrosa was not found in usable condition. Bracken-Grissom and colleagues, in a forthcoming paper, seem to have had just one Cerataspis monstrosa from to take DNA from. They used that DNA try figure out if it was a larval form of a better known crustacean.

The DNA work was tricky. They tried several times to use a sequence of DNA often used for barcoding, and failed repeatedly. Fortunately, other regions of the genome worked.

Thanks to Bracken-Grissom and colleagues, we now know that that turns into this:

This is Plesiopenaeus armatus, which is a very deep water living shrimp. Bracken-Grissom and colleagues give records of it living in waters of more than 1,000 m deep.

So what of Cerataspis monstrosa? Bracken-Grissom and colleagues recommend that the larva be given the adult name – Plesiopenaeus armatus. This is not a done deal, however. The larvae got their name first, and that would mean that it would normally take precedent. The authors note that they are applying for an exception to the rule on the grounds that the adult for the genus is much more often used, so renaming the genus from Plesiopenaeus to Cerataspis would cause unnecessary confusion.

Oh, and as for the human baby pictures above? They are, in order:

Harrison Ford, and...

Tobey Maguire.

Reference

Bracken-Grissom HD, Felder DL, Vollmer NL, Martin JW, Crandall KA. 2012. Phylogenetics links monster larva to deep-sea shrimp. Ecology and Evolution: in press. DOI: 10.1002/ece3.347

Larval photo from here; adult picture from here.

Harrison Ford pictures from here.

Save Siccar Point

This is Siccar Point. This is where we first learned that the Earth is ancient. Not just old, not just thousands of years, but so old that it seemed almost to have been around forever. It is arguably the birthplace of modern geology. The concept of an ancient Earth was important to Darwin’s thinking about evolution, too.

Now, there is a proposal that could damage this incredibly important location by digging a trench across is and filling them with concrete. Learn more here, including ways you can lodge objections.

Here’s the email I sent:

I'm an biologist and educator. I tell my students about the importance of Siccar Point in the development of science, and how geologists used Siccar Point to demonstrate the great age of the earth. That Siccar Point taught us something so fundamental about the history of the planet makes it a scientific landmark. As such, it should be preserved as best as possible.

Consequently, I object to the plan put forward by Drysdales Limited, because I am concerned about the potential damage done to this historic geological formation.

I think Siccar Point should be something like a World Heritage Site.

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

How students see scientific publishing, part 2

It’s fascinating to see how outsiders think a process works compared to how it actually works.

Like last year, I asked my biological writing students, “What happens to a manuscript between the author finishing writing and it being final form that an audience can read?” I asked them to make a little flowchart. This year, there seemed to be greater understanding that there was some sort of review, though only about half specifically mentioned peer review.

Like last year, students were uncertain about who was doing the reviewing. Some people said publisher, some said editor, and some said reviewers.

One of the more interesting points in discussion, though, was when I asked them, “Who makes the decision about whether a paper goes into a journal or not?”

The students were unanimous in their opinion: the publisher decided if an article was accepted for a scientific journal. They thought the role of the editor was to check for grammatical errors, consistency, and things like proper comma usage. And students considered the reviewers to be more like fact-checkers, rather than people evaluating things like the significance of the work, experimental design, and other bigger picture stuff.

I tried to explain that in scientific publishing, a “publisher” usually refers to a large entity, like a large multi-national for profit corporation or a non-profit organization. Individuals are rarely publishers, and publishers don’t have much say in day-to-day decisions. I don’t interact with publishers directly when I submit a manuscript; I’m getting emails from editors.

The names of the titles are no doubt contributing to the confusion here. It’s so logical to think that a decision to publish would be made by a publisher. Students hear us talking about editing manuscripts, and think that the language crafting is all the job entails.

I wonder at what point a student working in the sciences figures out how the publishing system works. At the undergrad stage? Early graduate career? Late career? Whenever that first manuscript goes out?

When did you figure out how a manuscript turns into a paper? And did you get someone explicitly telling you, or did you figure it out by example?

Related posts

How students see scientific publishing

Comments for second half of August, 2012

A post on Impact Factors at Reciprocal Science has a big ol’ comment thread, and I’m part of it!

How academics can create an online presence. Was surprised that someone’s first recommendation was... LinkedIn? Haven’t met anyone who’s gotten much out of that (and I say that as someone with a profile.)

The Tracing Knowledge blog talks about evidence of insect photosynthesis.

Life After Thesis wonders why more academics aren’t online in a significant way.

Hot button topics in science are tricky issues, as Unofficial Prognosis discusses.

Mike the Mad Biologist asks who we need to persuade to make changes to scientific publishing. (Hint: Follow the money.)

Neuropolarbear ponders whether to discuss the old science or the new science in his presentations.

Pondering Blather looks at the ever decreasing security afforded by tenure.

Neuroskeptic says that replicating experiments is not the critical thing to worry about in making a science credible.

Steve Caplan at No Comment tries to defend the idea that journal names are a good proxy for the quality of individual papers within, on average. I remain unconvinced.

Scott Berkun be hatin’ Prezi. I zoomin’.

This semester’s good news

Yeah, all I got is a meme. Sad. Hoping this fatigue will be gone and blogging will be back in force next week.

Tuesday Crustie: Red trim

This looks like something in the Australian genus Euastacus, but I don’t recognize the species. Maybe E. suttoni?

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

Insecure enough to lie, but too secure to fire?

A common claim by science deniers is that scientists lie to keep their jobs. There’s a premise in that claim: that scientists are working in conditions where they can be easily dismissed. But a lot of scientists are tenured academics, which is supposed to remove the fear of arbitrary dismissals.

I wonder what the overlap is with people who would claim that the tenure system makes it far too hard for a scientist to get fired. I bet the overlap is large, and that they don’t see any contradiction between holding those two positions simultaneously.

Famous for space, but down to earth

The news just broke that Neil Armstrong has died.

Earlier this year, a series of interviews with Armstrong appeared here, which I watched with great interest. I was alive when we walked on the moon, but I was too young to remember it. But I was fascinated by space travel as a kid. And after the moon walk, Armstrong had been famous for not being famous: he stayed out of the public eye when everyone knew his name.

The interviews made today’s new more of a shock. He looked so healthy in the interview. At one point in Part 3, the reviewer jokes, “There must be something in lunar travel that’s good for longevity.” Armstrong laughs and says, “I hope that’s true.”

I am so glad he did those interviews. For someone who was famous for being the first person to step on the moon, he came across in those interviews as being completely down to earth.

We probably could not have hoped for a better representative of humanity to make our first step on another celestial body.

Putting classes in drydock

Occasionally, ships are put into drydock. There are certain repairs and upgrades you just can’t do when the ship is in continuous operation. One of the biggest taks is just scraping accumulated crud off the hull. All the barnacles, tunicates, and other encrusting and enfouling critters.

My classes start Monday, and I’m way behind in preparing for them. One of the reasons is that we’re switching over to a new version of our online course management system (moving from Blackboard Vista to Blackboard Learn). There isn’t an easy way to import material from the old Blackboard into the new Blackboard, so I am going to have to do a lot of work re-entering the online component of the class again.

Sigh.

I’ve taught most of my classes several times now. While I try to change them and improve them every year (“constant improvement in the samurai way”), these tend to be little, incremental changes. I have rarely made deeper, structural changes and substantially revamped a class. I haven’t done things like remake the slides from scratch, or rethink the assignments I was asking them to do, and maybe chuck some out.

I can see where the stereotype of the professor getting up and pulling out the yellowing, aging lecture notes from twenty years ago comes from. The temptation to keep recycling a class and reusing material and giving the same assignments is strong. And I don’t want to be that guy.

While I was annoyed about the switch in course management systems at first, I realized that maybe this was an opportunity to refurbish the course. Put the class in drydock and scrape off all the accumulated crud, and start over.

How often do you put you class in drydock?

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

Let’s stop enabling bad speakers

Matthew Francis saw a bad scientific talk.

Nearly every sentence was unintelligible. ... (T)he speaker compounded the problems listed above by mumbling everything, and not speaking into the microphone so what was mumbled often didn’t even come through the public address system. Since the person’s slides were badly designed (thin gray lines on the plots, tiny fonts), the audience couldn’t get the information from either the audio or the visual. In fact, the crowd of physicists, specialists in the speaker’s own field, were not paying attention to the talk.

Matthew only refers to this individual as “the speaker.” Matthew says he doesn’t want to name this individual, because he is writing about the general issue, and not the specific talk. Fair enough. But we should start creating more of an expectation that scientific talks will be reviewed and critiqued. And names will be named.

If someone wrote a scientific paper that was as bad as this talk apparently was, nobody would have a second thought about writing a response to it, laying out the problems, and naming the authors. Yet it seems to be considered rude to criticize people by name when someone gives an incomprehensible presentation.

When was the last time you went to a speaker after their talk and said, “I don’t think your presentation was very effective”? Have you ever had anyone (besides a supervisor or lab members) give you critical feedback on how to improve your presentation?

The only example I can think of offhand was the National Academy of Science Sackler science symposium on science communication earlier this year. Because it was streamed live online, people on Twitter were able to comment about the deficiencies of some of the talks. And one person was able to get up and convey that frustration to the speakers.

I’m not saying, “Let’s have trial by backchannel for presentations.” This does not need to be immediate and destructive, but could be done with reflection and in a constructive tone. This is what good peer reviewer do for papers.

For that matter, we should be taking more steps to ensure that it never gets that bad in the first place. We have peer review before a paper is published. Maybe we should start having some sort of peer review before presentations, to make sure that slides are at least going to be legible. While this would not be possible for every talk at a conference, it might be possible for at least featured keynote talks to get a once over before the day they’re given.

I recently co-organized a symposium, and I was thinking about emailing my speakers and asking them to email me their PowerPoint deck so I could review it. I didn’t, not because I was scared, but just because I ran out of time. I’m kicking myself now, because I think I missed an opportunity.

We need to be more forthcoming with our colleagues when their presentation isn’t up to snuff.

Related posts

Science communicators need to lead by example

External links

#186) Science Talks: Wanna make ‘em better? Start having critics write REVIEWS (like the theater). I dare ya.

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

Good thing I’m not in a hurry

I submitted a manuscript yesterday, which made me happy. But as I was updating my CV, I looked at my other manuscripts in review, and my happiness was slightly undone.

I have one manuscript that I submitted almost exactly one year ago. I have had an initial positive review, but and still awaiting final acceptance.

I have one manuscript that is is two months in with not initial decision. Not too nervous yet (summer holidays can mean a slowdown in review time). But I’d be happy to read the first reviews any time now... any time at all. Any second. Now.

Then there is my most recent paper, which has been out almost two months. But it’s still up as a provisional PDF and not the final typeset version. I was wondering when I might see the final version, and was disappointed to read this analysis that found only 20% of papers or less were typeset in three months after their initial availability as an online pre-print.

I am not in a field that typically needs to move very fast, but there is room for improvement here.

Tuesday Crustie: You got your chocolate in my crustacean

Spotted on Facebook, via Reese’s.

The responsibilities of an academic are teaching, research and service fundraising

Two anecdotes.

First, last Friday, I was at a meeting of coordinators for our university’s graduate programs. Our vice-president for academic affairs was talking about the university’s plans to expand their graduate offerings. Why do we want more graduate programs, particularly doctoral programs?

He said, roughly, “We’ve managed to get some funding from agencies like NIH and the NSF. But there’s a lot of programs that we don’t qualify for because we don’t have doctoral programs.” (That’s not a direct quote, but I remember him specifically mentioning those two agencies.)

Second, a few weeks ago, I was in discussion with someone who was in charge of a a fairly new Ph.D. program in biology (not medical biology). He said that they were going to conduct searches for four new faculty members... whose main responsibility would be to write successful grant proposals to support their doctoral students.

It’s been rare to see such naked admissions that institutions see graduate students and faculty as cash cows.

At the program level, this could well be one reason why we have an over-supply of Ph.D.s in the job market now.

The latter might bother me even more. To hear that indicates to me that those poor souls are going to be evaluated for tenure just on whether they can raise money. That is not supposed to be what academia is about. Students, if you wonder why your professor is an incoherent teacher... this may be why. In a situation like that, why would you invest any time more than the bare minimum needed?

If you’re an advanced graduate student or post-doc, you might not want to fret about landing that glamour mag publication as much as you should be writing grant proposals at every opportunity. Federal agencies, state agencies, scientific societies.

Additional: I like this translation of academic speak by Dr. 24 Hours:

“Establish an Independant Research Program” = Get Grant Money or You're Fired.

Related posts

The root of problems: How external funding distorts institution’s priorities

Unsolved mysteries

I have a guest post over the blog for Things We Don’t Know. The post is about what this...

...tells us about one of the biggest questions in biology: how many species are there?

Read the guest post here.

Does a Ph.D. train you to head a lab?

I was stopped by this quote in Soapbox Science:

I feel people should be aware that, while a PhD program almost perfectly serves the purpose of training you to become a primary investigator, not everybody will be able to become one in the current job market (pretty obvious, right!).

I am not sure how well Ph.D. programs train people to be head scientists running labs.

I felt a doctorate trained me well to be a post-doc. But when I started my current gig, I had a lot of moments where I fell I hadn’t been warned what I was in for.

The first thing that happened was I botched my negotiation. Being god’s fool, I somehow managed to avoid disaster, but I could have been very badly burned if there hadn’t been some honourable people around.

I’d been a teaching assistant as a graduate student, so I wasn’t completely lost there. But there is a big difference between being a teaching assistant and running your own class from stem to stern.

But running my own lab has been... a mixed bag. It took longer for me to get my footing than I expected, and to have projects in the wings ready for students to pick them up. Judging by my success rate, I still have a lot to learn about “grantsmanship.” And I still don’t feel my management / supervisory style is all that it could be.

The big one, though, is bookkeeping and budgeting. I didn’t have to worry about tracking money in any significant way as a grad student or post-doc. Spending money at an institution is not like spending your own money. You have layers of people and paperwork that stand between you and purchases. You have obscure “enterprise finance” systems that seem designed to drive a person to substance abuse. I’ve learned that I despise trying to keep track of grant money.

I’m lucky, because of the kind of institution I’m in and the kind of lab I run, that I don’t do as much of this as if I was at a big research institution. To listen to people in those situations, grant writing and grant management is all they do. If I had landed that kind of job, I would have been woefully unprepared.

Additional, 21 August 2011: This article in Science Careers about early career NIH awards echoes the sentiments above:

But she doesn’t usually need advice for the science aspects, Olsen says; it’s laboratory management and interpersonal relationships. “I definitely feel overwhelmed at some junctures, trying to figure out the bureaucracy and managing other people in the lab, that kind of thing.”

In praise of Viking

1976.

I didn’t even have to look that up.

That was the year that the first machine made by human beings landed on the surface of Mars. Its name was Viking.

And it sent back colour photos.

I bring this up because with all the hoopla about the successful landing of Curiosity, people seem to have forgotten about the Viking missions. People have mentioned Spirit and Opportunity and talked about them as though they were the first things on Mars, rather than science being done on the Martian surface for over 35 years.

I’ve heard people say Curiosity is the first time we’ve had colour pictures from Mars, which boggles me, because I remember those images from Viking making the news when they were released. There were big gatefold pictures in National Geographic. (Pace was slower then; the pictures were in the January 1977 issue, about six months after the landing.)

Viking may not have had the dramatic landing of Curiosity. We couldn’t follow the news as closely as we can today. But it was Viking that blazed the trail. Let’s give it it due.

Photo from here.

Self archiving science is not the solution

I can’t watch “The Power of the Daleks.”

The British Broadcasting Corporation (BBC), feeling that television was a disposable, ephemeral medium, junked many tapes of television series like Doctor Who. They even junked notable ones like the first episode of Patrick Troughton’s second Doctor facing the best known and most popular villains of the entire series.

Archiving is a tricky thing.

The card game Legend of the Five Rings is about 15 years old. But it’s almost impossible to find material about the game’s influential first couple of years. A lot of key discussion happened on a company email listerv. The one copy someone from the company was keeping was lost when a hard drive crashed.

I went looking for a podcast of a story I’d heard on Quirks and Quarks about singing mice. I wanted to listen to the audio again. But their online archive goes back to 2006, and the story I remembered was from November 2005.

You might think. “Well, that’s just pop culture,” but the same issue plague science. Physicist Slava Turyshev, who is working on the Pioneer spacecraft, noted:

To study the Pioneer anomaly we needed the probe’s navigational data. But mission tapes were normally saved for only a few months and then thrown away, so you’re lucky if you can find what you need.

Today, some experiments generate so much data that chucking the data away is a necessary part of the process because we just can’t keep it all. This happens at the Large Hadron Collider, for instance.

Just as I posted this, I learned a personal subscription to Nature only gets you papers back to 1997.

I mention these because one of the ideas to reform the scientific publishing enterprise is one where journals are removed from the picture entirely. Scientific communication should be replaced by blogs and self archiving, according to some. This is not a vision I can get behind, because I’ve hung around with taxonomists.

Taxonomists are often accused of being too conservative and hidebound in publishing. The botantists required species descriptions paper and Latin species descriptions until very recently. But I have to say, as a group, they made me more aware of the importance of archiving than any other. Taxonomists are often routinely revisiting literature that is centuries old. How am I going to make sure someone can read my papers in the twenty-fifth century?

Björn Brembs argues that libraries can effectively take the place of journals. That is certainly an improvement over self-archiving, though I think we have a long way to go on that front. At our institution, one enterprising librarian started an institutional repository for faculty, where we could deposit not only our reprints, but more ephemeral work like conference posters.

But she quit. And since then, I’m not even sure who, if anyone, is in charge of the repository. It’s been a while since I deposited anything there.

While I personally plan to live forever, in the remote chance that some accident occurs where I don’t, how can I make sure my scientific contributions are available to researchers one hundred years from now? Two hundred? Three? Sticking my own PDFs on my own university server is not going to cut it. I can’t control what happens to my papers after my death. Maintaining the scientific record needs to be done by communities and institutions, not individuals.

Hat tip: This grew in part out of a conversation that bubbled up over at Living in an Ivory Basement.

Comments for first half of August 2012

Living in an Ivory Basement (my favourite blog title a long time) talks about publishing in PLOS One.

Is there wiring in the brain?

Chess ratings and Impact Factor

The use and misuse of journal Impact Factors continues to attract attention. I think Impact Factor has some usefulness in showing a journal is a bona fide scientific enterprise.

In my non-scientist life, though, I’ve seen other situations where people are aggressively pursuing some stat or another to prove their worth. When I was involved in the card game Legend of the Five Rings, there was a point where people were repeatedly calling for the game to use the Elo system to determine who were the best players.

Elo is not an acronym, but refers to Arpad Elo, who devised a system for ranking chess players. Like Impact Factor, it has sway. Players take Elo rankings pretty seriously for games where it is used. Many card gamers knew it from Magic: the Gathering.

I like this quote from Arpad Elo (written as part of a Chess Life article in 1962), because it showed Elo understood the problems of uncertainty well.

Often people who are not familiar with the nature and limitations of statistical methods tend to expect too much of the rating system. Ratings provide merely a comparison of performances, no more and no less. The measurement of the performance of an individual is always made relative to the performance of his competitors and both the performance of the player and of his opponents are subject to much the same random fluctuations. The measurement of the rating of an individual might well be compared with the measurement of the position of a cork bobbing up and down on the surface of agitated water with a yard stick tied to a rope and which is swaying in the wind.

Emphasis in the original.

Interestingly, after Legend of the Five Rings did adopt the Elo rating system, it did not prove to be “the answer” that some players thought it would be.


Picture of Elo from here.

Tuesday Crustie: Shake a claw

The Neuroethology congress was held last week. The congress had a banquet on on a ship on Thursday night, and this statue was outside the dock:

The statue could signify one of the lessons of neuroethology: listen to what your animals have to say.

Photo by past president of Neuroethology, Paul Katz. Thanks Paul!

Food and trust of science

Back in grad school, we had a speaker who was given a general public lecture. He was talking about the prospects for personalized medicine. The idea is attractive. Not all medicines work on all people. Sequence a patient’s DNA, and you can find out what medicines are likely to be ineffective.

This is not a post about personalized medicine, though. It’s a post about a question that got asked at this public lecture.

He basically asked, “Scientists used to say that butter was bad for us, and we should eat margarine. Not they’re saying that margarine is bad and we should east butter.” (I do remember that there had been a story about health risks associated with margarine in the news around that time.)

“Why should we trust any of you?”

My recollection of the answer isn’t as clear as the question. But I seem to recall that that question was brushed off lightly, with a sort of “There’s nothing to worry about.”

I sympathized with that man in the audience, and have gained ever more sympathy as time has gone on. I was reminded of it by a couple of things this weekend reminded me of this man’s question. On Ockham’s Razor, this speaker claims research does not show that cholesterol causes heart disease:

I stopped cutting all the fat off my grass-fed steaks, started frying my eggs deep in butter and began to avoid any product with the word ‘lite’ on it. I’m not on a diet but I’m about 3 kgs lighter and last time I had my cholesterol checked it was 12% lower.

Now, the scientifically minded may say, “That’s just anecdote,” but the point is that you have people making these sorts of claims all the time.

The second was a post from Biochem Belle on popcorn flavouring and Alzheimer’s disease, which has apparently been in the news of late.

Oooh, and on his 1 August podcast from his weekly call-in show on Triple J, Doctor Karl said 32,000 cases of lung cancer are tied to sitting down, 12,000 cases of endometrial cancer, 1,800 of ovarian cancer, and 49,000 each of breast cancer and colon cancer are caused by sitting. That’s a lot of cancer.

While Dr. Karl did explains some of the logic of how sitting could be related to health, those numbers sound incredibly definite. And Karl said sitting “caused” the cancer, not “increased the risk.” For more on how people might get those numbers, try Ed Yong’s article, “What does it mean to say that something causes 16% of cancers?”.

And then watch for research appearing slightly before Valentine’s Day about chocolate. There will be some. And it will probably say there are some mild health benefits if it is eaten in moderation.

As a professional scientist, I have an insider’s view on many scientific stories. It’s hard for me to pull out and try to imagine how a lot of stories sound to someone who is barely aware of science.

Another example of this: One of my students yesterday was talking about how she was talking to someone who thought fruit fly research was obscure, and her reaction was, “Um. No. Drosophila is not obscure. It is studied intensively by thousands of people around the world.”

When I listen to the reporting about research on food, I am back to square one. I never know what to make of it. Research on food and health seems to be never ending, often contradictory, and difficult to interpret.

I get the same vibe whenever I try to read about the use of nuclear energy. I am just lost.

David Dobbs recently wrote that science writers need to do a better job of portraying uncertainty in science, and not promote those with pat answers.

But when I look at how research about food is presented, I can see why people are impatient and distrustful. I can totally understand why people gravitate to those apparent pat answers when faced with what seems to be a never ending march of contradictory information.

Tenth International Congress for Neuroethology, Day 5

After a fairly late night on the cruise, plus the usual last day attrition, made for a slightly subdued day for many attendees. But not for me.

The last plenary talk of the conference was Toshiya Matsushima, who was discussing decision making in chicks. He was one of those speakers who is very quiet, almost soft-spoken, but who has a way of pulling you into his world. And he still threw in the occasional joke, with a low-key, but still funny, delivery.

He briefly mentioned how grateful he was for the support of the Society following the tsunami and subsequent Fukishima disaster. Then, he described a series of experiments looking at how chicks decide how to feed. They can train chicks to peck for food, and do various manipulations where they reward less food immediately, or more food after a brief delay. He again invoked the Heiligenberg rule (“Use the champion animal”) to say that chicks were champion feeders. There is high mortality among chicks, and they have to put on weight very quickly in the first few days after hatching.

He also recorded from the chicks’ nucleus accumbens, and found that there were some neurons that responded to the amount of food that was expected (the learned response), the expected delay, and the actual reward. He compared these to three judges who had to decide on a single sentence (the behaviour).

Then, he described what happens when you do surgery on this region of the brain. There are a couple of different effects. For one, the chicks become impulsive. The chicks also become more persistent, and will continue pecking even when they get no reward for much longer than normal chicks.

He ended his talk comparing scientific research to, of all things, bonsai trees. But it was a lovely metaphor. A bonsai is not a forest, but a single miniature tree. You cannot create a bonsai quickly; it takes decades. it may even be passed from generation to generation. But through this human art, you catch a glimpse of nature.

I did not get a relaxing coffee break, as I was working to make sure the speakers for the nociception symposium were all good to go. (Neuroethologists use video than most, and video is still exceptionally picky in presentation software.) Such is the life of a symposium co-organizer.

Dan Tracey was, um, our representative for the “evil four.” He's been working on nociception in Drosophila for about ten years. Although the title of the symposium was “Nociceptors in the real world,” Tracey said he was really talking about pain. He noted that people can study responses to light in both humans and flies, and both get to call it vision. It’s not that only the human researchers get to study “vision”; the fly researchers do not have to say they study “photoreception.”

With the genetic tools at his disposal, he and his lab has been making excellent progress on what genes and neurons are responsible for nociception in flies. For instance, he has been able to put channel rhodopsin in flies, and cause the maggots to do their characteristic thrashing behaviour of nociception by shining light on them. “This was the coolest day ever, because it worked.”

But he never loses sight of the behaviour. There are a lot of great ecological research questions about the relation of the maggot’s nociceptors with parasitoid flies that attack them. Tracey showed the maggots can actually shake off the parasitoid attackers, prompting him to say, “When you see a fruit fly, I want you to think of Sigourney Weaver,” in reference to her famous Aliens roles.

Robyn Crook is workings with a favourite of this blog, cephalopods. She was able to record neurons that act very much like nociceptors, which nobody had ever done in cephs before (as discussed here a couple of years ago).

Her take on nociception was to relate it not to short term stimuli, but in the context of long term injuries. Squid, which she works with, are often found in the wild missing the tips of their tentacles, for instance. She was able to show that the squid do change their defensive behaviours when given these mild injuries. They tested these with sticks with hairs on the end. “Behaviour has complex equipment. Duct tape is very important,” she deadpanned.

Co-organizer Ewan St. John Smith talked about his work on naked mole rats, a good chunk of which was published in Nature last year. Naked mole rats have a small number of common mammalian sensory neurons called C-fibers. And it is just the naked animals, not other haired mole rats that have this reduction.

Not only that, they are insensitive to acids. Somewhat surprisingly, all the ion channels of acid detection were still in the mole rat neurons, but there was a sort of genetic “shunt” that prevented the neurons from generating action potentials when exposed to acid. All of these seems to be related to the mole rats living almost perpetually underground in high carbon dioxide laden dens.

The last speaker was Victoria Braithwaite, who was talking about fish nociception. (You can find my review of her book, Do Fish Feel Pain? here.) She summarized some of her work on the nociceptive sensory neurons from about 10 years ago. Her more recent research is geared to showing not just that fish have nociception, but that they use that information in a way that is suggestive of pain.

One of the big arguments that she has faced from critics is that fish cannot feel pain because they have no neocortex. She argues that the relevant brain structures for processing pain in humans are the amygdala and the hippocampus, and fish do have equivalent structures in their brains.

L to R: Ewan, Dan, Robyn, and Victoria

All our speakers had lots of questions at the end of the session, and we were all able to continue the discussion over lunch.

I was incredibly pleased. I thought the symposium achieved everything we had set out to do. The talks were a great mix, and none felt out of place at a neuroethology meeting.

I had to leave immediately after lunch, and could not stay for the last contributed talk session. I was particularly bummed to miss the talk by my co-organizer Ashley, who was one of the very last speakers for the entire conference.

I got to the airport in what I thought was plenty of time, but my self check-in failed. So I went to stand in a line-up. A line-up that lasted over an hour. When I finally got to the front, I learned that my flight had been delayed. Again. And my connecting flight in Dallas was the last one of the day. I was almost certainly stuck in the Dallas airport for the night.

Externally, I laughed. Because you have to, as they say. Internally? “Crap crap crap crap.” I got one tiny little ray of hope: Dallas flights were also being delayed, so I might make it. But I only gave theft about a 10% chance. And I dropped that to 5% when the flight missed its delayed departure time by about 45 minutes.

But I made an excellent start on this blog post.

I got into Dallas about 10:00 pm, and the last flight back to McAllen was long gone. And I was indeed stuck in the airport overnight, left to wonder what god of travel I had so annoyed that have m last three trips delayed so much that I arrive at my destination on the wrong day. Fortunately, a computer can now make longe delays much more tolerable than they used to be.

Tenth International Congress for Neuroethology, Day 4

Today was a half day at the meeting. The organizers deliberately scheduled half a day of free time so people could muck around the Washington, DC area if they wanted.

The first morning talk was by Elke Buschbeck. She and her team have been busy studying insect eyes. But these are probably not the "fly eyes" that you think of when you think of insects. These are structurally different and called stemmata. The cool discovery she made a few years ago was a diving beetle which has bifocal stemmata. Her students had presented this two years ago at the Ninth Congress in Salamanca (had just come out in Current Biology, I think), so I knew part of this story. But I was still very interested to see the videos of this beetle in action.

What I don’t remember hearing before was that these baby beetles have a optical burqa. All the light sensitive cells in their eyes line up in a single narrow strip. Imagine your could read only this line of text, and you were blind to everything above and below it. That’s the diving beetle’s visual world at this stage. Buschbeck showed great video of the beetles coming in towards pray, and they “bob their heads,” scanning up and down so they can see the whole image.

It's a very odd way to make an eye.

Of the three concurrent sympsosia later, I went to one on invertebrate movement, which is sort of my old home territory. Most of it was familiar to me, but this factoid caught a lot of people’s attention on Twitter.

Lots of people know octopuses are brainy invertebrates. All told, they probably have around half a billion neurons throughout their body.

About two thirds, 66%, of those neurons are in the legs.

Octopuses have very distributed nervous systems, and some of their behaviour doesn't need to be controlled by the brain at all. The presenter, Binyamen Hochner, said that computation can occurs anywhere. And he didn't just mean outside the brain; he is essentially arguing that the body itself can carry out some computations.

For my afternoon, I went to the mall and ended up in the U.S. Botanic Garden. Looking at plants was about the right speed for me. A good mental palate cleanser. Then, off to the evening banquet on a ship cruising the Potomac (pictured above).

One more day, and it will be the best so far! Because tomorrow there is a symposium on nociception that I helped to organize. This has been in the works since the Salamanca meeting two years ago, so I am pretty excited to see it about to come together.

Tenth International Congress for Neuroethology, Day 3

Learned today that this conference has 563 attendees from 28 countries.

Today proved yet again that Ron Hoy’s “core four” (or “evil four”) is the stickiest sound bite of this conference. (Walter Heiligenberg’s advice, “Use the champion animal” is a close second, though.) There was only one featured talk today, by Constance Scharff. Her talk, on bird song learning, was a pitch to have songbirds “join the club” to turn the “evil four” into the “evil five.”

Scharff describe songbirds as the “champion” vocal learners. Not many animals learn by imitation of other animals, and even fewer learn vocalizations. One of my favourite moments of today was Scharff playing a recording of a German folk song... sung by a bullfinch. Obviously, this is not a normal thing for a bullfinch to do, and it must have learned how to sing that particular song by listening to humans.

In humans, there has been a lot of interest in a gene called FoxP2, because it has been specifically linked to speech impairment in humans. Inevitably, some people suggested that mutations in this one gene are an important aspect of what gives humans our highly elaborate vocal system - language.

Wile I am loath to simplify a complex story, since I complained about just that in the last paragraph, there are some indications that FoxP2 is needed for normal song learning. Using RNA interference and a variety of other techniques, they were able to knock down FoxP2 expression in songbirds. Songbirds treated this way were not able to learn anywhere near as well as the untreated controls.

There were three concurrent sessions after this. I went to one on navigation, which featured research on birds (relating magnetic sense to polarized vision), fish, bats (both about navigating in 3-D space) and bees (how they “stick the landing”). If you check the #icn12 hash tag on Twitter, you’ll also find tweets on a session of nervous systems coping with lack of oxygen. If any reader was at the motor program symposium, I'd love to hear some comments!

The business meeting had several awards, news, and choices for the congress in 2016. Without a doubt, however, the emotional highlight was a retrospective of the late Bob Capranica, a pioneer of amphibian neuroethology and, in later years, big supporter and booster of the field. He created and administered a prize for young neuroethologists out of his own pocket. Recently, the Neuroethology society took over management of the prize, and it now bears Capranica's name. Bob Diego earlier in the year, but Pat Capranica was there to receive an award for the work that she and her husband Bob had done in promoting neuroethology. She received a standing ovation.

Tenth International Congress for Neuroethology, Day 2

Ack! Can't believe we're already past the 40% mark for this conference! Some highlights from today...

Opening the day was Ole Kiehn on tracking the spinal cord circuits for locomotion. Ron Hoy’s talk from yesterday clearly made an impression, as Kiehn referred to humans as “the fifth evil species.” Keihn's work also echoed Hoy's talk in that it showcased how people trained in traditional electrophysiology are increasingly using genetic techniques, like optogenetics.

And I got “Bingo!” during Ole's talk when I saw someone a few rows ahead of me checking Facebook.

The second half of the morning was taken with the Young Investigators symposium, with four great talks, one of the highlights of the meeting so far.

Antoine Wystrach lit it up with a talk on ant navigation. I particularly enjoyed how he hinted that his lab bought something clandestine to generate... Vibrational stimuli.

Basil al Jundi had some more navigation with insects using celestial cues, with some particularly fun videos of dung beetles, which use light to roll their balls of dung in straight lines.

Michael Yartsev gave a talk that in other meetings, might be very controversial. He was showing a series of experiments in bats that showed that one of the major theories for how place cells work (developed using rats and involving theta rhythms) could NOT explain place cells in bats (no theta rhythms in bats). It was a strong demonstration of the limitations of using single model organisms and the power of comparative methods.

Lauren O’Connell had what was arguably the quote of the day, explaining monogamy: “Monogamy is tolerating your partner being around you.” Again, Lauren's work had a huge genetic component, showing how neuroethology in increasingly becoming neurogenetic ethology.

The afternoon plenary had Malcolm Burrows showing a wide array of videos of insects jumping. Insects that were good at it, bad at it, legs bending like archer's bows, insects jumping off water. But the highlight was perhaps when he went to pull out ap cicada that he had found that morning, a relative of the frog hopper he was talking about.

"Oh no, it's gone." It had escaped, and could be seeing flying around the lights near the ceiling. "If he gets hot, maybe he'll sing to you."

There were three symposia on the afternoon; I happened to go to one on mating signals. this was followed by another featured lecture by Ed Kravitz. Ed used to work with animals close to my heart, crustaceans, but in the last decade or so turned to work almost exclusively with one of “the evil four,” fruit flies, primarily because of the advantages of genetic tools. Afterwards, Ron Hoy got up and complemented it as one of the best examples of actual ethology cal work he’d seen using fruit flies. (Peer pressure, maybe?)

Now, as you may have gathered, there are a lot of plenary and special lectures at this meeting. I had some discussions about this over dinner. I am not sure it is all that good to have so few voices given the lectern. It must be nice for those who get it, I’m sure. But it certainly doesn’t help diversity when so much of the meeting is by established voices, many of whose have give featured lectures at this meeting before. Now that this meeting is every other year rather than every three years, this sameness may become a bigger issue than in the past.

I also had a short but very animated chat with Kathryn Knight, the news and views editor of The Journal of Experimental Biology and keeper of their Facebook page about scientific publishing. Key phrases: “collateral damage of push for open access,” the relative quality of PLOS One, American attitudes towards taxes, and how different kinds of biological researchers view their budget totals (especially regarding open access fees), and how much sense people other than scientists can make of the primary literature.

Would live to elaborate, but have to get up in not too many hours.

Tuesday Crustie: West Virginia’s rarest

If anyone ever asks you, “What is the rarest crayfish in the state of West Virginia?”

You can tell them, “Well that is difficult to say, but a good candidate would be the digger crayfish, Fallicambarus fodiens.”

You might win a pub trivia bet with that. Under a particularly bizarre set of circumstances.

I know this not because it is part of my general background knowledge, but because I was checking a new paper by Loughman and colleagues on burrowing by crayfish. Burrowing crayfish are very hard to study, like many digging and burrowing animals are. You need a lot of effort to pull them up out of their burrows.

This paper did both collection and modelling for F. fodiens and another burrowing species, the little brown mudbug (seriously, that’s its official common name), Cambarus thomai. For the digger, one of the best predictors of whether you could find this species was whether the surrounding forest was over one hundred years old.

The odd thing is, this relationship with old growth forest seems specific to West Virginia. The authors note that you can find digger crayfish in other states in “in roadside ditches, residential situations, and agricultural settings.” The authors suggest that in West Virginia, the little brown mudbug outcompetes the digger crayfish in disturbed habitat, and the little brown mudbug doesn’t live everywhere that the digger does.

It does help point out, however, that not all forests are the same. Sometimes, you have to keep the old, old stuff around.

Reference

Loughman ZJ, Welsh SA,Simon TP. 2012. Occupancy rates of primary burrowing crayfish in natural and disturbed large river bottomlands. Journal of Crustacean Biology 32(4): 557-564. 10.1163/193724012X637339

Tenth International Congress for Neuroethology, days 0 and 1

Man, I am having no luck with travel these days.

I arrived at the airport about an hour early, as usual. I tried automatic check-in, but it wasn’t working, so I went into the line for the counter. I think I was about 5 or 6 in line.

I didn’t move for about 40 minutes. But after about 10 or so, a huge long line formed up behind me. I overheard someone say that the flight had been completely cancelled. Sure enough, a few minutes later, I got an automated call from the airline telling me that I was rebooked on a flight leaving at 3:00 pm. A four hour wait.

Fortunately, the McAllen airport has free wifi. And it’s amazing what’s tolerable when you have free wifi and something to take advantage of it. A few games, some Netflix, and the time just whizzes by.

Even the replacement flight was late getting off the ground. And it was frustrating because the departure time kept sliding, a little bit at a time, so I was never sure if I could sit down for an actual meal. I could have done, but kept getting less than satisfactory bites. But we finally got on the way to Dallas about 7:45 pm. I reckoned that I’d spent as much time in delays as I had been scheduled to spend travelling, total. In the end, we touched down at about 11:25 pm. Ugh.

For stupid lack of preparation reasons, I did not make it to campus that night. But on the plus side, I was able to follow the landing of the Curiosity rover on Mars more or less in real-time on Twitter at 1:30 am (no wifi at the time for anything more substantial). Amazing stuff.

On the plus side, I played a bloody awful lot of Cut The Rope Experiments. Which, now that I think about it, kind of feels appropriate for Neuroethology. Lots of three star levels... I am only four stars short of claiming them all.

Setbacks aside, I caught the first train of the Metro to the University of Maryland. I was surprised at how many people were on the 5:00 am train, but I suppose I shouldn't have been.

I got on to the University around 6:30 am or so, found some breakfast and free wifi at a nearby McDonalds, and saw the first signs of the conference at quarter after seven. I made my way to my room in student residence, had a super quick shower and shave (too fast - nicked myself) and walked into the ballroom just as the very first plenary talk of the conference was starting.

I could not have cut it any closer.

But with only one day into the meeting, a few interesting trends are already emerging. People are worried about how they are going to sell neuroethology to funding agencies.

In his opening talk, Art Popper discussed this at some length. He had the good fortune to find several issues related to his research that had clear policy implications. for example, he talked about noise generated by pile drivers and how that could affect fish stocks. Popper said he found it gratifying that policy makers really did listen to scientific recommendations.

Popper (and several others) mentioned the landing of the new Mars rover Curiosity as something that go people excited about science. He repeated the common refrain that scientists do not do a good job of communicating what they do to the general public. (Yet no social media workshop? Hm...)

This was followed by a set of talks that were mainly historical in nature, with some guessing about prospects for the future. The predominance of what Ron Hoy called the “core four” model organisms - mouse, worm, zebra fish, and Drosophila (which others started to call the evil four) was also traced back to funding agency's priorities. The NIH wanted to support research that emerged from the human genome project, And the emphasis on genetic models arose from that.

Hoy gave something of a rabble rousing speech, saying that the field is very much in transition. The core techniques are changing fast, with more genetics and less electrophysiology. It is rare to have jobs advertised for “neuroethologist.” Hoy speculated that the future of neuroethology for the next decade may lie more in small liberal arts universities than major research institutions.

In the final talk of the night, Jim Simmons also kept coming back to how he is looking for ways to pitch his research. He said, “We need to convince founding agencies that we, and our animals, have solved problems that they consider unsolvable.”

I tweeted a lot from the sessions. Search #icn12 on Twitter for more short notable quotes. But as for now, I have been up for about 38 hours and I think the long expected crash is almost here.

Neuroethology bingo

Tomorrow, I am getting on a plane and heading to the Tenth International Congress of Neuroethology at the University of Maryland. I’ll be blogging throughout the week, and tweeting with the hashtag #icn12. I’m particular excited to be co-organizing a symposium on nociception that will be held Friday!

For the amusement of fellow conference attendees (click to enlarge)...

Fashioned after similar bits of tomfoolery at Nothing in biology makes sense! and Dynamic Ecology.

How the cow got its spots

Why do some mammals have spots, stripes, or other sorts of markings on their fur? Usually, this has been chalked up to camouflage or because the patterns might be sexy. But a new idea has been making the round this year: that it helps keep bugs away.

In March, Egri and colleagues published a paper suggesting zebra stripes deterred biting flies. Having tested stripes, the same team are back in a new paper to test spots. In their new paper, the team is working with slightly less exotic animals, but with more practical implications: cows.

If you’ve seen cows in a field, you’ve probably seen them swishing their tails to bat away flies. Flies are not just an annoyance: they can affect cows so much that they seriously harm the cows’ health. The flies bite and suck blood, and can transmit disease this way. Plus, the distraction can be so great that the cows don’t feed enough and lose weight.

To test the idea, the team set out boards painted with varying amounts of spots, but with the same proportion of black and white. They covered the boards with a glue, so that if a fly landed on it, it would be stuck, allowing them to easily measure the attractiveness of the surface. The more small spots, the fewer flies they found on the board. They tried this with the boards in different orientations, but the results kept coming out the same.

The team then moved on to a more realistic, cow model. Covered in glue, naturally – potentially annoying any cow tippers who happened to be in Szokolya, Hungary, where the experiment was carried out. The results were the same: lots of small spots meant few flies captured. Dark brown cows had lots of flies landing on them.

What is going on here? The team suggest that this all happens because of one important fact about the flies: they lay their eggs in water.

How do you get from that to cowhide? Like this:

Flies lay their eggs in small pools of water, so they need to have reliable ways to detect bodies of water.

Light reflected off water is polarized, and many insects, including these flies, can see polarized light. Thus, the flies have a built-in detection system for, and a preference to move to, polarized objects.

The dark fur of cattle polarizes light more than the white fur. (This is the one point in the study where the researchers used actual cows, not just painted models.)

The team goes on to suggest that besides having some agricultural applications, humans might take a few lessons from this research, since flies that bite cattle can just as easily bite humans:

Seems to be working: no flies on her.

References

Blahó M, Egri Á, Bahidszki L, Kriska G, Hegedus R, Åkesson S, Horváth G. 2012. Spottier targets are less attractive to tabanid flies: on the tabanid-repellency of spotty fur patterns. PLOS ONE 7(8): e41138. http://dx. doi.org/10.1371/journal.pone.0041138

Egri Á, Blahó M, Kriska G, Farkas R, Gyurkovszky M, Åkesson S, Horváth G. 2012. Polarotactic tabanids find striped patterns with brightness and/or polarization modulation least attractive: an advantage of zebra stripes. Journal of Experimental Biology 215: 736-745. http::/dx.doi.org/10.1242/​jeb.065540

Cow photo by Brenda Anderson on Flickr; dress photo by VancityAllie on Flickr; both used under a Creative Commons license.

Objectivity

Which is the better film: Alien or Aliens?

I thought this was a matter of opinion. and maybe some debate. The two have the exact same rating on IMDB, and Aliens has an ever-slightly higher metascore of critical reviews.

But I was informed yesterday that the answer is definitely, most assuredly, beyond any shadow of doubt is the first one: Alien.

I was told that this was a matter of “objective quality – as determined by the field and form of film,” and that “it’s not really beholden to personal taste or opinion.”

As a scientist and movie fan, I was surprised.

As a scientist, I put great stock into objectivity. I’d hoped that I have a good grasp on what it means when something is objective. For instance, one of the major things you can do with objective qualities is to measure them, with numbers, usually on an interval scale. There are generally agreed upon units for objective measures: meters, grams, degrees. You can create instruments that measure that quantity.

Admittedly, just because something has numbers attached to it does not mean that it is objective. For example, there are many psychological tests where two tests claim to measure the same thing that end up disagreeing with each other. But numbers are usually a step in the right direction.

As a movie fan, I felt I’d missed a memo somewhere. What are the SI units for quality? What instrument is used to detect and measure the presence of film quality?

And can the same measurements be made for other artistic media? Can the quality of television series be objectively measured by the same criteria as movies? Comics? How about painting? Guitar playing? Synchronized diving? (Have seen comments this week that if a competition needs judges, it’s not a sport.) If so, that might finally be able to stop hearing, “Eh, the book was better.”

And if quality is objective, a lot of movie critics are out of jobs. And I might as well stop writing my movie review blog.

I was reminded of this quote by David Hume:

If we take in our hand any volume; of divinity or school metaphysics, for instance; let us ask, Does it contain any abstract reasoning concerning quantity or number? No. Does it contain any experimental reasoning concerning matter of fact and existence? No. Commit it then to the flames: for it can contain nothing but sophistry and illusion.

All of which is a long way of saying: Aliens is totes better than Alien, dude!

(Incidentally, if there were to be an SI unit for measuring quality, I would propose that it be the Pirsig, in honor of Robert M. Pirsig, whose novel Zen and the Art of Motorcycle Maintenance (no jokes, please, I’ve heard them all) is all about the nature of quality. Great films might be measured in kiloPirsigs; Your Highness would be measured in nanoPirsigs.)

Comments for second half of July, 2012

Scicurious looks at work-life balance. How much of a move is too much to expect from prospective scientists?

A NeuroDojo post about Impact Factor makes a cameo at Byte-Sized Biology.

Why don’t scientists comment on articles at the journal website?

Gaines on Brains asks whether you be super-strong when you need to be. Problem with questions like this is that it’s easy to hear stories about people “lifting cars” without key details – like, that it was only raised a couple of inches.

Neuroskeptic asks if referees should be expected to catch fraud. If they don’t, should their names be revealed?

Biochem Belle asks how much more money funding agencies can put into postdocs.