30 April 2010

The Zen of Presentations, Part 33: PowerParody

Making fun of PowerPoint has gotten too easy, frankly. Too many people have written too much about how many people use it badly.

But this one made me laugh hard.

It’s coming out of this much forwarded New York Times article about the use of PowerPoint by the military.

The Daily Show With Jon StewartMon - Thurs 11p / 10c
Afghanistan Stability Chart
www.thedailyshow.com
Daily Show Full EpisodesPolitical HumorTea Party

I suspect this bit was partly inspired by Peter Norvig’s famous Gettysburg address parody, but this one has a Star Wars clip. And that automatically makes everything better.

Crustacean nociception: Comparative

One of the things I like about our new PLoS ONE paper is that it lengthens my list of species for I have published original research by 23%.

  1. Spiny sand crabs, Blepharipoda occidentalis (Paper)
  2. Pearly sand crabs, Lepidopa californica (Paper)
  3. Mole crabs, Emerita analoga (Paper)
  4. Squat lobster, Munida quadrispina (Paper)
  5. Signal crayfish, Pacifastacus leniusculus (Paper)
  6. Cricket, Teleogryllus oceanicus (Paper)
  7. Yabby, Cherax destructor (Paper)
  8. Balmain bugs, Ibacus peronii (Paper)
  9. Slipper lobsters, Ibacus alticrenatus (Paper)
  10. Spanner crab, Ranina ranina (Paper)
  11. Spiny lobster, Panulirus argus (Paper)
  12. Sea squirt, Ascidia interrupta (Paper)
  13. Marmorkrebs, Procambarus sp. (Paper)
  14. Louisiana red swamp crayfish, Procambarus clarkii (Paper)
  15. Grass shrimp, Palaemonetes sp. (Paper; pictured)
  16. White shrimp, Litopaneaus setiferus (Paper)

It’s hard for me to believe that this is the first time I’ve actually published data with Procambarus clarkii, which is used so often, and which I’ve had in the lab for a long time.

And I’m hoping to add to this list at least one more time before the end of the year.

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

29 April 2010

Crustacean nociception: The worry

Global warming. Evolution. Vaccines. Lobsters being cooked in pots.

The “lobster pain” question may not as headline-grabbing and contentious as the preceding issues on the list above, but it has something in common with all the rest.

Many people have strongly held opinions about the matter that don’t rely much on evidence. Animal rights people make “Being boiled hurts!” buttons. People associated with fisheries say things like, “No brain, no pain.

People don’t debate the issue, they trade position statements. And they often say quite witless things in the process. Sometimes, arguments achieve a sentence to error ratio of 1:1.

Some people will hate our new paper on crustacean nociception and some will love it, not because of the science, but based on how it fits with their pre-existing beliefs. I’m betting some readers will fly right past the most important sentence in the paper:

We are not claiming that crustaceans do not feel pain.

That’s important, because it tries to maintain nuance, in case people try to simplify our research findings to fit their pre-existing positions. And sadly, I think it’s a matter of when, not if, someone tries to take the results in this paper out of context and try to make it say something it doesn’t. I’m half-expecting someone to accuse me of being in the pocket of “big fisheries.”

To those on both sides of the issue, I ask you to do the experiments. I don’t mean this in the literal sense that people should go buy an electrophysiology rig. I mean it in the sense of saying evidence matters. I know that is hard. The same day this paper was published, I found not one, but two articles about how resistant people are to evidence, even if – or perhaps especially if – it’s coming from a scientist.

If crustaceans have nociceptors, I want to know it. If they don’t have nociceptors, I want to know it. I don’t care who shows it, and I don’t care which way the outcome is. Stop the vicious circle of arguing in a vacuum, so we can make some informed decisions.

Picture from here.

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

28 April 2010

Crustacean nociception: The journal, PLoS ONE

I’ve got to hand it to the folks behind PLoS ONE.

When I told people we had a paper coming out in PLoS ONE, multiple people spontaneously said, “That’s a good journal,” or even “Wow!” *

This is a far cry from what most people thought when PLoS ONE debuted a few years back. The stated editorial policy of only reviewing for technical competence and not importance made people worry that PLoS ONE would look like this:


Somehow, PLoS ONE has managed to avoid that fate. I think it’s managed to shed that image because it has become so massive. It’s on its way to becoming the biggest journal in the world in terms of number of articles (it was #3 last year). I don’t think it’s because everyone is sending their best stuff there, but when you have a lot of people sending stuff in, there’s more than enough cream to rise to the top.


I also think part of the reason PLoS ONE has started to be viewed as a bit prestigious is that many researchers are still reluctant to pay publication fees. That publication fee creates friction, and friction helps make something seem valuable.

I am glad that is piece is in PLoS ONE, since the “lobster in the pot” question is frequently asked. In fact, when we had a guest lecturer here recently, she mentioned she had been asked the question in her intro biology course the week before. So open access is a good thing for this paper, as I’m hoping it might help provide a reasonable “key” into the question.



I wrote all of the above a couple of weeks ago, well before I read The Scholarly Kitchen and its alternative view on PLoS and particularly PLoS ONE. The discussion following is lengthy and lively.

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

Dumping ground ohoto by D'Arcy Norman on Flickr; cream photo by Chiot’s Run on Flickr. Both used under a Creative Commons license.

* The “Wow!” factor may have been an expression of the surprise that I’d published anything at all.

27 April 2010

Tuesday Crustie: Buoy

When you think of barnacles, you think of animals that are fixed in place. But they are not all like that...


The photographer tentatively identifies this floating barnacle as Lepas fascicularis, but searching around suggests that that name is no longer valid. It might be Dosima fascicularis, which are given the common name of buoy barnacles.

Diversity is wonderful.

Photo by Willapalens on Flickr. Used under a Creative Commons license.

Crustacean nociception: Origins, part 2

And now, the continuing backstory of our new PLoS One paper (previous post here)...

The idea of crustacean nociception hung around in the back of my mind as a good project in the first few years of 2000s. Periodically, I would go onto Google Scholar and elsewhere looking for papers, not just on crustacean nociception, but invertebrate nociception generally. I built a quite nice series of lectures for my neurobiology class along the way from that.

Around this this time, I started to see how often the question came up, and how badly botched the answers were. I blogged about it, and I got ever more annoyed, not just by the lack of an answer, but by how people were making assertions that had no basis in research.

A couple of students working with me did some very preliminary trials, looking for a way to test crustacean nociception experimentally. My first graduate student, Sandra, got a little bit of preliminary data that went into her master’s thesis. But it just wasn’t enough to push forward with the project.

Finally, Sakshi got on board, and we finally started to get the data that’s in this paper.

To give you an idea of how long we’ve been slogging away at this project, we started collecting data late 2007. We thought we were going to have this done in a couple of weeks, but the results didn’t cooperate. We gave a poster at a summer meeting Crustacean Society meeting in 2008 (visible here). Sakshi gave a talk at the Society for Integrative and Comparative Biology meeting in early 2009. Actual paper last week. So it’s been well over two years in the making.

So much of a research project is a story of false starts and points where you really wonder if you’ll see the light at the end of the tunnel. We had more than our fair share of those, starting from the very first experiments, where we weren’t getting the expected results.

None of that comes across in the technical paper. It’s nice to give at least a hint of that, even though, as I mentioned, I’m only telling a very small part of the backstory here.

Catch me at the International Association of Astacology or the International Society for Neuroethology meetings this summer, and I’ll tell you more!

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

26 April 2010

“Don’t mention abiogensis!” – You should, actually

ResearchBlogging.org“Origin” means beginning. So it’s unfortunate that the best known book on the subject of evolution is On the Origin of Species. Because the theory of evolution by natural selection is not, strictly speaking, about the origin of life.

A recent article by Paz-y-Miño and Espinoza made that rookie mistake. And they got called on it. And quite right, too. The letter writers, Rice and colleagues, however, are upset not just because Paz-y-Miño and Espinoza use the theory too loosely.

They’re scared.

The first reason they give to separate evolution from the question of the origin of life (a.k.a. abiogenesis) is:

(S)tudents often hold more tightly to a supernatural account for the origin of life than they do to a supernatural account for how the diversity of life arose(.)

This sounds dangerously like self-censorship.

I can almost hear Basil Fawlty’s voice in my head: “Whatever you do, don’t mention the origin of life!”

We talk about the branching pattern of classification as evidence for evolution. We talk about commonalities of living things as evidence for evolution. When you examine those pieces of evidence for evolution, it is a logical inference that life originated on this planet once. To completely separate natural selection and abiogenesis does a disservice to both.

Darwin, as usual, was ahead of the game and saw the two were logically connected. The last chapter of Origin (first edition), he wrote:

(A)ll living things have much in common, in their chemical composition, their germinal vesicles, their cellular structure, and their laws of growth and reproduction. ... Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.

Rice and colleagues also argue that abiogenesis is more the domain of physics and chemistry than biology. This sounds like an easy excuse for timid teachers: “Not my department, have a nice day.”

Scientists working on the origin of life problem are going to be testing hypotheses that life originated following the regular laws of chemistry and physics. That is, they will be testing materialistic hypotheses. Yes, some people are going to have problems with that for religious reasons, and won’t like that science does not allow for the immaterial. Yes, scientists currently have fewer responses to religious objections to abiogenesis.

But there is no point in trying to hide the science around the origin of life under the rug in an effort to get people to buy into evolution. It’s a cowardly way to teach science.

References

Paz-y-Miño C., G., & Espinosa, A. (2009). Acceptance of Evolution Increases with Student Academic Level: A Comparison Between a Secular and a Religious College Evolution: Education and Outreach, 2 (4), 655-675 DOI: 10.1007/s12052-009-0175-7

Rice, J., Warner, D., Kelly, C., Clough, M., & Colbert, J. (2010). The Theory of Evolution is Not an Explanation for the Origin of Life Evolution: Education and Outreach DOI: 10.1007/s12052-010-0225-1

Graphic by Arenamontanus on Flickr. Used under a Creative Commons license.

25 April 2010

Hoping these are the only quakes caused today

It is now April 26, Coordinated Universal Time. Today is a good day to take a stand for rationality. Inspired by Jen McCreight at Blag Hag (see here and here)...



23 April 2010

Big big love in wetas?

ResearchBlogging.orgWeta is not just the name of a special effects studio; it’s the common name for one very large insect (pictured) that is found in New Zealand. Like many animals on New Zealand, it’s under a bit of pressure from introduced mammals, so there are definitely conservation implications if you can understand the mating system of the animal.

Wetas make an interesting case study for studying body size and mating, because they are large for their lineage, and there’s also a big size difference between the males and the females. In this particular species of weta (Deinacrida rugosa), females are about twice as heavy as males.

There’s a lot of permutations and combinations to figure out what factors are important in mating in these species. Having a large body can have a lot of advantages in the mating game. It can help you compete with other members of the same sex in a physical contest. But another way being large can help you compete is that bigger bodies can often mean bigger reproductive organs, and more gametes, which for males translates to more sperm.
Is having a large body size advantageous in either sex?

Four years of chasing wetas in New Zealand, radio-tagging them (yes, they’re big enough for radio tags), letting them copulate in buckets and burrows, and authors Kelly and company are getting closer to some answers.

Somewhat unexpectedly, they did not find any statistically significant relationship between body size of mating wetas. Big boys didn’t mate with big girls or small with small.

Second, heavy females received significantly less sperm than light females. This is again a bit unexpected, given that in invertebrates, large females almost always are able to produce more offspring. Typically, you find males will expend as much sperm on the highest quality females as possible. Additionally, male body size doesn’t limit how much sperm the males can produce, so there was no evidence of “the spirit is willing but the flesh is weak.”

Why? One possibility is that weta males just don’t adjust their sperm allocation for mate quality. If so, this would be very surprising, given how often males in how many different species have been shown to be able to do this. Maybe female size isn’t an indicator of fecundity, though that also seems a bit hard to believe.

The authors also float the idea that large females are so sexually attractive, that males act as if they “assume” large, high quality females will be mated multiple times, and they produce less sperm so as not to “over-invest” in a competetive situation. The authors admit themselves that their data don’t support that; there isn’t a statistically significant relationship.

Reference

Kelly, C., Bussière, L., & Gwynne, D. (2010). Pairing and insemination patterns in a giant weta (Deinacrida rugosa: Orthoptera; Anostostomatidae) Journal of Ethology DOI: 10.1007/s10164-010-0211-7

Photo by mollivan_laura on Flickr. Used under a Creative Commons license.

22 April 2010

Crustacean nociception: Origins, part 1

As I mentioned before, our new paper in PLoS ONE took a very long and winding road from idea to publication.

As an undergraduate, I helped my supervisor, Jennifer Mather, prepare a talk, “Ethical treatment of invertebrates: how do we define an animal?” Jennifer wanted to speak on this partly because Canadian Council of Animal Care guidelines had listed experiments with invertebrates at the same ethical level of concern as vertebrate tissue. Interestingly, that’s where most invertebrates remain to this day (see Appendix XV-B), although there are increased concerns for “cephalopods and some other higher invertebrates.”

I helped Jennifer make some slides for her presentation. I drew some cartoons on them for fun; things like a clam saying, “Where did the expression ‘Happy as a clam’ come from?” The talk was given at an Animal Behavior Society symposium (first conference I went to!). Her talk was ultimately published. * So I started thinking about invertebrates, their nervous systems, and what that implied for their care, early in my academic career.

In 2001, Ed Kravitz wrote an article for the International Society for Neuroethology newsletter. He described the experience of being interviewed on TV as part of a story about the ongoing question of whether boiling lobsters is inhumane.

In response to the question of whether lobsters feel pain, I said that we didn’t know.

Emphasis added. Of course, because Ed is a scientist, he went on to give a longer, more thorough answer.

I added that since pain is a perception we often don't know whether people feel pain either, unless we ask them, and that pain thresholds vary greatly among individuals. I mentioned that pain is a higher cortical function in humans and that there is no structure resembling a cortex in the lobster brain. In response to questions about the many minutes of suffering and struggling by lobsters to get out of pots of boiling water, I mentioned that neurons in the lobster brain cease to function at temperatures above 27° Celsius (about 80° Fahrenheit) and that in boiling water the brain would quickly reach that temperature. I felt it highly unlikely, therefore, that the banging around in the pot was struggling to escape and instead suspected that heat-induced contractions of the massive tail and limb musculature of already brain-dead animals was the cause. In case people were still worried about the suffering issue, however, I mentioned that after cooling an animal on ice to anesthetize it, the brain of a lobster could be immediately destroyed with a scissors cut between the eyes.

Ed’s answer was correct, but it still bugged me. It bugged me we didn’t have an answer backed by good evidence, just extrapolations and guesses (albeit educated geusses). People had studied crustacean nervous systems intensively for decades. You can find beautiful pictures of lobster brains by Gustaf Retzius from the nineteenth century. It seemed to me that whether crustaceans had nociception (about as close as we’re going to get to “pain” scientifically for invertebrates in the near future) was an empirical question that should have a reasonably straightforward, factual answer.

To be continued...

* And that’s one of those moments where you go, “Wow, has it really been more than 20 years?”

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. DOI: 10.1371/journal.pone.0010244

21 April 2010

File under, "We didn't listen to the warnings."

Last night, I was thinking about the fragility of a world economy made dependent on high-efficiency travel.

Watching the news? No, I was watching Doctor Who. And not the new series with Matt Smith, no. I was watching some old school Who: “The Seeds of Death.”

That’s right: back in 1969, writer Brian Hayles was worried about the risks of globalization and how easily interdependent economies can be disrupted if travel stops. It’s a teleportation system called “T-mat” in the show rather than good ol’ airplanes, but still. And the parallels don’t stop there.

A major part of the plot concerns the abandonment of rockets... and now we’re looking at the last space shuttle flight with no replacement on the near horizon.

The cause of our current woes? Eyjafjallajökull, a volcano in Iceland. (And seriously, you cannot tell me the name of that volcano sounds like the name of a Doctor Who baddie. You just can’t.) The cause of the woes in “The Seeds of Death”? Ice Warriors!

Crustacean nociception: Introducing my co-author

Continuing on the “extras” with our new paper in PLoS ONE this week on crustacean nociception, allow me to introduce the paper’s first author...


Sakshi was the perfect person for this project. She is a double major in biology and philosophy. She was part of a team that competed in the national Ethics Bowl competition this year and finished in the top half. That’s fantastic mix for a project that has such obvious ethical implications.

We had started working on crustacean nociception from a completely different angle and approach. Sakshi pushed for us to take a different approach, which – though not straightforward (okay, often incredibly puzzling and frustrating) – was ultimately the right way to go.

Proof positive that it’s not always the boss who comes up with the good ideas.

Indeed, one of the reasons I’m happy about it was how little I did. Sakshi owned this project. And is she a post-doc? No. Grad student? No. Undergrad researcher and proud of it. (Gloat: This is the second paper this year I’ve had with an undergraduate co-author; this is the first. Also open access.)

Another advantage of having a co-author? I don’t drink, but Sakshi does. So this was the first publication I ever got to pop open a bottle of champagne when we got the acceptance email.

But the best reason to have a co-author? The full contact hugs when you can get when you tell ‘em the paper’s accepted. I wouldn’t trade that for anything.

Additional: This is how the paper showed up in my RSS feed this morning. Sakshi as the author, and me as “et al.” Further evidence of my dispensability on this project.


Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

20 April 2010

Crustacean nociception: The embargo lifts

There are some things I don’t blog about, even though I blog a lot.

One of those things is that I don’t say anything about is my ongoing research. Journals are notoriously twitchy about work being presented in other forums besides their own pages before publication. I don’t want to give the game away on projects before they are completed, accepted, and out there for people to see.

And this time, the paper was embargoed until now. Which, even though I know intellectually is something that happens to every paper in the journal, still felt a little bit sexy.

Today, my co-author, Sakshi Puri, and I have a new paper out in PLoS One that has had a very long fuse. It’s related to a problem that I’ve addressed multiple times on this blog (see links at bottom): the “lobster in the pot” problem, or, “Do crustaceans feel pain?”

“Do crustaceans have nociceptors for extreme pH?” is open access, like all PLoS ONE papers, so it’s free for all to read.

I’m going to be blogging about this paper over the next week or so, because I think there’s some interesting backstory that doesn’t fit into the technical paper. Think of the paper as the movie, and these posts as the bonus features on the DVD.

I also think there’s something to be said for follow-through. Fortunately, that something was largely said by Randy Olson.

But even having said that, if you ever catch me in person – at a conference, say – I can tell you some stories about this paper’s trek to publication that I won’t be telling you here on the blog.

Related posts

Fighting the forces of ignorance - 15 May 2003
Ignorance may not be bliss, but perhaps it is painless - 15 February 2005
Shell shock: Is the new way to dispatch a lobster a better way? - 26 November 2009

Reference

Puri S, Faulkes Z. 2010. Do decapod crustaceans have nociceptors for extreme pH? PLoS ONE 5(4): e10244. doi: 10.1371/journal.pone.0010244

Tuesday Crustie: Teaser

Today’s Tuesday Crustie is a teaser for something up later this afternoon...


White shrimp (Litopenaeus setiferus).

I’m always struck with shrimp how different they look when alive, with all their fine appendages in action, to how they look after they’ve dies. Sadly, this is an animal that people are more familiar with seeing dead on a plate with some dipping sauce than alive.

The next decade in neuroscience

Wired asked some neural specialists, “What will transform our understanding of the brain in the next decade?

They didn’t ask me. (Pout.)

If they had, I think this would have been my response – partly cheeky, partly serious. My answer to “What will transform our understanding of the brain in the next decade?”:

Nothing.

This won’t be due to lack of effort, but due to a lack of a coherent theory of mind. How brains make minds is what people want to understand. Understanding neural circuitry or synaptic transmission better won’t transform how most people think of brains if they don’t illuminate mental states. The next decade will see large accumulations of facts waiting for a theory to unify them. I don’t think that theory is going to come next decade.

Tangent: Of the answers Wired did get, I’m astonished that António Damásio thinks this decade, new information “will strike the last blow against the mind (brain)/body problem.” As far as I can see, “the mind/body problem” has been, is, and will continue to be, to neuroscience what creationism is to evolution: the zombie idea that nothing will kill.

19 April 2010

Lemme see your war face!

ResearchBlogging.orgPeople in the military are highly trained to perform at high levels under horrible situations. It’s a reasonable hypothesis to think that these individuals would have different cognitive performance and brain activity than civilians.

A new study by Paulus and colleagues tries to get inside the brains of some of these military personnel using the darling technique of the moment for humans, functional magnetic resonance imaging (fMRI).

The authors recruited veteran Navy SEALs, and compared their behavioural and neural responses to emotional faces. They showed pictures of people who were showing angry (maybe a little like the one shown right), scared, or happy faces, and the subjects had to match the emotion shown to another picture on a screen. The subjects did this task while the research team was scanning their brains.

Now, the thing of it is, there is no explicit prediction about what sorts of behaviour is expected between the soldiers and the controls. That’s a shortcoming of this study, because the authors did find significant differences between the SEALs and controls. But the SEALs were...

Slower. Sometimes.

Wait. What?

Now, “slow” is not the first thing you’d expect a Navy SEAL to be. But they were only slower to match fearful and happy faces. Response time of SEALs to angry faces? Same as control.

Now, here is perhaps another oddity of this study. Paulus and company describe several differences in neural activation of the two groups, related to the insula. An interesting finding is greater neural activation in the SEALs in response to angry faces. They argue that this suggest the military personnel are using greater neural processing to stimuli related to being in combat, implying that “angry” faces are more relevant to someone in the military than other faces.

None of the neural differences seem to relate to the differences in response time they found. Without any sort of correlation, the fMRI findings are facts in isolation. To their credit, the authors admit this. They chalk up the few differences between the test groups as perhaps due to a small sample and the nature of the task. They don’t much hint, though, at how they might test this “increased neural processing power” hypothesis. Or, for that matter, how they might expect that extra brainpower to manifest itself in behaviour.

The title claims to show “enhanced threat detection” in the SEALs. But “detection” is a description of behaviour, not brain activation. If SEALs do not outperform controls on the behavioural task, then the title is a bit misleading.

Additional: Neuroskeptic also put up an analysis of this paper, like 5 minutes, after I’d put up mine.

Reference

Paulus, M., Simmons, A., Fitzpatrick, S., Potterat, E., Van Orden, K., Bauman, J., & Swain, J. (2010). Differential brain activation to angry faces by elite warfighters: Neural processing evidence for enhanced threat detection. PLoS ONE, 5(4): e10096. DOI: 10.1371/journal.pone.0010096

18 April 2010

Happy birthday to my research assistant


The guy on the right is my occasional research assistant. He helps out from time to time by shoveling through a bunch of sand looking for sand crabs, and runs animals from South Padre Island to the main campus for me. He’s celebrating his 70thbirthday today, and he’s my dad.

Happy birthday, Dad! Have a great day, and thanks for letting your kid be a goof.

And that bit goes for you too, Mom. (She’s the one on the left.)

(And incidentally, if you think there’s something wrong with a man making his septuagenarian father do hard physical labour, relax: he was only 69 when this picture was taken. Next thing you know, you’ll be telling me I can’t have small children working 15 hour days.)

Photo by Jessica Murph, taken January 2010 on South Padre Island. Thanks, Jessica.

16 April 2010

Comments for first half of April 2010

Projectsteph talks about how a doctorate can be good training even for those who don’t want to remain in research. I point out that Seth Godin made a similar point less than 24 hours later.

Good, Bad and Bogus asks if journalists should report on research that hasn’t been peer reviewed. I think generally not. I neglected to mention that science journal often do report on results from conferences, which are rarely reviewed.

Canadian Girl Postdoc in America crunches the numbers on how many women are getting into academic jobs. I relate some calculations for my own department, and conclude I may not see parity between men and women before I die. Crap.

Scicurious at Neurotopia completed her doctorate. That deserves two languages’ worth of congratulations.

Skeptvet has a very nice table about words as scientists use them compared to how non-scientists hear them. But Carl Sagan gets mentioned in the comments, and I couldn't let that slide.

15 April 2010

Simon Singh’s libel case dropped

Yeah, you’d better drop it, British Chiropractic Association.

And they did.

Simon Singh, who I wrote about last week, was being sued by British Chiropractic Association for libel. I’m happy for Singh, but this statement in the Guardian coverage makes me happier:

The sudden end to the case will strengthen the campaign for reform of the libel laws, which Jack Straw, the justice secretary, is considering. It is also a specific pledge in the Liberal Democrat manifesto.

Genius is overrated

I sometimes think that one of the biggest problems of engaging people in science, either as a career or as an audience, is the notion that science is practiced by geniuses.

Not very many people think of themselves as geniuses, so they make themselves believe up front that they won’t be able to do it ot understand it.

The arts face a very similar problem. There’s this notion out there that it’s about creativity, and waiting for the muse, when often the reality is that 90% of the job is just showing up and doing the work.

Every cool science story that you read here, there, or elsewhere almost always has an extraordinary amount of grunt work behind it. I wish that element of science got a little more acknowledgement, though I’m not sure of the best way to do that.

Photo by Lamont Cranston on Flickr. Used under a Creative Commons license.

14 April 2010

Mind controlling an ant... with a fungus

ResearchBlogging.orgRecently, I talked about a wasp that is able to use its venom to turn a cockroach from a freely moving individual into a soulless zombie. It’s a feat that stretches your imagination of how one animal could exert that much control over the nervous system of another.

As it happened, I cam across a paper that might just go one better. Another insect is the victim (an ant, this time), but the Svengali isn’t another animal. It’s a fungus.

The fungus is Ophiocordyceps unilateralis, here pictured growing out of a very, very dead ant. Andersen and colleagues wanted to test one of Richard Dawkins’ famous ideas: that the idea of the “extended phenotype.” After infection, how precise is the ant’s subsequent change of behaviour? And can it be shown that this actually benefits the infecting agent in a way much greater than chance?

This fungus infects an ant species (Camponotus leonardi) that lives high up in the forest canopy, many meters above ground. But the corpses of infected ants were in very precise locations that were very different from the location of the ants in the colony:

  • Jaws clamped into the vein of a leaf
  • Close to the ground (but not on it)
  • On the north-northwest side of a tree

It’s so precise, you almost can’t help but imagine the inside of the head of an ant, with a fungus sitting behind a steering wheel. The authors were able to show that this position was particularly advantageous to the fungus by moving the corpses of the ants to different locations, which quickly resulted in the bodies being lost to the wild.

The authors also did some detailed analysis of how the fungus spread through the ant’s body after the ant died. This is fascinating stuff, I’m sure... to a mycologist. But one key point is that the fungus can’t start reproducing until some days or weeks after the ant has died.

For me, this raises so many interesting neurobiological questions. Some seem fairly easy to explain, in principle; ending up on the north side of a plant is probably due to changing the animal’s response to light. The final “death bite” of the ant into a leaf seems particularly tricky to explain. What chemicals are the fungus releasing into the ant’s brain that is leading the ant to such specific locations, and perform such exacting behaviours?

And if all of that wasn’t enough specificity: there’s a few other ant species in the are (Polyrhachis spp.) that the fungus can infect, but rarely does. When those animals are infected, their corpses are found significantly higher in the trees than the preferred species. This hints that the fungus can’t control this ant species so well as the one it usually infects. Is this a difference in the brains of the ant, where the fungus infects, the cocktail the fungus produces, the immune response of the hosts, or something else?

Answering some of these neurobiological questions may be a bit tricky. Ants aren’t the easiest things to do neuro on – very small. But there will be some great questions for the masochistic scientist willing to do it.

Reference

Andersen, S., Gerritsma, S., Yusah, K., Mayntz, D., Hywel‐Jones, N., Billen, J., Boomsma, J., & Hughes, D. (2009). The life of a dead ant: The expression of an adaptive extended phenotype. The American Naturalist, 174 (3), 424-433 DOI: 10.1086/603640

Photo by myriorama on Flickr, and used under a Creative Commons license.

13 April 2010

Tuesday Crustie: Lipstick


Barnacles (Pollicipes polymerus) from one of my old stomping grounds, Vancouver Island.

Photo by Minette Layne on Flickr. Used under a Creative Commons license.

Elevators versus stairwells

This Obesity Panacea post on staircase signs reminded me of a bugbear I’ve been meaning to write about for a long time. The Obesity Panacea post notes, “people don't use staircases that are hard to find,” but there’s another factor that I think impacts on staircase use.

Here’s a picture of an elevator on campus.


The elevator is well lit. There’s a television to look at while you’re waiting. Some have carpeting, maybe even some hardwood accents. In short, getting onto an elevator is an aesthetically pleasing experience.

Here’s a stairwell in the same building:


Dimly lit. Nothing but bare concrete. Unkempt. If I didn’t know I was in an academic building, I’d half expect to find a wino pissing in the corner.

Could it possibly look more like a place you are actively discouraged from using? You might as well put up a sign that says, “Enter at your own risk” or “The elevator that the fun people take is around the corner, loser.”

Why don’t architects make nice stairwells? Why not light them properly, put them in places that get sunlight, put some paint on the walls?

And we wonder why people don’t want to take the stairs, are less active, and are becoming increasingly obese.

12 April 2010

Blondes beat brunettes on beach

ResearchBlogging.orgThe joke around some beach communities is that you can never be too thin, too rich, or too blonde. I don’t know about the first two, but a new paper suggests being blonde on a beach may be good, but you can be too blonde – if you’re a mouse.

Animal colours provide some classic cases of adaptation and natural selection. For instance, most people with even a passing familiarity with biology know about peppered moths and industrial melanism. Fur colour in mice isn’t quite as famous as moth colours yet, but it might be getting there. I discussed mouse colour being hyped as “one for the textbooks” in a previous post. I suggested that the field experiments supporting some of the work were a little obscure and not well described.

Some people agreed with me. Alright, nobody said anything to me personally, but it would explain a new paper from the same lab. Sacha Vignieri, Joanna Larson, and lab leader Hopi Hoekstra go back to the field to get some more direct evidence for how mouse coat color influences survival in the field. The first couple of paragraphs do an excellent job of explaining why this story is worth revisiting 60 years after experiments showing that different fur colours were advantageous in different environments.

The team went to northern Florida, the scampering grounds of a field mouse (Peromyscus polionotus; pictured) that shows two distinct fur colours. They needed to go there not for the mice, but because that’s where the mouse predators live.

The authors didn’t need any mice, because they made their own.

Now, before you get this image of some sort of Frankenmouse experiment (“It’s alive... and squeeking!”), Vignieri and colleagues made models of mice out of plasticine.


Okay, they were a little more realistic than that.

You might think plasticine is a poor thing to make a mouse out of. Mice are furry, and plasticine... isn’t. True, but from a distance, the shape alone is enough to fool some predators.

(I can just imagine some poor, hungry predator coming down thinking, “Food, food, at long last, food!—Wha...!? This isn’t food! Damnit!”)

The big advantage to using plasticine models over other kinds is that when something attacks them (“So... hungry!”), they leave behind too or claw marks. This way, you can actually make a reasonable guess as to whether the predator was, say, a mammal or a bird. They also measured the colour of the soil they placed their plasticine models on, so they were able to test how closely they matched.

They tested two locations. On an beachfront island, the soil was very light coloured. Some ways inland in a park, the soil was quite a bit darker.

It might be to the predators’ credit that the non-moving, non-furry plasticine mice didn’t get attacked all that often. Of 2,688 chances predators had at them, 28 models were recovered with predator marks; another 12 went missing. And, as expected, the mice models that didn’t match the soil colour had the most attacks. The light coloured mice on dark soil getting the worst of it, but the authors attribute this to a higher rate of predation overall in habitats with dark soils.

But light coloured mice on light soil suffered from increased attacks if the mice were too much lighter than the soil. This is a nice example of stabilizing selection, where predation is constantly nudging mice to match their local environment as closely as possible.

In other words, it was possible for mice to be “too blonde.”

But before brunettes start gloating: the same was true for very dark coloured mice on dark soil.

But while blonde mice may have a selective advantage over brunette mice on the light-coloured beaches, brunettes could console themselves by remembering there’s a lot more inland than there is beach.

Reference

Vignieri, S., Larson, J., & Hoekstra, H. (2010). The selective advantage of crypsis in mice. Evolution DOI: 10.1111/j.1558-5646.2010.00976.x

Mice with coin photo from here. Plasticine mouse photo from here. Blondes from here.

09 April 2010

Mind controlling a cockroach

ResearchBlogging.orgThis post was chosen as an Editor's Selection for ResearchBlogging.orgMind control sounds impressive. But if you qualify that by saying, mind control of a cockroach, you might think, “Dude, it’s a roach. How hard can controlling its mind be?”

While roaches may not be among nature’s deepest thinkers, jewel wasps (Ampulex compressa, pictured below) pull off an impressive level of control by stinging the cockroach. The wasp walks the roach to the wasp’s nest, lays an egg on the roach, and the roach remains inside the nest and allows itself to be eaten by baby wasps. Importantly, the cockroach isn’t dying or immobilized or paralyzed – it just isn’t running away. (Video below, from supplementary material for this article.)



Obviously the wasp is injecting some sort of complex chemical cocktail in its venom, but what does it do to the roach’s nervous system? Gal and Libersat perform a series of experiments to pinpoint just how the wasp venom is working.

The wasp stings near the front end of the cockroach, where there are two major cluster of neurons: the brain (which gets called the supra-esophageal ganglion here) and the sub-esophageal ganglion (or, as some countries foppishly call it, the sub-oesophageal ganglion). The brain sits ahead of the “throat,” as it were, and the sub-esophageal ganglion sits just behind it.

Intuitively, you’d expect that the wasp would be targeting the roach’s brain. When we think of the place that actions are started, that’s what we think of. But this is a somewhat backbone-centric view of things, as most invertebrates have taken an “eggs in many baskets” approach to their nervous systems: they’re less concentrated in one place. It was already known that the wasps do sting the brain, but do they also work their hoodoo on the sub-esophageal ganglion?

Gal and Libersat first showed that when they removed the sub-esophageal ganglion from a cockroach, wasps given the opportunity to sting it took much, much longer compared to control. They interpret this as the wasp “looking” for its target, and it just keeps digging around in the roach’s body, looking for the missing neural tissue.

Then, they showed in intact roaches that placing a small drop of venom on the sub-esophageal ganglion significantly impaired the cockroach’s walking and escape running. When the venom was placed on the brain, though, there was no difference in behaviour compared to the control animals.

Not only did they see behaviour of whole animals depressed, when Gal and Libersat recorded from isolated sub-esophageal ganglia in a dish, they saw a significant decline in both spontaneous spiking, and spiking elicited by either wind or touch. And, as anyone who’s ever tried to hit a cockroach knows, these animals are very sensitive to wind and touch are normally very effective at running away from them. It looks like the initial movement away from these stimuli is not broken, but the normal running afterwards is messed up by the venom.

All of these experiments suggest that the sub-esophageal ganglion is really critical for the wasp’s mind control trick. This region is probably involved in controlling the initiation of voluntary locomotion (much like some of the command neurons in crayfish I wrote about a while ago).

But if so much of the wasp’s strange hypnotic power is exerted by controlling the sub-esophageal ganglion, the authors can only speculate on this: why does the wasp sting the roach’s brain?

Reference

Gal, R., & Libersat, F. (2010). A Wasp Manipulates Neuronal Activity in the Sub-Esophageal Ganglion to Decrease the Drive for Walking in Its Cockroach Prey PLoS ONE, 5 (4) DOI: 10.1371/journal.pone.0010019

Photo by TGIGreeny on Flickr, used under a Creative Commons license.

07 April 2010

I could be sued for libel in the UK

Many readers will probably be aware of the struggles of Simon Singh (pictured) in UK court. Singh has been sued of libel over a story he wrote about chiropractic practices. Singh said there was no good scientific support for many of the claims of chiropractic. The British Chiropractic Association sued him for libel, without any evidence on the face of it that Singh said anything untrue. Because the law lets them.

Regardless of the outcome of his particular case, there’s a larger issue, namely the way libel labs in the UK work. Singh lists reasons for libel reform:

(a) English libel laws have been condemned by the UN Human Rights Committee.

(b) These laws gag scientists, bloggers and journalists who want to discuss matters of genuine public interest (including public health!).

(c) Our laws give rise to libel tourism, whereby the rich and the powerful (Saudi billionaires, Russian oligarchs and overseas corporations) come to London to sue writers because English libel laws are so hostile to responsible journalism. (Again, it is exactly because English libel laws have this global impact that we welcome signatories to the petition from around the world.)

(d) Vested interests can use their resources to bully and intimidate those who seek to question them. The cost of a libel trial in England is 100 times more expensive than the European average and typically runs to over £1 million.

(e) Two separate ongoing libel cases involve myself and Peter Wilmshurst, and we are both raising concerns about medical treatments. We face losing £1 million each. In future, why would anyone else raise similar concerns when our libel laws are so brutal and expensive? Our libel laws mean that serious health matters are not necessarily reported, which means that the public is put at risk.

If you haven’t done so, consider signing the petition for libel reform at http://www.libelreform.org/sign. And consider spreading the word.

06 April 2010

Tuesday Crustie: Slaters

One day in Melbourne, Garry said something to me about slaters. As happened on more than one occasion while I was living in Australia, I looked at him with complete vacuity. Then, we played a quick 50 point round of my favourite game show at the time, Explain it to the dumb Canadian.

After several moments of the sort of frustrating dialogue you one person tries to find some way of explaining something very simple to someone with no reference point (e.g., explaining “ballet slipper pink” to someone blind; explaining Gwar to someone who has taste), the light finally dawned that he was talking about something like these:


“Pillbugs!”, said I. And Garry agreed, and we were finally back sharing some common understanding.

So there you have it: A quick tale of two scientists divided by a common language. Some day, I’ll tell the “texter” story.

This particular beast is Porcellio scaber, I think.

Photo by ivantotuga on Flickr, used under a Creative Commons license.

April carnivals

The Circus of the Spineless (#49, for those playing along at home) is being hosted by fellow Texas resident, Xenogere.

The Carnival of Evolution (#22, for those with the home game) is available for your reading pleasure at Beetles in the Bush. And I’m pleased to announce that the June edition of Carnival of Evolution will be hosted right here at NeuroDojo!

And if you find something good through either of those carnivals?

05 April 2010

Fashion! Turn to the left! Fashion! Turn to the right!

Dr. Becca was singing the praises of her new lab coat. It apparently references Lost.

Well, Dr. Becca, you are not the only one to have a cool partner. For not too long ago, I received as a gift, this:


Now, I will admit Dr. Becca’s lab coat may have a bit of an edge in the artistic department. The embroidery is more substantial. But, Dr. Becca, Ph.D., I will see your lab coat and raise. Do you have...

TEH GOGGLEZ?!?11?1!!?


(My people get me. The crazy, geeky, me.)

03 April 2010

Class advertising gone awry

Snapped this picture in the hall of my building: advertising for a fall class put up by a professor.


And we wonder why students have problems writing.

02 April 2010

Another impediment to scientific progress

As a faculty member in the University of Texas system, there are two major ways my salary increases.

First, I can get promoted to a new rank. And, well, that typically only happens twice in an academic career: once when you’re promoted from assistant to associate professor, and once when you’re promoted from associate to full professor. Obviously, those raises are few and far between.

Second, I can earn merit raises. This is an annual evaluation of my achievements in teaching, research, and service. There’s a complex formula to determine this, but not surprisingly, more published science gets you more points, and potentially a bigger raise.*

Why does this system potentially stifle scientific progress?

This year could be the most productive year of my career to date. I’ve got two peer-reviewed papers so far (one out, one in press), a letter in Science, a contribution to the Open Laboratory 2009 anthology, and I’ve got several other projects that could get published this year.

But.

From a purely rational economic point of view, it would be blindingly stupid of me to be publish anything this year.

Nobody is expecting to get any merit increase this year. Our university has been asked to make a budget cut of several percentage points due to the recession (as many institutions are). Travel budgets are among the first to go, but merit often also goes.

If I were smart, I should hold off on publishing my research during this academic year. I should submit things so that they’ll be published in the next academic year, when there’s at least a possibility that there might be merit money in it for me.

So I’ve just been given a financial incentive not to publish research as soon as I can. But it’s bloody hard for me to take the strictly rational route that economists tell me I should take in maximizing my own utility! As a scientist, I want my work out there as soon as possible. I want to be moving on to new projects, not sitting on completed manuscripts, waiting for the financial fortunes of the state to improve.

Has anyone else pointed this out to politicians and administrators and those who talk about scientific competitiveness, innovations that lead to economic recovery, and so on?

* Those of you playing along at home will notice that there is no cost of living increase.

Picture from Very Evolved.

01 April 2010

PLoS ONE Post of the month runner-up

One of my recent posts on brain size and bird migration was a runner-up for the PLoS ONE blog post of the month.

I was kicked to the curb in this category GrrlScientist. Good for her!

Who gets to be a scientist?

Is Richard Dawkins a scientist?

“How can you ask that? He’s probably only one of the most famous scientists in the world!”

I don’t advertise myself as an actor, even though I was an extra once. Or as an artist, even though I did some cartooning some time ago. And I even got paid for it.

Dawkins has a doctorate in science, is a great synthesizer of other people’s science, one of the greatest advocates for science around, but when was the last time he did any original science? When did he last analyze any data?

How about Randy Olson? He also has a doctorate, was a proper professor, but went to Hollywood and hasn’t published a peer-reviewed paper in years, as far as I know.

Or Sam Harris, who I talked about yesterday? Two publications? There are some undergrads with two publications. That’s not the typical track record of a professional scientist.

The “general public” is famously unable to name a single living scientist. That they cannot may be due in part to a lot of people being described as scientists when they are not actively involved in science.

Professional scientists have clear marching orders: Test hypotheses by generating data, and publish the results. (Yes, I know theoreticians don’t necessarily generate their own data, so don’t come bugging me.) Should scientists, as a profession, be a little more assertive about who gets to use that professional label?

Fun while it lasted

My many months of enjoying a Top 10 listing in Brain, Behavior and Evolution for my last review article have abruptly come to a close this month. My review article is nowhere to be seen...

I do think that the creation of a new section – Highlights and Perspectives on Evolutionary Neuroscience &ndash that is not paywall protected may have had something to do with the sudden reorganization of the top 10 this month from the previous months. The free stuff will undoubtedly dominate the top 10.