29 April 2011

A note to those in high school

I thought about what I liked in high school, and realized...

Choose what you like in high school well. It’ll be with you a lot longer than you think.

It is sad how little progress I’ve made.

28 April 2011

Flight of the dodo

Contrary to popular belief, dodos can fly.

They just have spectacularly bad luck in their flights suffering from looooooooong delays.

Yesterday, Randy Olson (blue shirt, above) was on our campus, talking about science, filmmaking, evolution and much more. He was here as part of a program by the Office of Graduate Studies.

We had hoped he would arrive on Tuesday to make the screening of Sizzle: A Global Warming Comedy, but he got stuck in Houston for almost an entire day. Ironically, he had been in San Antonio before that, and could have driven here faster than his flight turned out to be!

The audience reaction to Sizzle was very positive, and myself and my colleagues did a bit of discussion afterwards.

Randy and I finally met at a screening at Cine El Ray, where we saw a screening of Innocent Voices. There was a bit of discussion about both the movie and Randy’s work afterwards.

Wednesday was the big day, with a workshop with our Teaching Academy on communication, followed by viewing some student and university videos, an informal session, and finally a screening of Flock of Dodos.

In the Q&A after the screening, Randy talked a little bit about his next film project, which will feature what many people say is their favourite part of both Flock of Dodos and Sizzle:

Randy’s mom, Muffy Moose, now 87.

If you saw Flock of Dodos, you saw a little bit of the life history of Randy’s parents near the end of the movie. Muffy was born in the Philippines, met Randy’s father there, and was shipped out on the eve of the war, where she became a model. His father was a survivor of the Bataan Death March. The film will be about the history of the Philippines in World War II, viewed in part through Muffy’s experiences.

The working title is Muffy’s War.

The day for me ended with a geeky fanboy moment. I got my copies of Don’t Be Such A Scientist and Flock of Dodos signed.

Cosmic coincidence department: We learned that his cameraman on the highly-viewed Science Cheerleaders video (which I wrote about here), Brandon Garcia, was one of our students! He friends with several of the grad school staff, including Denisse Cantu (far left in top picture).

27 April 2011

Review: Written in Stone

ResearchBlogging.orgI expected this book to be about the fossil record, but it’s more accurate to say it’s the record of the fossil record.

By which I mean this:

Each chapter covers one animal group, usually (but not always) that has undergone a major transition in form. Land mammals to whales, fish to tetrapods, and dinosaurs to birds are all featured. The narrative of each chapter, however, follows the history of the science rather than the science of the history.

There are wonderful stories here that I had not heard before, and the characterizations of the scientists themselves are rich. These were the book’s greatest strengths for me. I particularly enjoyed the description of the showmanship of Albert Koch, who tidied up with his spectacular (though rather dubious) whale skeletons in the mid 1800s.

The book is illustrated, but the illustrations are rather small. They are often old woodcuts with a lot of fine detail, but because of the creamy colour of the mid-grade paper, it’s often a bit difficult to make out some of the detail. The typesetting itself is also a touch on the small and dense side, again making the book feel like a more difficult read than it actually is.

As I read Written in Stone, though, I kept wondering, “Who is this book for?”

It’s likely tough going for a reader without a university degree. The discussions often run into some rather technical discussions of anatomy. Maybe an undergraduate with a comparative vertebrate anatomy class under her belt might be less flummoxed than me, but I often found such sections tough going.

It’s not exactly for people who are looking for how the fossil record provide evidence for evolution. Other books, like Jerry Coyne’s Why Evolution is True, lay out that evidence in a more straightforward way.

It’s not for invertebrate fans. Despite the ammonites on the cover, most of the chapters are about vertebrates. Now, I love me some charismatic megafauna, but the invertebrates aren’t given their due. On many key issues of interpreting the geologic record, understanding the pace of evolution, and documenting extinctions, the backbone of evidence is provided by invertebrates (pun intended).

It seems like Written in Stone is for people with undergrad degrees in biology who never got much instruction about fossils in their career. Alas, that audience is larger than I would like it to be.

During graduate students’ oral examinations, I often ask them, “How old are the oldest fossils on Earth?” Few master’s candidates give me a decent answer. And I picked that question because I once read that it is one that a high school graduate should be able to answer.

I wouldn’t recommend this book to just anyone. It’s a book that I would recommend enthusiastically to some people (if I knew them reasonably well). It will reward many readers handsomely.


Switek B. 2010. Written In Stone. Bellevue Literary Press, pp. 1-320. ISBN: 978-1934137291

26 April 2011

Tuesday Crustie: What a happy lad since the day he lost his strings

ResearchBlogging.orgSquat lobsters are not terribly well known, and this is a new species in a genus that even I didn’t know about: Uroptychus.

This species is being split off from Uroptychus naso (“naso” means nose), which is found in the western Pacific. The new species was spotted because of genetic surveys. Two lineages of mitochondrial DNA were found in samples, which prompted a closer look at what had been thought to be a single species.

Once they had spotted the genetic difference, the authors went back and tried to look for morphological differences. The authors describe these as “slight” - subtle variation in rows of setae and the like. And the authors describe two new species from the re-examination. It’s a nice example of how genetic work can lead to the discovery of cryptic species.

This one has a more northern distribution, ranging up to Japan. And it has a wonderful name, in reference to its relative, and its prominent rostrum.

Uroptychus pinnochio.

And people say scientists have no sense of humour.

Next week, I’ll showcase the other new species and talk a bit about the geography related to the three squat lobsters.


Poore GCB, Andreakis N. 2011. Morphological, molecular and biogeographic evidence support two new species in the Uroptychus naso complex (Crustacea: Decapoda: Chirostylidae). Molecular Phylogenetics and Evolution: In press. DOI:10.1016/j.ympev.2011.03.032

25 April 2011

Publishers submitting intelligent design materials for consideration in Texas

Despite that evolution is the law in Texas, intelligent design keeps cropping up with regards to the state K-12 education.

The Texas Freedom Network is reporting that applications for instructional materials for Texas classrooms include intelligent design materials; in particular, they mention International Databases. The Texas Education Agency has material from this publisher online, but it is password protected.

If the Texas Freedom Network’s information is correct, these materials are unsuitable. This example is given:

Teacher instructions such as: “students should go home with the understanding that a new paradigm of explaining life’s origins is emerging from the failed attempts of naturalistic scenarios. This new way of thinking is predicated upon the hypothesis that intelligent input is necessary for life's origins.” (Module 8, “Teacher Resources,” Slide 3)

That’s about as blatantly religious as one can get without mentioning God.

It’s important to note that these are applications only. It doesn’t mean they will be approved.

Well, at least we’ll have something to talk about after Flock of Dodos screens on Wednesday.

A new refereeing format for peer-reviewed journals

Peer review currently consists of writing, and reading, lengthy critiques and recommendations and completed forms. Other refereed activities have developed a much faster, more concise method of communication that journals would do well to consider adopting. (Click to enlarge.)

Inspired by philosophy referee hand signals.

22 April 2011

Credential evaluation

“Strong support for the argument that video game violence is indeed harmful.”

What would that strong support be? According to this story, it’s whether authors have published a scientific paper about media violence.

Read that carefully. It’s not about scientific papers on media violence, it’s about the authors of scientific papers on media violence.

Here’s the deal. There’s a court case. California wants to be able to ban the sale of video games to people under 18 based on the violence content. People get to file amicus briefs to offer their opinions for the court to consider. The authors of this study decide to look for evidence that video games cause violence by examining the scientific credentials of who wrote the court briefs.

They compared whether the amicus brief authors had published papers about media violence. Again, they’re not saying anything about the papers, just whether a brief author has written any in that area. In theory, someone who published a study on media violence that showed no effect, but who argued in favour of the proposed laws, you would be counted on that side, even if your research didn’t support a link. (Admittedly, that seems unlikely.)

In both sides of the case, authors with published scientific articles on media violence are in the minority. Those arguing the side claiming that violent video games are not problematic have a smaller percentage.

Still, most of the people writing briefs don’t have scientific expertise on the subject, which in and of itself is worrying.

But is comparing the percentages valid at all? Who decides who gets to submit amicus briefs? If briefs are submitted voluntarily, there could be any number of biases in the generation and selection of briefs.

Another piece of evidence that is considered “strong support” is by analyzing the impact factor of the journals the brief authors have published in. Impact factors have many problems, but their use here is weird. Again, the authors are not examining the impact factors of journals that published articles on media violence (as far as I can see), but whether the amicus author had published in high impact journals, ever.

Sorry, but that is not “Strong support for the argument that video game violence is indeed harmful.” It’s barely support at all. If they had said, “Supporters for laws limiting violent video games have more expertise than those opposing such laws,” there would be no problem.

It would have been better to look for peer-reviewed articles cited in the briefs. Than start rating those articles for the quality of their evidence, using basic criteria like:

  • Is the paper actually about video games? (I.e., is it relevant?)
  • Was it a randomized, double blind experiment?
  • How big was the sample size?
  • How big was the effect size?
  • Has the finding been replicated?
  • How often has the paper been cited?

Credentials are important, but they shouldn’t be a substitute for evidence.

Caveat! The paper that this research will be described in will not be published in May. It is possible that the actual research is better than the story in Science Daily (which I’ve been baffled by before).

Hat tip to Julie Dirksen.

21 April 2011

Extra extra DNA in giant neurons of slugs

ResearchBlogging.orgYou have two copes of your DNA in almost all your cells. The notable exceptions are your sperm (if you’re a guy) or your eggs (if you’re a gal). So if you measured the DNA in a cell in your body, you should get the same amount in any cell, regardless of the type of cell or the size of the cell.

Many molluscs, like Limax maximus here (same genus, different species than used in this research) have big, honkin’ neurons. This is what has made some slugs, particularly Aplysia californica, valuable animals to people who want to record the electrical activity from neurons. Somewhere along the way, someone measured the amount of DNA in Aplysia, it seemed suspiciously high.

There are many ways that you could end up with large amounts of DNA in a cell. The cell might form from several smaller cells that have been fused together (this happend in some giant axons in squid). An alternative hypothesis is that the neurons have extra DNA because the DNA has replicated without the cells dividing.

Yamagishi and colleagues tries to test this using slug. Reasoning that the effects they were seeing were related to regular growth, they fed one group of slugs a lot of food, the controls slightly less, and starved a third group for a few weeks. At the end of this, they successfully grew groups of slugs that differed in the size of:

  • Their bodies;
  • Their brains;
  • Specific regions within the brain, and;
  • Individual giant neurons in the brain.

That bigger bodies mean bigger brains is not unusual; this is a well-known scaling effect. It’s also not surprising that the main cause of the size increase is in the size of existing neurons, rather than increased numbers of neurons, because most invertebrates seem to have fairly rigid numbers of identified neurons across a wide range of sizes.

The authors are most interested in whether these extra giant neurons in the well fed animals also have additional DNA (they do) and how it gets there. To test this, they added a dye called BrdU that will show up in cells that are actively making DNA. Usually, this means in cells that are actively dividing.

This is one of the critical pieces of evidence, showing BrdU-labelled neurons in the subesophageal ganglion, with the starved animals on the left and the overfed animals on the right:

This is the full sized picture as it appears in the journal. It’s almost impossible to make out the actual, crucial data points on the right side instead of the profusion of arrows. In the PDF, you can zoom in rather large and convince yourself those data points are there... but by jove, you shouldn’t have to go to that trouble.

It’s also a bit puzzling as to why the normally fed control group isn’t in many of these comparisons.

This all suggests that the neurons are undergoing mitosis (genetic duplication) without cytokinesis (physical separation of the cells). This might be happening because neurons are metabolically very active. They have to synthesize and transport all their proteins quite long distances from the nucleus. And because the number of cells doesn’t change much in invertebrates, growth could put significant demand on a cell’s ability to deliver enough material.

That said, it isn’t a simple relationship. You would expect that because muscles vary tremendously with body size, motor neurons would show this tendency to have more DNA more than, say, interneurons. But that turned out not to be the case.

It’s not clear from these experiments if the neurons are duplicating the entire genome in the cell, or whether they are being more selective, and only duplicating key components – particular chromosomes, say.

It’s also not clear how the signals of more food and more growth gets picked up by the neurons and turned into a signal to make more DNA.

That this was all tipped off by an observation in one species and confirmed in another suggests that this is widespread among molluscs. But would it be expected in other species, too?

I prediction that this loading up large neurons with DNA will be found in other invertebrate, but will be rarer in vertebrates. Arthropods and some worms also have giant neurons and stereotyped numbers of neurons, so they would seem to be facing the same problem as molluscs. Vertebrates seem to have more variable numbers of smaller neurons, so I would expect it to be more rare there.


Yamagishi M, Ito E, Matsuo R. 2011. DNA endoreplication in the brain neurons during body growth of an adult slug. the Journal of Neuroscience 31(15): 5596-5604. DOI: 10.1523/JNEUROSCI.0179-11.2011

Picture by rhonddawildlifediary on Flickr; used under a Creative Commons license.

Science 3.0 neuroscience blogging contest

Science 3.0 is sponsoring a neuroscience blogging contest, for both new and old posts. You have to scroll down to find the entry form, on the right hand side.

20 April 2011

Education can set people free, in more ways than one

I’m a bit behind on my podcasts, but I had to point to this one from All in the Mind about a week and a half ago, about why people kill.

I found this piece from guest James Gilligan completely fascinating:

When I was directing the mental health services for the Commonwealth of Massachusetts in the United States we did a study to find out what program in the prisons had been most effective in preventing re-offending or recidivism after prisoners left the prison. And we found one program that had been 100% successful over a 25-year period with not one of these individuals returning to prison because of a new crime.

And that program was the prisoners getting a college degree while in prison.

You know, when you’re an educator, it’s easy to be so bogged down in the day to day routine of marking and managing students and preparing assignments that the idea that education can be transformative is something that you just give lip service too.

It takes something like that to make you realize that education truly can transform people for the better.

19 April 2011

She’s packed her goodies and gone

The very first episode of Doctor Who I ever saw (“The Seeds of Doom”) opened with Elisabeth Sladen frantically digging around in snow, trying to find the Doctor.

And it was so wonderful to see her back in The Sarah Jane Adventures, where her part was such a great counterpoint to typical television heroes (young and male). She was an action hero at an age when most actresses have to play the nurses in Shakespeare plays or the grandmother.

She died of cancer today at the age of 63. Very sad.

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

A research and education park in South Texas

A press release from the city of McAllen is reporting that planning has started on a new research and education park in the area. It will focus on manufacturing.

With the region becoming the North American hub for advanced manufacturing, Patridge said NAAMREI partners recognized the need for a research and education park.

“Today’s manufacturing product life cycle must respond rapidly to the needs of the customer,” he explained. “By having research and development facilities close by, our companies will be able to speed up the time it takes to go from concept to consumer.”

This is great news for our area, as it creates the possibility of transitioning the region from a late nineteentheen century economy (agriculture and manufacturing) to a more modern economy (science and technology).

I’m not sure what an “education park” is, however.

Tuesday Crustie: Candycane

Stenopus hispidus is sometimes called “candycane shrimp,” which is much more fun than its other common name, banded coral shrimp. Love the length of the antennae on these ones!

Photo by Nemo's great uncle on Flickr; used under a Creative Commons license.

18 April 2011

The Zen of Presentations, Part 39: Unsaid

This is probably the most effective short presentation I’ve seen in a long time.

Unfortunately, I can’t embed the video here. But what you will see if you click the link above is American Congressman Joseph Crowley confronting the House of Repesentatives with nothing but an easel pad. (The clip is less than 90 seconds, so don’t be put off!)

He says nothing. But the expression on his face shows that he means every word he doesn’t say.

It’s powerful.

In a presentation, there is an almost overwhelming urge to fill up every second with your words. It’s easy to forget the power of silence. It’s as Claude Debussy said:

Music is the space between the notes.

A well placed pause can give emphasis. It can give someone the few second they need for something to sink in.

Sometimes, it’s better to shut the hell up.

Additional: Found a version of the video that can be embedded, though the linked version looks better.

15 April 2011

Hundreds of Harvards

Peter Thiel is still promoting his notion that higher education is a bubble waiting to burst. I wrote a slightly paranoid response to this before, but he said something interesting in his new piece:

“If Harvard were really the best education, if it makes that much of a difference, why not franchise it so more people can attend? Why not create 100 Harvard affiliates?”

The first answer is that we do have hundred of Harvards across the country, just without the name. They’re the many public and private universities. They have the same mission as Harvard: deliver higher education.

The second answer is that sensible people realize that the difference in education between Harvard and other universities is nowhere near as great as the differences in price and exclusivity of those universities.

Seth Godin notes that a lot of what is dictating university choices – certainly for people trying to get into what are seen as “elite” universities – has a lot to do with people trying to create their own personal brands, not the education they get.

Like Thiel, Godin rightfully raise questions about the cost of an “elite” education.

Does a $40,000 a year education that comes with an elite degree deliver ten times the education of a cheaper but no less rigorous self-generated approach assembled from less famous institutions and free or inexpensive resources?

That people in this country get so hung up on a small number of schools is part of a larger social issue: the American class system.

Malcolm Gladwell points out that the importance of going to the “right” school is a particular indication of the inequalities of American society (which are getting deeper, by all accounts). In Canada, the University of Toronto or McGill could reasonably claim the title of being the Canadian equivalent of Harvard. But in Canada, few would think a University of Toronto bachelor’s degree is somehow so much better that a University of Lethbridge bachelor’s degree.

While some elements of Thiel’s analysis are correct, I think he’s wrong about a coming “pop!” in higher education. Too many employers want employees the bachelor’s degree. I can’t quite envision all the Fortune 500 companies suddenly saying, “We are no longer going to require our entry level positions to need bachelor’s degrees.”

I can see higher education shrinking and stratifying – that is, proportionately more kids from rich families. I don’t think that would be a good outcome, as education has traditionally been a means of creating social mobility.

The Scholarly Kitchen makes similar comments, totally independent of mine!

“Follow the yellow brick road!” “WHAT ROAD?!”

Averil Macdonald has an interesting take on science education from Physics World in 2006 that I just discovered.

It is a myth that students avoid difficult subjects - if they did, then veterinary science and medicine would not be oversubscribed, nor have more female applicants than male. ... Students flock to difficult subjects because they are difficult yet seem to offer the promise of prestige, status and money. ... until you can show them what they can get out of science - the jobs and the business opportunities - they will not see that it has anything to offer.


There is a second problem besides that students don’t see the job opportunities. Even if a student does get that there are jobs for scientists, they have almost no clear idea how to get to them.

Let’s say that you are excited by WordLens, an app that came out last year for smartphones that translates signs from one language to another. It’s the sort of technology that not too long ago, I wouldn’t have believed I would see in my lifetime. You want to get a job working on creating a real-time audio translation device (a la Star Trek’s universal translator). One person could speak into it and you would hear a translation slightly later, for all major languages.

Man, even I barely have an idea of how to start on that sort of career path... and I’m a professional educator and scientist. What hope does a high school student have in figuring out how to navigate that career path?

In contrast, high school students see a very clear pathway to other professions. Bachelor’s degree with good GPA, then medical school. At the end of it, you are a physician who can either work for others in a hospital, or work for yourself. All the health professions have this advantage over other most science careers: a completely unambiguous career path.

This matter is relevant to the many who keep saying we need to improve science education, including business types. It’s not going to matter how many “technical jobs” are out there if each one is so dramatically different from the others that the road to each one is obscure.

Hat tip to Karen James.

Also, now that I’ve reached the end of this post, I wonder if this is just a very long way of saying, “I agree with Drugmonkey”?

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

Comments for first half of April 2011

Bone Girl and I prove great minds think alike.

The Scholarly Kitchen talks about how China rewards researchers for publication. This could be the best thing to keep the United States a world leader in science. Seriously.

BenchFly asks about the advantages and disadvantages of researchers focusing their research narrowly.

Dr. Becca thinks she could have done better at negotiation.

I make a cameo appearance on Genomeweb with one of my recent posts on tenure.

I also make a cameo appearance at Cephalove.

14 April 2011


Texas legislators did not particularly like the national attention the State Board of Education brought to the state in the last couple of years.

Several bills have gone forward to try to curb the excesses that went into the making of the last set of K-1 science standards. To my knowledge, none have passed yet. But the most recent is being heard now, which would specify the nature of the experts brought in to review proposed standards.

I had not known that the Board already increased the standards for “experts” earlier this year. But they are still not terribly demanding: a bachelor’s degree and demonstrated experience.

The American Independent is reporting on Bills are going forth that would require experts have doctoral degrees and five years of university teaching – that’s generally going to mean someone who is almost a tenured professor.

You may recall that Don McLeroy, chair of the Board during the revision of the science standards, famously said someone had to “stand up” to experts.

Not looking for tail, revisited

ResearchBlogging.orgIn today’s “Science is incremental” department...

A couple of of years ago, I wrote about a paper with the counterintuitive finding that peahens do not prefer peacocks with large tails. At the time, I bemoaned that the authors hadn’t done an experiment. They hadn’t manipulated anything, and were dealing with a trait that varied little across males they were studying.

I am pleased to report that Dakin and Montgomerie have done an experiment. There’s a lot going on in this paper, but the critical one for me was that they measured, then changed, the number of visible “eyespots” in the peacock’s tail. The males whose eyespots had been removed had fewer copulations than those that were intact.

That said, the number of eyespots and the length of the tailfeathers in the intact animals didn’t correlate well with mating success.

The females, then, are paying attention to the tails... but the deviation has to be fairly large before they care. The experimental removal of eyespots put the peacocks in the bottom 10% of the range that has been reported for wild peacocks. I’m still waiting for someone to figure out how to add feathers on to a peacock to see if that would make a super successful male.

Peahens are not mating randomly, though, so what they use to assess a “high quality male” once you get past a certain threshold for the size of tail is not clear.

Related links

Not looking for tail


Dakin R, Montgomerie R. 2011. Peahens prefer peacocks displaying more eyespots, but rarely Animal Behaviour: In press. DOI: 10.1016/j.anbehav.2011.03.016

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

13 April 2011

Astrology I can get behind

From Geeks are Sexy, the Geek Zodiac! It’s like the Chinese Zodiac... only geekier. (Click to enlarge.)

I am rather pleased to be born in the year of Daikaiju.

Hiding the doomsday device: camouflage and venom in stonefish

It’s ugly as sin and poisonous as hell.

This is a stonefish (Synanceia verrucosa). There are several species in the genus, and they all look like algae covered rocks. They also have one of the most dangerous venoms known to science.

ResearchBlogging.orgIf you go look for stonefish in Google Scholar, you will find a bucketload of papers on stonefish venom. You find research on molecules that have been isolated from the venom, clinical cases of poisoning, development of antivenoms, and more molecules extracted from venom. Indeed, you’re hard pressed to find any papers that treat the fish as more than a venom-making machine.

I’m not going to delve into the venom itself here. Instead, I want to talk about how venom fits into the ecology and evolution of stonefish.

Stonefish are ambush predators that make their living by burying themselves in sand. And they are able to completely conceal themselves in only a few seconds.

Once hidden in sand, they wait for fish to come by. Stonefish have lost a couple of joints between jawbones that many other fish have, so they are able to extend their mouth further some of their relatives. This reach, plus suction generated by opening the mouth, is enough to draw many smaller unsuspecting fish to their doom. Stonefish are also clever enough to use movements of the exposed fins of their back to “herd” fish back into the strike zone.

The strike itself is over in about 50 milliseconds. For comparison, human reaction times are typically around 200 milliseconds.

Stonefish are relying on camouflage and surprise to make their living.

What do they need venom for?

Stonefish aren’t using their venom to catch their prey, like venomous snakes do. That suggests that the venom might be a defence.

The problem is that camouflage and venom is a bizarre combination. When you look throughout the animal kingdom at species that use toxic chemicals as defences, you tend to see bright colours! You don’t built an ultimate weapon and not tell anyone. You want to advertise that you have a defence. Poison dart frogs are a classic example.

Yet, weirdly, Cameron and Endean noted, “venomous fishes often adopt a sedentary or station-keeping mode of life.”

And I cannot find any references to fish that routinely eat stonefish.

An alternative hypothesis is that stonefish are venomous because their ancestors are venomous. But this doesn’t work, either. A massive tree of relationships by Smith (2006) puts sea robins and other non-venomous, but bottom-dwelling, fishes as the closest relatives to stonefish. Furthermore, prowfishes and velvet fishes, which are lineages of fishes that branch off from stonefishes, are not venomous.

There seems to be no clear functional reason that I can find for stonefish to have the feature that most compels our attention. I am sure there’s a great doctoral dissertation for a grad student who want to work on that problem!

If there’s a grad student who want to work on a species that is both incredibly dangerous and hard to see, that is.


This talk was inspired by one of my seminar students, Luis, who gave a talk on stonefish, and another student (Philip? Was that you?) who asked what ate them.

Related posts


Camercon A, Endean R. 1973. Epidermal secretions and the evolution of venom glands in fishes Toxicon 11(5): 401-410. DOI: 10.1016/0041-0101(73)90115-3

Grobecker D. 1983. The ‘lie-in-wait’ feeding mode of a cryptic teleost,Synanceia verrucosa Environmental Biology of Fishes 8(3-4): 191-202. DOI: 10.1007/BF00001085

Smith W. 2006. Venom Evolution Widespread in Fishes: A Phylogenetic Road Map for the Bioprospecting of Piscine Venoms. Journal of Heredity 97(3): 206-217. DOI: 10.1093/jhered/esj034

Photo by Nemo's great uncle on Flickr; used under a Creative Commons license.

12 April 2011

Tuesday Crustie: Crustaceans... in... space!

Today is the fiftieth anniversary of manned space flight, which is an anniversary all humankind should celebrate. Now, I’m younger than Yuri Gagarin’s historic flight into space... but older than Neil Armstrong’s trip to the moon. I’m a space age kid.

The Soviets claim the first human in space, but who can lay claim to the first crustaceans sent into space?

ResearchBlogging.orgAll the references to crustaceans in space I have seen talk about good ol’ brine shrimp (Artemia). Why put Artemia in space? There are several reasons. They’re small, for one, which is a prime consideration considering the cost of putting anything into Earth orbit is directly related to mass.

One good scientific reason for putting brine shrimp into space is brought out by Spooner and colleagues (1992). Brine shrimp can put their eggs in tough cysts that can almost entirely dry out, and development stops until they get into salt water again. This means that you can put brine shrimp into space, start them growing, and be sure that all of that development did in fact occur in space. With almost any other animal, you will have a mix of growth on the ground and in space.

Which nation put crustaceans in space first? Wikipedia notes some went up in some of Russia’s Foton missions, which started in 1985. But then, we all know Wikipedia’s not without its shortcomings. With a little digging, I was able to find an earlier spaceflight: Artemia had gone up in Apollo 16 in 1972 (Planel et al. 1974). This record seems to be held by the Americans.


Spooner BS, DeBell L, Hawkins L, Metcalf J, Guikema JA, Rosowski J. 1992. Brine Shrimp Development in Space: Ground-Based Data to Shuttle Flight Results. Transactions of the Kansas Academy of Science (1903-) 95(1/2): 87-92.

Clément G, Slenzka K. 2006 Animals and plants in space. In: Clément G, Slenzka K (eds.), Fundamentals of Space Biology, pp. 51-80. DOI: 10.1007/0-387-37940-1_2

Planel H, Soleilhavoup JP, Blanquet Y, Kaiser R. 1974. Study of cosmic ray effects on Artemia salina eggs during the Apollo 16 and 17 flights Life Sci Space Res 12: 85-89.

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

11 April 2011

Back to the start

It feels good to have a new paper on sand crabs.

I did my doctorate on sand crab digging, and one of the attractions of working here was the opportunity to follow up on some of that work.

But that said, this project got started in a roundabout way. My co-author, Unnam, was in our university’s honors program. She started with research projects with me fairly early in her undergrad career. That she started early meant that we had some time to try a few things that were a bit off my usual research path. We worked on several projects that were aimed at getting preliminary data, but they weren’t quite panning out.

Meanwhile... I had been collecting sand crabs on and off since I’d gotten to Texas. I’d see variation in colour, and somewhere along the line, realized that this was a puzzle. Why were some battleship gray, like miniature versions Blepharipoda that I did so much work with on my doctorate? And why were some white, much more like the west coast L. californica that I'd also seen during that work?

I suggested this to Unnam almost as a back-up plan, in case some of the other stuff we were working on continued to give us grief. Getting DNA data can be tricky, but how could you not get data on colour?

Well, the other projects did give us grief, so this one kept going.

And getting solid colour data wasn’t as easy as we first thought. Digital cameras are finicky things, auto-adjusting brightness and colours. This made it tricky to compare pictures of different animals.

Though trickier than we thought, in the end, Unnam successfully defended her honors thesis about a year ago. She’s now in medical school in Galveston, and we’re both pleased to have this paper get a wider audience than her honors committee.


Nasir U, Faulkes Z. 2011. Color polymorphism of sand crabs, Lepidopa benedicti (Decapoda, Albuneidae). Journal of Crustacean Biology 31(2): 240-245. DOI: 10.1651/10-3356.1

08 April 2011

Carnivals for April 2011

I’ve been fortunate to host two of my favourite blog carnivals right here on NeuroDojo this month. You can find Encephalon #85 here and Circus of the Spineless #61 here, too.

Oh, among carnivals I didn’t host this month....

Carnival of Evolution #34 is over at Quintessence of Dust.

07 April 2011

Neurotransmitter release without calcium

ResearchBlogging.orgWhen I was in graduate school, my boss went to an IBRO conference that contained a point / counterpoint pair of talks about what triggered the release of chemicals from one neuron that could be picked up by another. One researcher argued that calcium rushing into the neurons was the sole cause of the neurotransmitter release. The other argued that there wasn’t enough evidence to say definitively that calcium was both necessary and sufficient for neurotransmitter release.

A new paper may make both speakers wrong. Shakiryanova and colleagues claim to have found neurons that release neurotransmitter without calcium being involved at all.

My initial thought when I read the title of this paper was, “How silly of me to think that every neuron would have to use calcium to trigger neurotransmitter release. We see so much variation in neurons. Some neurons use calcium instead of sodium for spikes, and some neurons don’t spike at all. Why couldn’t there be a case of some neurons using something besides calcium?”

How do you prove the neurons don’t use calcium? And what do they do instead of calcium?

The basic experiment is very simple. Record from a presynaptic neuron, and target cell – a muscle in this case – and take out the calcium. If the target cell can still do anything in response, there’s your proof, more or less.

Now, the details are much more complicated. Because this is in a fruit fly maggot, they’re using genetically modified flies that have a neuroactive chemical that glows under the right light.

There were two different chemicals that could trigger the neurotransmitter release. One is called forskolin. It activates adenylyl cyclase, which in turn activates cyclic adenosine monophospate (also known as cyclic AMP), and that causes neuroactive chemical release.

The other chemical is something I’m more familiar with: octopamine, which has received a lot of attention for its role in regulating behaviour in invertebrates. For maximum effect, octopamine makes the neuron release calcium stored inside it, and that triggers neurotransmitter release, so calcium hasn’t been completely cut out of the system.

Many of the experiments are... complicated... for anyone who isn’t familiar with Drosophila mutations and cyclic AMP chemistry. This is indirect way of me saying that I struggled to make sense of this paper. This paper is acrotastic, swimming in abbreviations and symbols.

I am left with many questions. It’s not clear to me what the source of either forskalin or octopamine might be in this system. The authors seem to be suggesting that these chemicals are causing a sort of slow, gradual release of neurotransmitter. Some non-spiking neurons release some neurotransmitter tonically, so perhaps this system is a little like those.

If I understand right, calcium is still the only way known to trigger neurotransmitter release from an action potential. But I can’t help but think that it’s just a matter of time before someone finds a neuron where the spike triggers some other ion to rush in and cause neurotransmitter release.

Tangent: The authors call octopamine a “homolog” to norepinephrine. In evolution, “homolog” means “related by common ancestry,” which doesn’t apply to molecules. In molecular biology, “homolog” often means “similar sequences of DNA,” or some other long polymer, which also doesn’t apply here. Anyone familiar with some other meaning of the word I’m no familiar with?


Shakiryanova D, Zettel G, Gu T, Hewes R, Levitan E. 2011. Synaptic neuropeptide release induced by octopamine without Ca2+ entry into the nerve terminal Proceedings of the National Academy of Sciences 108(11): 4477-4481. DOI: 10.1073/pnas.1017837108

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

06 April 2011

Faux rigeur

Dear journal editor:

I’m perfectly okay with having manuscripts rejected.

I don’t mind in the least that you didn’t send it out to external editors for review.

But don’t try to convince me that you gave a 24 page scientific manuscript an “in depth examination”...

In eight minutes.

Even the Journal of Universal Rejection takes longer than that!

Reading the abstract and deciding it didn’t fit the journal is fine. Trying to cover that decision under the guise of faux rigeur is insulting.

Luckily, I can’t stay too mad. There’s a new season of Mythbusters starting tonight, and this import arrived in my postbox today:

Four knockout tracks, one standout, and no real clunkers. Can’t stay mad with that in my earphones.

P.S.—While this is easily a personal rejection record for me, I cannot, alas, claim it as a record, as I got one report of a manuscript rejected before it was submitted.

The center of knowledge

A BBC report making the rounds last week suggests China will soon overtake the United States in science. The article is perhaps a little too quick to declare a new champion.

The figures are based on the papers published in recognised international journals listed by the Scopus service of the publishers Elsevier.

In other words, this is a measure of quantity, not quality. Quantity is important, but there have been numerous articles suggesting that there are some systemic problems with Chinese publications, not the least of which is rampant plagiarism. For instance, here’s a Nature article from last September about Chinese journals:

Wu Haiyun, a cardiologist at the Chinese PLA General Hospital in Beijing, says that only 5–10% of these journals are worth saving, and the rest are “information pollution”.

About a month later, Nature said this in an editorial:

Lack of monitoring and regulation in China means false CVs and scientific misconduct are rife there.

It’s because of reports like these that when we want to joke about low-impact journals in our department, we use the Chinese Journal of Irreproducible Crap as our (made up) example of a crummy journal.

Still, I do agree that all the trends are pointing to China emerging as a scientific leader.

But I’m interested in a bigger question: What are the factors that make a place a hotbed for ideas?

When Neil deGrasse Tyson spoke on our campus last week, he spent some time talking about why so many of the visible stars in the night sky have Arabic names. And this he traced back to a period around the turn first millenium when Baghdad was the undisputed centre for learning and scholarship in the world.

What I find interesting is that such centres of innovation and learning have cropped up and moved repeatedly over the years.

Alexandria was once the place intellectuals went to to learn. Athens held the title for a long time. You almost can’t think of the word “Renaissance” without thinking of Italy. And who would have picked Scotland as an intellectual powerhouse of the 18th century?

When I wrote about peak science last month, I was speculating on whether there might some limits on how much scientific investigation we can do. But while I think the claim is too bold globally, does this pattern of one location becoming the world’s “intellectual capital” for a few decades, then fading, show that the “peak science” hypothesis holds locally?

What factors lead to a city or country becoming a recognized place for scholarship? Is it an unpredictable “lightning in a bottle” effect, where by sheer chance, you get a small critical mass of hard-working, bright individuals?

Or are there common factors in all of the great centres of learning throughout history? For instance, is it just about money? Do intellectual revolutions occur in cities and countries with the most booming economies? Tyson seemed to argue that it was more than that, saying that there were several examples of countries that were world powers, but not intellectual centres.

It would be fascinating to put global statistics on research papers, patents, research investment, percent of population with university degrees, and similar indicators, on Gapminder. The only thing I can find that seems related to universities is “Expenditure per student, tertiary (% of GDP per person).” Paging Hans Rosling...

I’m sure this would be a question ripe for exploration. Does anyone know if there are history books written yet on the historic centres of learning? Because it seems to me that there might be lessons for the United States and China in looking at what happened to those ancient (and not so ancient) centres of learning.

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

05 April 2011

Promoting the Head Dodo

This morning, I did an interview for the City of McAllen local community cable station to promote Randy Olson’s upcoming visit to our campus.

When I did a couple of radio interviews last year, I heard a lot of room for improvement. And it’s also a bit terrifying to do an interview for a book that includes a whole bunch of advice about communication in just this sort of situation! I kept thinking questions like, “Am I being concise enough?”

But I am bediviled by Es in this video! I get the E wrong in STEM – it’s there for engineering, not education! D’oh! And the E in my last name has mysteriously gone missing...

Tuesday Crustie: Smash!

The colours on this particular stomatopod (Neogonodactylus oerstedii) make me think of The Hulk. The Hulk is, of course, not only known for his classic green colour, but for smashing things. This stomatopod is also a smasher. In case you haven’t see how truly superhuman these animals are, get over and watch Sheila Patek’s great TED talk on the subject.

Not all members of this species are this particular shade of green, though. Michael Bok writes more about this species here at the Arthropoda blog.

Photo by Mike Bok of Flickr; used under a Creative Commons license.

04 April 2011

Swimming in poison

I’ve had one career: scientist.

My dad, on the other hand, has been a musician, mobile home salesman, jeweler, car salesman, Chicken Delight manager, and a few other things besides. But one of his last jobs before retiring was to be a safety officer at the Shell Waterton natural gas plant in the foothills of southern Alberta.

A little while ago, I asked him about one of the biggest safety challenges. I remembered him talking about when he would come home from work, which they usually referred to by the chemical formula: H2S.

Without a doubt H2S is at the very top of the list for the deadliest safety hazard in a gas plant. The H2S is contained in the gas (coming into the plant) before it is stripped out. Should a leak occur, the gas is colourless, odorless and heavier than air, so settles in low spots. The colourless and odorless properties make it extremely hard to detect without proper equipment. Exposure can cause death within three minutes.

Safety people wore H2S detectors and monitors and breathing apparatus and air was available in all buildings. There was an alarm system for the entire plant.

This chemical, hydrogen sulfide, is so nasty because it messes with the energy production in your cells. Your mitochondria get messed up and can’t generate energy. It’s like the power switches in every cell of your body get flipped off, one at a time. Imagine turning off the lights in a big warehouse: one section goes dark. Then another. Then another...

Because all multicellular organisms have mitochondria, hydrogen sulfide in high enough concentrations should be a poison to almost any living creature.

But this unassuming little fish is able to survive levels that would kill almost anything else.

ResearchBlogging.orgThis fish is Poecilia mexicana, a relative of aquarium (and evolutionary biology) favourites like guppies and mollies. As you might guess from the second half of its name, it lives in Mexico – southern Mexico, to be exact, where there are several small rivers with very high levels of hydrogen sulfide. The high levels of hydrogen sulfide are due to the geology of the area: the hydrogen sulfide is in the ground springwater that feeds the rivers.

It’s not only that the hydrogen sulfide levels are high that makes these rivers difficult to live in. Because sulfur reacts with oxygen, the oxygen levels in these rivers are low.

And it’s not the only species; P. sulphuraria also lives in such rivers. In fact, between the two species, it looks like these fishes have invaded these dangerous rivers three separate times. The close relative of these fish do not withstand hydrogen sulfide, so the ancestors of all the locals didn’t have some built-in resistance to the poison.

Given than hydrogen sulfide’s main effect is at the subcellular level, it’s surprising that all these lineages of fish show substantial changes in their body shape: fishes in the high hydrogen sulfide streams have larger heads than those that do not. The selective pressure is probably not the hydrogen sulfide, but the low oxygen in the streams. Larger heads mean more space for bigger gills, which intuitively means more oxygen uptake. This hasn’t been tested physiollogicaly yet, though.

There are also some changes in the fin position in P. sulphuraria compared to their relatives in less toxic streams. This does not seem to have any adaptive significance. They do seem to indicate that this population is off on its own independent evolutionary pathway, however.

Curiously, small fish tolerated the hydrogen sulfide much better than large ones. The reason for this is not discussed in the discussion, and I can’t figure out a reasonable hypothesis for why.

How do these become superfish, impervious to this poison? All animals make some hydrogen sulfide naturally, and so naturally have chemical pathways to get rid of tiny amounts of hydrogen sulfide. Presumably, these pathways have been ramped up to the max in these fish. This remains to be tested physiologically.

Ramping up those defenses against the hydrogen sulfide may not come cheap, though. These are not “superfish,” whose genes are spreading through nearby streams because of their ability to tolerate this poison. The mechanism and the cost of tolerating the hydrogen sulfide remains to be seen. There’s still much to do to understand how these fish were able to make it in these hostile environments.


Tobler M, Palacios M, Chapman L, Mitrofanov I, Bierbach D, Plath M, Arias-Rodriguez L, García de León F, & Mateos M (2011). Evolution in extreme environments: replicated phenotypic differentiation in livebearing fish inhabiting sulfidic springs Evolution DOI: 10.1111/j.1558-5646.2011.01298.x

Photo from Michael Tobler’s own website.

This post is part of the National Evolutionary Synthesis Center (NESCent) competition for the Science Online 2012 conference.

01 April 2011

Circus of the Spineless #61: Legs!

Welcome to the 61st edition of the monthly celebration of the little (and occasionally not so little) animals that run the world!

When hosting a blog carnival, one of the biggest challenges is figuring out how to organize the posts.  Last time I hosted the Circus, over at the Marmorkrebs blog, I sorted by presence or absence of exoskeleton – that is, into crunchies and squishies.

This time, the circus is larger, and I needed something with a little more resolution. Something a little more complex than a simple binary division. So...

No legs

Reporting from the lower mainland, Wanderin’ Weeta has some sea squirts in her camera lens lens.

Meanwhile, out on my old stamping grounds of Vancouver Island, Island Nature has some meadow slugs for you.

Okay, I’m homesick now.

One leg... okay, a stalk

This fun post at Uncharted Atolls features two kinds of echinoderms, including crinoids. Which are not to be confused with Krynoids.

Cool invertebrate. Deadly galactic weed. Know the difference!

Six legs

Six legs means hexapod, which means insects, which means a lot of beetles!

The Pashford Pot Beetle? Lovely! Also in serious trouble, according to Dave Hubble’s Ecology Spot. Dave also examined how beetles in Britain are responding to climate change.

Beth Jones, stepping in at the SciAm Guest Blog looks at whether the Asian long-horned beetle can be contained.

There are some lovely little butterfly at Wild Sri Lanka and Trees, Plants and More.

Bees in Art has an artistic representation of wood boring wasp.

Six legs and a pair of nasty-ass raptorial appendages

Real Monstrosities describes some stompatopods thus:

Superheroes usually arrive in ridiculous costumes resplendent in triumphant, “look-at-me, look-at-me, I-really-want-you-to-look-at-me” colours. Many Mantis Shrimps do the same, while others are best described as “brown”. I wonder if they’re the bad guys?

Honestly, the things you learn doing a carnival. I had no idea that stomatopods’ raptorial appendages were modified mouthparts. Embarrassing for a crustacean biologist to admit.

Eight legs

Don’t look, Mom! (My mom hates spiders.)

Hey! That's not a beetle! Well, you can see how a blog title like Beetles in the Bush might give a person the wrong impression when you suddenly come across a jumping spider.

Here on NeuroDojo, I started off the month examining whether very small spiders with very small brains could make very complicated webs.

Okay, Mom. You can look now.

Despite the title of this post – “Entomology of Star Wars. Episode III: Bears in Space” – tardigrades are not insects: wrong number of legs.

If you think it would be tough to keep track of eight legs, it can be: it’s very hard for octopuses to learn how to coordinate their legs and their eyes. Oh, this is one of my own posts here at NeuroDojo.

And yes, horseshoe crabs have eight legs– it’s just hard to tell in these pictures from Rebecca in the Woods.

Nine legs

Don’t be silly. That would violate the law of bilateral symmetry.

Ten legs

While true crabs have ten legs, I focus on just the big, sexy claw of fiddler crabs in this NeuroDojo post, and ask if the boys’ll wave them at any female. Even the wrong species.

Several decapods get caught in fishing nets at Trees, Plants and more. Yup, this would be one of those “More” posts in the blog title.

Many legs

I put this section in to prove that myriapod bloggers are slackers. Thirteen thousand species, and you can’t even give me one post, guys? Sheesh.

The next edition of Circus of the Spineless will be hosted by Squid a Day. The circus is looking for the next stop on its tour after that, so if you would like a chance to be a part of this show, email ringmaster Kevin Zelnio.

Comments for second half of March 2011

LoonieChemist makes me homesick. Mmmmmm. Smarties. Twice.

Scicurious and I are not only fellow neuroscientists.... we’re dinophiles.

Brian Switek continues on with the Brontosaurus retrospective at Dinosaur Tracking.

Bradley Vortek looks at how much brain you need. I wonder about one of the references that everyone has heard of, but may not have been published.

Jeff Toney at Dean’s Corner claims that students don’t read newspapers. That’s not what my students told me.

Jonathan Eisen, at Tree of Life, does something I’ve also started doing: a post describing the backstory to one of his recent papers.

Janet Stamwedel at Adventure in Ethics & Science, shows some wonderful sketches of ecological concepts.

At Demin and Tweed, Jeremy Yoder beat me to a great story of eggs and evolution. He blogged it, and now I don’t have to.

Namnezia got tenure!

Dr. Becca is thinking about her new lab space.

I make a cameo appearance at Worst Prof Ever.

When it comes to crayfish, I’m such a pedant. But don’t let me acting as part of the crayfish mafia discourage you reading this post at Student Voices about crayfish management.

Science Professor looks at why a search committee sometimes come up empty.

At Body In Life, Flavia Di Pietro wonders if “nociceptor” is a loaded definition.

A new paper in PLoS ONE says intelligent design can be taught next to evolution in Texas. And that isn’t true.

How comparative is your research? 2011 update

This week has been good. I had a new paper officially accepted and a preprint go up on Monday. Today I discovered another new paper had moved from “in press” to “published.” That journal, The Journal of Crustacean Biology, doesn’t “do” preprints, which means I’ve had two new papers hit in one week. Perhaps more importantly...

The bragging list of how many different species I’ve published papers on can be updated!

  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 fallax f. virginalis (Paper)
  14. Louisiana red swamp crayfish, Procambarus clarkii (Paper)
  15. Grass shrimp, Palaemonetes sp. (Paper)
  16. White shrimp, Litopaneaus setiferus (Paper)
  17. Benedict’s sand crab, Lepidopa benedicti (Paper; pictured above)
  18. Tapeworm, Polypocephalus sp. (Paper)
  19. Nematode, Hysterothylacium sp.(Paper)

Will have “stories behind the papers” posts on these soon! Bedtime for me.


Carreon N, Faulkes Z, Fredensborg BL. Polypocephalus sp. infects the nervous system and increases activity of commercially harvested white shrimp (Litopenaeus setiferus). Journal of Parasitology: In press. DOI: 10.1645/GE-2749.1 (DOI link not working yet; abstract and preprint available here.)

Nasir U, Faulkes Z. 2011. Color polymorphism of sand crabs, Lepidopa benedicti (Decapoda, Albuneidae). Journal of Crustacean Biology 31(2): 240-245. DOI: 10.1651/10-3356.1