31 July 2009

Rearranging the chairs on the Titanic: Gen Bio classes and informed citizens

Science magazine has an article (password protected), “Universities Begin to Rethink First-Year Biology Courses,” that starts out thus:

Introductory biology courses are often the last academic exposure nonscience majors at U.S. colleges have to science. Unfortunately, say science educators, the courses too often leave a bad taste in the mouths of students who spend more time in lectures than on experiential learning and in regurgitating facts rather than understanding the concepts behind them. As voters, those graduates apply their misconceptions of science to shape national policies on everything from evolution to stem cell research.

Okay, I’ll accept those premises, but I disagree with the conclusion:

So improving introductory biology is seen as a critical step toward raising the nation's scientific literacy.

Sigh. Don’t waste your time.

If the goal is to give university students a wide view of scientific knowledge that will make them better and more informed citizens, then make courses that do that.

Instead of bemoaning that many university students only take one science course in their first year and trying to sex up that one class, do something different. Change the curriculum so that all students take an integrative capstone class in science in their last year of study. Require them to take more science classes; make students take not just an introductory class, but an advanced class.

I’m not saying this would be easy. I know full well how constrained the degree plans at many institutions are.

But introductory courses cannot, and should not, bear the weight of the whole broad academic fields. Introductory courses are meant to provide students with an introduction to a particular discipline. A single general biology courses is not going to create an informed and scientifically literate citizenry who also appreciates chemistry, physics, social sciences, and mathematics, and so on.

Nobody would ever say, “We want the general public to have a better appreciation of design and art and craft, so let’s really pump up those Gothic literature courses.” Not that there’s anything wrong with Gothic literature, but I doubt it would greatly inform my understanding of painting or drama or sculpture or dance.

If we want university graduates to have advanced knowledge in an area, they must take advanced classes.

Is the aquatic ape hypothesis fringe science?

I admire today’s TED talk by Elaine Morgan as a great presentation, but I have reservations...

Morgan promotes the “aquatic ape” hypothesis. This suggests that the many anatomical features that distinguish humans from chimpanzees and bonobos were due to humans being aquatic at some point in their evolutionary past. It is not a loopy idea by any means, and is quite an interesting explanation.

Unfortunately, some of Morgan’s claims of why this hypothesis hasn’t got traction are very close to the sort of rationalizations that all manners of denialists use. Rather than admitting there are any weaknesses in the evidence, she instead chalks up resistance of the hypothesis to vague and shadowy forces of vested interests: “academia” and “paradigms”. She doesn’t call it a conspiracy; Morgan is clearly too sophisticated for that. (And I don’t mean that in a derogatory “Oh, she thinks there’s a conspiracy but just doesn’t use the word” way; I think her view is more smart and subtle than most wacky conspiracy “theories.”)

In that sense, yeah, I think the aquatic ape hypothesis is fringe science. Sorry, Elaine.

Human paleontology is its own very specialized field, so I make no claims of expertise here, but it seems to me that what is missing from the aquatic ape hypothesis is that it hasn’t been able to generate predictions. Pretty much every piece of evidence advanced for an aquatic past is, “Here is a distinctive anatomical feature that we already know about, and it makes sense if we had an aquatic past.” In other words, it’s always retrospective and ad hoc evidence – another warning sign.

One logical prediction to me would seem to be, “If we had an aquatic past, then we should routinely find hominid fossils associated with ancient lakes, rivers, and other water bodies.” To the best of my knowledge, that hasn’t been the case. When the aquatic ape hypothesis starts making useful testable predictions, it’ll move into the mainstream.

Additional: After writing this, I found AquaticApe.org, which indicates much the same thing. I admit confirmation bias may be playing a role here, though.

Questioning everything

Question everything graffitiBaltimore columnist Mary Spiro has a comment about a paper the Nature just retracted. The paper was retracted because two paragraphs were plagiarized.

Spiro also talks about the difference between the paper, which talked about “sperm-like” cells and the press releases, which talked about “sperm” cells. Which is a big difference.

Much of Spiro’s article is sensible stuff, but I get just a touch nervous by the very end, to which I add emphasis.

Science provides humanity with solutions to problems and answers to questions. But for science to retain the interest and trust of the public, all parties involved must do their due diligence to validate the quality of the scientific research produced and how it is reported. In other words, question everything.

I’m reminded of a story I heard once – I freely admit it could be an urban legend, but whether it actually happened or not doesn’t change the point. If anyone knows the source of this story, I’d love to hear about it.

An instructor decided that he was going to give his students a lesson in critical thinking and announced to his class that every lecture would contain one lie. This, he hoped, would make the students more willing to question what he was saying.

He had to stop that practice before the class ended. The students became obsessed with trying to ferret out the one lie, and it completely destroyed their ability to learn the material.

As a scientist and a skeptic, I’m all in favour of questioning and criticizing. But I can’t do it all the time; I don’t think anybody can. Well, not anybody sane, that is. How do you decide if if something needs greater than usual scrutiny?

  • How extraordinary is the claim? I think Carl Saga used to say that extraordinary claims need extraordinary evidence. Strong claims need strong evidence, or at least principled reasons behind them.

  • How consistent is the claim with other known science? This is why things like dowsing and homeopathy and various forms of fringe goofiness are subjected to relentless scrutiny: even if the effect were real, the proposed mechanism is at odds with other well-established scientific theories.

  • How far from the source is the claim? The amount of distortion that happens because people don’t read original materials, but second-, third-, or greater degrees of separation through compilations and repackaging is huge.

“Question everything” is one of those mantras that works great in theory, but lousy in practice. There is such a thing as paranoia.

30 July 2009

The biggest debate about science?

Today’s post, I am a lazy blogger and mostly compile other people’s responses to something Colin Stuart asked on Twitter:

What do you, good folk of Twitter, believe to be the most pressing debate about modern science?

I thought that was a great question, so wrote:

The most important debate about science is how to convert scientific information into public action.

And I really wanted to see what other people had to say. The wording of “about” science is important here; it’s not asking for the most important debates in science. A few broad themes came up...

Public trust and public policy

I see debates re cloning, GM, MMR, stem cell etc. all as symptoms of a single 21stC malaise: who to trust, who to believe? - ruthseeley

the woeful lack of scientific literacy in the media. - cromercrox

Perceived lack of acknowledgement of importance of science/evidence in govt., policy-making etc. (another pov) - EvidenceMatters

To teach the public to be comfortable with uncertainty. - silentypewriter

How to accurately communicate to the public what we know we know and what we don't know we don't know. - JATetro

I think most pressing science issue is lay mistrust of science. Without some consensus, much else is moot. - nparmalee


I think the most "pressing" debates all stem from what to do energy/environment/health wise with this many people on planet - ktg72

most pressing debate: at what point does human population growth override the need for medical progress? - museumoftechno

Climate change

How to stop climate change and avoid being the cause of a mass extinction event? - imascientist

Global warming: a habitable planet would be useful - loopysue_p

Surely how to tackle global warming - what could be more pressing? - twitandtweeter

As others have said, nothing really compares to global warming, i.e. the continuing existence of the human race! - jjaron

most pressing debate? Actually, I think climate change. Major public sketicism + large possible effects, for the lose. - Luna_the_cat

Science as profession

In that case, the most pressing debate is whether and how to fix the broken scientific publishing, funding & career system. - kejames

Depends on which pov. Researcher - poor funding, career prospects in UK. Public - 'balance' of reporting and science apps. - EvidenceMatters

peer review reform - blandiloquent


the future of space exploration. i.e., to decide that the time has come to get ourselves a space elevator. - doroncalo

Robot overlords

the rise of the machines. nano tech and it's viral future. interests and scares me most. - ColtSeaversPS

'in' modern science = e.g. the singularity, abiogenesis; - kejames


The development of Hover-boards. Only 6 years away!!! - FantasticMrOx

29 July 2009

Long sperm are speedy sperm

ResearchBlogging.orgAnimals compete in all sorts of ways, even right down to the cellular level. Sperm competition became a prominent idea in ethology in the early 1980s, driven by theoretical considerations coming from sociobiology and the technical innovations of early DNA fingerprinting. It’s been long enough that you’d expect some fairly clear generalizations about sperm and genetics in the context of sperm competition, but Mossman and colleagues indicate there’s still work to do.

Zebra finchMossman and colleagues argue that when you look across species and compare them, long sperm are faster – and you’d predict sperm competition would favour fast sperm. When you look within a single species, they claim, the pattern is not so obvious. They decide to look at this in zebra finches (Taeniopygia guttata), a well studied bird.

They had a colony of birds in which they knew all the relationships (for the genetics), they got sperm samples to look at the morphology of known individuals, and to measure the speed of the sperm.

The measurements of sperm are actually fairly complex. For instance, which sperm do you measure? They measured the speed of all sperm, the top 20%, and the fastest single one they measured. They took all those measures and ran them through stats to get a single value that incorporates information from all three measurements. Similarly, the authors didn’t just measure sperm length, but several features.

When you correlate all those features, the longest sperm turn out to be the fastest ones.

But in order for either sperm length or speed to be important evolutionarily, it has to be heritable. This involved looking at the relationships of hundreds of birds and linking those with the sperm characteristics they’d examined, and sperm length and speed are very heritable. Of course, since each is correlated with the other, heritability would be a package deal.

Nevertheless, as every researcher knows, correlation does not imply causation. Follow-up research might focus on an experimental test of the relationship between sperm length and speed. One way might be to see if breeding experiments, perhaps using an animal that’s a little faster breeding than zebra finches, could generate fast-and slow-swimming strains.

There’s also a prediction that males with large, fast-swimming sperm should have a selective advantage over other males if females are able to mate with multiple males. This seems to be true in “domestic fowl,” as the authors put it (I think that means “chickens”), but testing in zebra finches would be a logical thing to do.


Mossman, J., Slate, J., Humphries, S., & Birkhead, T. (2009). SPERM MORPHOLOGY AND VELOCITY ARE GENETICALLY CODETERMINED IN THE ZEBRA FINCH Evolution DOI: 10.1111/j.1558-5646.2009.00753.x

Picture by user marj k on Flickr, used under a Creative Commons license.

28 July 2009

Tuesday Crustie: Giving you the eye

Scyllarides latus
Slipper lobster (Scyllarides latus). Slipper lobsters are fairly closely related to spiny lobsters, more so than they are to clawed lobsters.

I did research on a couple of different slipper lobster species than the one shown here, and am always sort of surprised that slipper lobsters are not better known. I think they’re very charismatic crustaceans, with all sorts of interesting shapes and colours.

From user Joachim S. Muller on Flickr, used under a Creative Commons license.

27 July 2009

Escaping flatland, or: How fish remember where they’re going

ResearchBlogging.orgWhat do you do when you’re trying to get somewhere, and you get conflicting information? The person in the passenger’s seat swears he knows which way to turn, but the GPS unit in your car tells you to go the opposite direction. Problematic. Indeed, possibly relationship-changing depending on who’s in the passenger seat.

Still, humans generally have it easy when it comes to navigating. Our decisions are usually “turn left” or “turn right.” We are close to flatlanders when we are moving around our environment. Animals animals that fly, climb, or swim have to take the vertical dimension into account when getting around much more than humans do.

A new paper by Robert Holbrook and Theresa de Perera look at how fish remember positions in space. They put small tropical tetra, Astyanax fasciatus (shown below) through their, um, paces? (can fish pace?) in a classic Y-maze. One arm ends in a bare cul de sac. The other end of the rewards the fish with food and the sight of another individual of the same species. (This species of fish has an eyeless variety found in caves, but that’s not what was studied here.)

Contrary to urban legend, fish do have memories and can learn – even the much maligned goldfish. The Y-maze used in these experiments rotated, so they could train the fish to turn left or right to get to the reward, or swim up or down to get to the reward. The fish learned these two tasks at the same rates.

Astyanax fasciatusThe authors then trained fish when the Y-maze was rotated at a 45° angle, so their choices to get the reward were, say, “up and left” or “down and right.” The fish learned this task, too. But when the maze was flattened out, the fish continued to make the correct left or right turn. But when the maze was straightened vertically, the fish couldn’t pick the correct up or down turn when the maze was oriented vertically.

The last experiment was to train the fish when the maze was slanted at 45°, then, instead of straightening in, turn the maze to the other 45° angle. Based on the experiment above, where the fish remembered the left or right turn, you might expect they would turn left or right, depending on which direction they had been rewarded. But the fish, if trained to swim up and left, would swim up and right after the maze was rotated. If trained to swim down and left, they would swim down and right after the maze was rotated.

In this experiment, the vertical dimension had primacy, not the horizontal. But the both directions weren’t the same to the fish. Fish trained to swim up took longer to learn the task than those trained to swim down.

The authors don’t have a ready explanation for why the horizontal “left / right” memory gets primacy in one experiment but not the other. Their bigger point is that the two components are processed by the fish independently of each other. This would probably be quite interesting to neuroethologists studying spatial navigation, who could probably start to look at what sorts of neural circuits might handle these two lines of information.

A concern with this paper is the small sample sizes in the experiments. They used only four or five fish for each one. Would it have been so hard to get to double digits, guys? Then at at least you could use some more powerful statistics. Combined with the the apparent ease of conducting the experiments, it makes this paper feels very slight (much like another recent paper in this journal).


Holbrook, R., & Burt de Perera, T. (2009). Separate encoding of vertical and horizontal components of space during orientation in fish Animal Behaviour DOI: 10.1016/j.anbehav.2009.03.021

24 July 2009

I’m too scared to dance: Bee dancing changed by corpse viewing

ResearchBlogging.orgOne of the most famous findings in animal behaviour is that the dance of honeybees in the hive is correlated with the location of their food. The dance depends on the distance of the food, the direction of the food, the quality of the food, and, according to a new paper by Abbot and Dukas, how dangerous the food is.

Strictly speaking, it’s not that the food is dangerous (although that’s kind of what the title of the paper implies), but that the food is in a location that has cues that the bee associates with danger. Abbot and Dukas set artificial flowers for bees to find and feed at. At one flower – the “dangerous” flower – they placed two “recently killed” bees. Then they waited back at the five and recorded the dances of the bees that had visited those flowers. They also alternated which flower had the corpses.

The bees visiting the “dangerous” flower were significantly less likely to dance at all, and when they did, they dance for shorter periods of time.

The authors interpret this result as bees being sensitive to “predation risk.” This is perhaps a little too specific. My impression is that when something preys on a small insect, there usually isn’t much of a corpse left behind.

This is an very interesting finding, but the paper is disappointing because it is so slight. This is one simple experiment. It wouldn’t have killed the authors to run a few more experiments, because there are a bunch of very, very obvious ones to do. This is surely a classic case of authors “salami slicing” down a longer series of studies into tiny minimum publishable units.


Abbott, K., & Dukas, R. (2009). Honeybees consider flower danger in their waggle dance Animal Behaviour DOI: 10.1016/j.anbehav.2009.05.029

I don’t need no badges, but I like them anyway

Here are my merit badges from Order of the Science Scouts of Exemplary Repute and Above Average Physique.

Troop badge: Okay, I had to fudge a little on this one, because I kind of am into the business of total world domination. (I’m Dr. Zen, for cryin’ out loud! A name like that, and people have expectations...)

 Talking science badge: I’m an instructor. I’m paid to talk science.

 “I blog about science” badge: You’re reading the evidence that I’ve earned this one. I also have the Marmorkrebs blog. Speaking of which, that qualifies me for...

 “Inordinately fond of invertebrate” badge: I’ve worked with octopus, so I guess I can’t bitch about the symbol being a cephalopod instead of a crustacean.

I’ve done science with no conceivable practical application” badge: Sometimes, you have to be honest.

 “Cloner” badge: Marmorkrebs again.

 “Experienced with electrical shock” badge (Level I)": Easy one for someone who does electrophysiology. And relax, it's only to small bits of tissue, not entire animals.

“Science has forced me to seek medical attention” badge: It was a loss of footing on some rocks while holding glass.

“Somewhat confused as to what scientific field I actually belong to” badge: Do I study a neuroscience, neurobiology, ethology, neuroethology, evolutionary biology, carcinology, zoology...? It's all biology, I suppose.

“World’s foremost expert on an obscure subject” badge: Nobody knows sand crab digging like this guy.

“I’ve eaten what I study” badge: In my defense, I have not eaten my subjects anywhere near as much as other people would like to eat my subjects. I don’t much care for seafood. And I think I’ve only had the same exact species as I’ve published on once (a small taste of Balmain bugs that I didn’t order).

“I actually grew up and became a marine biologist” badge: I do work with a lot of animals that need salt water.

“Broken heart for science” badge: Some stories are not for telling.

“I somehow convinced someone to part with a lot of money for science” badge (Level I): My REU program.

“I use twitter to spread science” badge: I’m DoctorZen over there.

Update, 22 June 2013:

The “I attended ScienceOnline and connected to a web of science leaders & communicators” badge. 2013!

23 July 2009

A fellow traveller removing waste

As I’ve been struggling with the curse of paper in my own office this week (still not done), it’s so good to read that I’m not the only one. I particularly like the disposal highlights list.

How did bats get underfoot?

You think snakes on a plane are crazy? Bats! On the ground!

ResearchBlogging.orgBefore humans arrived on New Zealand, the only mammals living there were bat species. One of only two remaining native Kiwi mammals is Mystacina tuberculata, the lesser short-tailed bat.

This bat’s second claim to fame is that it walks. Only one other bat, the vampire bat, does this, and vampire bats don’t spend anywhere near the same amount of time on the ground as M. tuberculata does. That there are no other land mammals in New Zealand has been suggested as a reason that these bats are such ground huggers. This was suggested by analogy with birds, which are often flightless on islands that don’t have large predators. Indeed, New Zealand provides an example here with the kakapo, which Douglas Adams famously described as the world’s largest and least able to fly parrot.

This is an appealing idea, but tricky to test. You can’t really test an evolutionary hypothesis with only one species, and there are no other species in this bat’s family.

Mystacina tuberculataThis new paper by Hand and colleagues brings in a second species in this family by way of the fossil record. Importantly, the fossil, Icarops aenae, was not found in New Zealand, but in Australia. Australia famously has an abundant array of marsupials mammals, so bats and birds in this environment would be expected to remain mostly skyborne.

Now, even with the help of an online digital skeleton of this species, I’m way out of my depth with the anatomy described in this paper. (Hey, I’m an invertebrate biologist. This has fur and a backbone. Sue me.) But I appreciate the logic of the analysis.

Based on various molecular and fossil evidence, the fossil predates split that leads to the genus Mystacina in New Zealand. Thus, if walking was due to the predator=free environment provided by New Zealand, then you would expect limb morphology typical of other bats.

The fossil limb shows a lot of ground-dwelling adaptations.

It’s not a smoking gun killing the “lack of predators” hypothesis by any means. There are a raft of assumptions about distribution, timing of divergence, that are important in interpreting the results. Plus, it’s entirely possible that a lack of predators allowed an already ground-dwelling group of bats to go even further towards a land loving lifestyle. Nevertheless, it seems that this line of bats may have already touched down (in the ecological sense of their habitat) before they touched down (in the geographic sense) in New Zealand.

Predator from TV's PrimevalAlso, these lesser short-tailed bats are good candidates to evolve into the terrifying predators that will outcompete humanity in the distance future, as seen on the television show Primeval. Primeval's predators are fast on their feet descendents of bats that don’t fly.

Which goes to show that New Zealand could be the source of the things that kill us all. ;)


Hand SJ, Weisbecker V, Beck RMD, Archer M, Godthelp H, Tennyson ADJ, Worthy TH (2009). Bats that walk: a new evolutionary hypothesis for the terrestrial behaviour of New Zealand's endemic mystacinids BMC Evolutionary Biology, 9 DOI: 10.1186/1471-2148-9-169

DOI not working yet; click here for abstract.

22 July 2009

Science is my sword

Previously, I argued that science was never meant to be the reserve of the super intelligent. How did it become viewed as something that was elitist instead of democratic?

Science is like a sword: effective in the hands of the most rank and unskilled amateur, devastating when wielded by a skilled master.

It’s pointless to ask if successful researchers owe more to scientific methods or their intelligence, since those with both will outdo those who have only one.

Science has become practiced by a few by virtue of its own success. As the questions to be tested have become ever more subtle, it has taken more and more time just to establish the working knowledge necessary not to duplicate previous work. Also, the types of equipment needed to answer many of these very subtle questions are often beyond the realm of what most people are able to get their hands on.

Even MythBusters, one of the best examples of DIY science there is right now, often has resources beyond what the average person can cough up. Sure, building a giant ball of Lego is easy in principle... until you realize how many pieces are needed. Just because you know what experiment to do doesn’t mean you can pull it off.

21 July 2009

Tuesday Crustie: Briney black

Brine shrimp (Artemia monica).

From user djpmapleferryman on Flickr, used under a Creative Commons license.

Truth for the hard of thinking

ThalesScience is hard, according to common expression. After all, when something is easy, what is it compared to? “It ain’t rocket science,” which ends the race in a dead heat with, “It ain’t brain surgery.”

And this feeds into people’s feelings of inferiority where science is concerned. There is this idea that science can only be practiced by the very bright.

This is strange, given that arguably, science was conceived as a way that anyone could find truth about matters. Let’s compare science to the other methods of finding truth that preceded it.

Philosophy was a way of getting at truth that was always seen as an intensely rarefied and intellectual endeavor. In other words, it really was only for smart people. The first Western philosopher, Thales (pictured), was said to have fallen into a well while contemplating the stars. The maiden who rescued him asked how he could know what was in the heavens when he did not know the ground at his feet.

Religion was another way of uncovering truth. But much religion revolves around revelation. Those not blessed with revelation had to hope to be blessed with faith. But those not blessed with faith were kind of out of luck.

Science was a way for both smart and stupid people to get at the truth.

Not very bright or blessed by the divine? Here’s what you do. Look for patterns. Stick to numbers and things that are verifiable. Make predictions. Do tests. Compare the outcomes with predictions. Do that, and you will get answers to your questions. In other words, science spelled out methods that anyone could use. In that sense, science is emphatically not the elitist exercise it’s come to be seen as.

How did science become seen as something that only geniuses could do? That’s some idle speculation for another post.

20 July 2009

Quote of the moment, July 2009 edition

OdoAfter spending most of the weekend chucking paper from my office and still having a long way to go before I hit anything approaching “clean,” this quote from Star Trek: Deep Space Nine felt appropriate:

Humans have a compulsion to keep records and files — so many, in fact, that they have to invent new ways to store them microscopically. Otherwise their records would overrun all known civilization.

(For the sticklers, that’s Constable Odo in the episode “Necessary Evil.”)

Indelible marks

Apollo 11 astronautsI don’t remember the Apollo 11 mission.

I was rather young at the time, when memories tend not to solidify into more permanent things. But like the astronaut’s footprints on the moon, the mark the Apollo left on me was indelible. The mission that the world is celebrating and remembering spurred my interest in science and shaped my consciousness in ways that I cannot even begin to imagine.

I had the publicity picture of the Apollo 11 astronauts here on my wall. I wrote to NASA and got a big package of stuff from them that I poured over. I visited Cape Canaveral when I was 10 on family vacation. I was fascinated by the thought of space travel, and the possibility of routine flights to the Moon and a mission to Mars. At the time, it seemed it might happen in my late 20s...

Needless to say, I’m not in my late 20s. An opportunity was missed after Apollo. The International Space Station is wonderful, but it seems such a tentative step after the astonishing ones of Apollo. I don’t think there has been an achievement after the moon missions that has had the same impact on kids that NASA’s manned space program had on me.

I’m not alone. A new Nature survey found that half of the respondents said the Apollo missions inspired them to pursue science.

17 July 2009

How to deny anything

As someone who has an interest in skepticism’s idiot cousin, denialism, I’ve learned that the topic changes, but the patterns of arguments are amazingly consistent. Over at the Tetrapod Zoology blog, Darren Niash shows that these patterns of arguments aren’t restricted to conspiracy theorists. Sadly, scientists with an axe to grind will pull them out too. The paper in question concerns the relationship between birds and dinosaurs.

Here’s a short list of techniques that you too can use anytime you find the evidence against your position!

  • Never assert anything. Your goal is only to find shortcomings in your opponent’s claims. If It doesn’t matter if your criticisms are inconsistent as long as you’re criticizing.

  • Ignore relevant information. Just pretend it doesn’t exist. Go back and pull out references from decades ago that could not have taken new information into account.

  • Act like you’re being suppressed. Say there are a lot of people with vested interests who don’t want your ideas to get out. Even though we live in a time that makes it almost impossible to silence anyone.

The Scincus that swims through sand like a snake

In old Disney comics, Scrooge McDuck would often be shown swimming in his money bin, diving through the coins like an exuberant dolphin. Leading many young minds to wonder, “How does he do that?” Coins don’t move like water; they’re arguably closer to something like dry sand.

ResearchBlogging.orgA new paper shows that one lizard may not be able to get through McDuck’s nine cubic acres of money, but it comes a lot closer than anything else we know about so far. Scincus scincus is a cute little lizard a few inches long, whose common name, “sandfish,” tells you a lot about its behaviour.

These lizards dive through sand like Unca Scrooge dives through silver dollars. Previously, people had suspected they paddled though the sand using their legs, much like some fish might use their pectoral fins in addition to their trunk. The problem with testing an hypothesis like this is that sand has this irritating property of being opaque – a problem I had significant personal experience with, I might add. I solved it using wires and recording from muscles.

Scincus scincusMaladen and colleagues went to high speed X-ray videography. I suspect that they probably spent a long time trying to find a combination of materials with the right combination of transparencies to X-rays, but they did it. And they found that the sandfish might better be described as a sand eel. The swimming that these lizards did (rather fast, about 10 cm per second) was entirely driven by the trunk. The legs were simply held in position and didn’t play a part after the animal got under the sand. There are some fantastic movies of this in the supplemental material.

From here, the paper looks into the physics of the situation. To be entirely honest, it’s fairly difficult stuff for me. When they write:

It is remarkable that η does not change significantly
for different φ...

I have to take their word for the remarkable nature of those Greek letters. I am rather hoping that some physics blogger out there can walk through the granular materials math in this paper.

Maladen and company end by noting that they have helped to show how organisms can exploit the alternately solid-like and fluid-like properties of sand to move through it. And this is indeed a substantial achievement, but what if you turn that around? If animals can do this, why haven’t more done so? To the best of my knowledge, no animals besides other lizards swim through sand like sandfish do. And I doubt that this is due to visibility problems; I think it is just that digging organisms are relatively rare.

There is so much nice stuff in this paper that I might forgive them for citing a sand crab digging paper from the 1970s instead of more recent and more detailed articles.


Ryan D. Maladen, Yang Ding, Chen Li, & Daniel I. Goldman (2009). Undulatory Swimming in Sand: Subsurface Locomotion of the Sandfish Lizard Science, 325 (5938), 314-318 DOI: 10.1126/science.1172490

Sandfish photo by user thew...g's on Flickr. Used under Creative Commons license.

16 July 2009

No spikes in this worm: Motor neurons without action potentials

ResearchBlogging.orgIf you know a little bit about neurons, even really basic stuff, you probably know that neurons send signals with action potentials (a.k.a. spikes). What fewer people know is that there is great diversity in how neurons signal. There are many sensory neurons and interneurons that work entirely without action potentials.

I once asked my Ph.D. supervisor, Dorothy Paul, “Is there such a thing as a non-spiking motor neuron?” Dorothy did most of her research working on non-spiking sensory neurons in the west coast mole crab, Emerita analoga. She didn’t give me the answer, but told me it was an excellent question and I should think about it. Some time later, I heard another student asking the same question to another researcher at a poster at a Society for Neuroscience poster, and the person said, “No.”

This paper says the answer is, “Yes.” There are non-spiking motor neurons.

Qiang Liu and colleagues did their research on the little nematode worm, Caenorhabditis elegans, and were able to take advantage of the huge knowledge of the genetics of this beast, and our ability to manipulate this animal’s genes. They recorded the output of muscle cells using standard electrical recordings, but instead of using electricity to stimulate the motor neurons controlling those muscles – the classical way of doing things – they genetically engineered the worm.

The authors were able to make the worms express a protein called channelrhodopsin in certain neurons. Rhodopsin is a visual pigment that responds to light. When you flash a light on these worms (did I mention they’re transparent?), the channelrhodopsin opens up a channel that allows electrical current to flow into the neuron. Thus, you can use a flash of light to fire neurons of your choosing.

In neurons with action potentials, activity is like a light switch: flipping the switch harder doesn’t make the light from the bulb any brighter. A key set of data is to increase the light intensity stimulating the motor neurons (shown by different line colours in the figure here), and record the response of the motor neurons. If there was a classic action potential in the motor neuron, you’d expect there to be no response until you hit a threshold, and always the same response in the muscle. But the effect is more like a dimmer than a switch: the greater the light intensity to the motor neurons, the more the muscles responded. This is just what you would as expect for a non-spiking neuron.

There rest of this paper revolves around characterizing the synaptic connections between motor neuron and muscle in much more detail. It mainly looks at how the strength of connections between the cells change with repeated stimulation of the motor neurons.

This is not the first demonstration of non-spiking motor neurons. Another nematode, Ascaris, probably claimed that honor two decades ago (Stretton and Davis 1989). So while I did learn quite a bit from this paper (I didn’t know about the Ascaris work) and am impressed with the techniques in this paper, I am still a bit puzzled as to why it’s in Proceedings of the National Academy of Science (PNAS). PNAS is one of those exclusive high profile journals, sometimes disparagingly called a “glamour mag,” that publishes on what it considers to be “high impact” science. I guess this paper made it in because C. elegans has become such an important model organism, because this paper doesn’t show any previously unknown or unexpected kind of phenomenon.

But considering that the Ascaris work was published before I asked my supervisor about non-spiking motor neurons, I suppose that the phenomenon could stand to be much better known in the neurobiology community.


Liu Q, Hollopeter G, Jorgensen E. 2009. Graded synaptic transmission at the Caenorhabditis elegans neuromuscular junction Proceedings of the National Academy of Sciences 106(26): 10823-10828. DOI: 10.1073/pnas.0903570106

Davis RE, Stretton AO. 1989. Signaling properties of Ascaris motorneurons: graded active responses, graded synaptic transmission, and tonic transmitter release. J Neurosci 9(2):415-425. http://www.jneurosci.org/cgi/content/abstract/9/2/415

15 July 2009

Interest and inferiority

A short but insightful point about science education from the I Was Lost But Now I Live Here blog:
(T)he reasons people claim to be uninterested in science fall into two categories: problems of interest (”it’s boring”, “it’s irrelevant”, “it’s hard”, etc), and problems of inferiority (“I’m not smart enough”, “it’s not for someone like me”, “it doesn’t match what I believe”, etc). If you can frame the problem correctly, you can form a better solution. For example, if the problem is that it requires too much sustained concentration (i.e. “it’s hard”), then present the science in shorter snippets. If the problem is that the audience feels intellectually inferior, then reassure them that the material isn’t supposed to easy. I think the most important ideas we can convey to non-scientists are that science is about solving mysteries, failure is part of the process, and science is intrinsically a human endeavor. In fact, I started thinking that instead of tricking people into liking science, we should get more people to like the scientists themselves.

Comments for first half of July

Uncertain Principles has a post on science popularization which I threw in my 2 cents.

Over at the Sciencewoman blog, I put on my Grad Program Coordinator hat to comment on, “What should I look for in a grad program?

And the recurring question of lobster pain comes up again; I provide references.

Deep Sea News asks how conferences should treat bloggers, and I answer.

I add corny geek jokes to a list. Cluelessly added one that was already there...

And finally, I join a post railing against the incorrect use of homology.

Do you know this man?

Recognize this nattily attired fellow? No cheating now!

Dave Gibbons
You don’t?

Even though he was responsible for one of Time magazine’s top 100 novels in 2005? Shouldn’t you know someone who was responsible for a major, critically acclaimed work of art that is credited with revolutionizing the medium?

I mention all this because in discussions about science, science outreach, science education, and all the various permutations thereof, it is often lamented that when asked to name a living scientist, the general public will often retreat to naming someone dead, or naming someone who isn’t a scientist. (Yeah, that’s right, I’m lookin’ at all you people who say, “Al Gore.”)

But maybe we have unrealistic expectations there. There are a lot of creators who have a huge impact on our world who don’t get a second glance as they walk down the street. Can you name a single living chef running a five star restaurant? Or a zillion other occupations? Can you name a single living speech therapist?

For that matter, I was browsing through a blog post and read that E.M. Izhikevich is “one of the most important people in neuroscience right now.” This surprised me just a little, since I do neurobiology, but I’d never heard of this person. Okay, neuroscience is a big field, and I’m in a tiny little patch of that big field, but still, I do try to keep up.

Maybe we should not expect scientists to be more famous than other professions. I’m reminded of Whoopi Goldberg, who at the end of end of Inside the Actor’s Studio, talked about fame: Fame was accidental, she said, and so it was unrealistic to have “Become a famous actor” as a goal. But she noted that fame had nothing to do with being a great actor.

Maybe we should concentrate on people knowing and enjoying the work, and not be trying to create a cult of personality around researchers. We ain’t never going to be rock stars. It’s not our job.

P.S. – For the record, the gentleman pictured is Dave Gibbons, the artist for The Watchmen.

14 July 2009


Today, I listened to five K-12 science teachers who had been in our department for the last six weeks doing research internships. They were the first in a new program we have called STRIDES, which I think stands for South Texas Research Internships... something something. We had a real cross section of teachers with different experiences, teaching different grade levels.

It was fun.

It was interesting to hear their reflections on things they learned. For instance, several of them mentioned that they really noticed the high level of vocabulary used in a research setting – the precision that comes with technical terms, and they talked a bit about how they could try to bring some of that to their classrooms.

But more importantly, it was great to see how energized they were by working in a lab, on a bona fide original research project, for a few weeks. I think those teachers are really going to have a chance to light a few fires when their school year starts up again.

Tuesday Crustie: Look up

Scopimera intermedia
Sand bubbler crab (Scopimera intermedia).

From budak on Flickr, used under a Creative Commons license. Spotted on The Annotated Budak.

Change in your pocket? Buy a lobster

File under, “Things I never thought I’d see”: a lobster vending machine in Osaka, Japan.

Spotted in 12 Bizarre Vending Machines – which is not for delicate sensibilities. They really will put just about anything in a vending machine in Japan.

Different topic, same problem

As the world prepares to celebrate the 40th anniversary of a human being walking on the Moon, this article looks at those who deny it happened.

Because I am interested in belief, there’s quite a bit to chew on.
Ted Goertzel, a professor of sociology at Rutgers University who has studied conspiracy theorists, said “there’s a similar kind of logic behind all of these groups, I think.” For the most part, he explained, “They don’t undertake to prove that their view is true” so much as to “find flaws in what the other side is saying.”

Mark Fenster, a professor at the University of Florida Levin College of Law who has written extensively on conspiracy theories, said he sees similarities between people who argue that the Moon landings never happened and those who insist that the 9/11 attacks were planned by the government and that President Obama’s birth certificate is fake: at the core, he said, is a polarization so profound that people end up with an unshakable belief that those in power “simply can’t be trusted.”

If you took all the people who denied the moon landing, evolution, climate change, that HIV causes AIDS, that vaccines do not cause autism, the Holocaust, and maybe one or two other ideas that require wild conspiracies... I wonder how large a majority they would form.

And is there any way of reaching such people? Sometimes, I despair...

13 July 2009

Bye Anita

It pays to advertise, even on coral reefs

Cleaner fish are undeniably photogenic. They are colourful little fish that much larger fish will sit still for and allow the cleaner to dart all around them, even into the waiting jaws of their “clients,” while the cleaners feast of many small surface parasites. Cleaner fish provide one of the classic examples of mutualism in the animal kingdom, proving that evolution does not always mean bloody competition.

ResearchBlogging.orgHow do “client” fish recognize cleaner fish from a quick snack, particularly given that there are many different species of cleaners? Karen Cheney and colleagues tackle the problem not just from many different angles, but from many different lighting conditions.

First, they found all cleaner fish had either blue or yellow in their colouration, compared to only about 2/3 of a control group of fishes. They also confirmed a previous finding that all cleaner fish had a long stripe on the side.

But why blue and yellow? Is there any particular reason for these particular colours? It is just evolutionary happenstance, where one random colour became established, and later, all the others without it were selected against?

Cheney and colleagues hypothesized that these colours are used because they stand out strongly against the background. Demonstrating this is tricky, because what we see as a colour in a nice, brightly lit aquarium is not necessarily what another fish will see in the natural habitat, for several reasons. First, fish may not see colour like we do. Second, water filters out different wavelengths of light, so the colours change as you descend. Third, the major light source is overhead, whereas aquaria let in light from all sides.

To test this, they did some computer modeling using the known visual properties of several fish species, and seeing how they responded to different colours in front of an average coral reef background. Blue, of almost any shade, came out as the most conspicuous for all species for fairly long distances. Yellow was particularly conspicuous against black – such as the long black stripes that cleaner fish have. It was also highly conspicuous against blue water, the other major visual element in a coral reef habitat.

To top this all off, Cheney and company took some fish models, painted with different colours and patterns, into coral reefs. One was a realistic representation of a local cleaner fish, and the others had some variation of colour pattern. Just knocking out blue from the model significantly dropped the response of client fish (figure shown; click to enlarge).

Blue alone is not enough to attract clients, as several models with blue colours in the wrong places fared no better than the blue-less but otherwise realistic models. The ever more radical departures from the realistic colour scheme showed even more declines in client responses, but none of the “duds” were significantly different from each other.

The authors suggest that cleaner probably evolved before the conspicuous colouration, which is a sensible hypothesis. Just because something is conspicuous does not guarantee a client’s appropriate response. In fact, it is difficult to imagine a scenario where a highly visible colour preceded the evolution of the cleaning behaviour.

This research does a very clean job of examining the signaling end of partnership between cleaner and client. Hopefully, someone will pick up with this on the receiver end, and start examining the sensory capabilities of the client fish that enable them to recognize cleaners and react appropriately to those signals.


Cheney, K., Grutter, A., Blomberg, S., & Marshall, N. (2009). Blue and Yellow Signal Cleaning Behavior in Coral Reef Fishes Current Biology DOI: 10.1016/j.cub.2009.06.028

Picture: New Scientist gallery