31 March 2010

Doing ethics like science?

Earlier this year, Sam Harris gave a talk at TED, which was just released, and given the title of “Science can answer moral questions.”

Having watched it, and read its follow-up, I have to say I’m a bit puzzled. I don’t see anything controversial or novel here. And I think the title is wrong.

Harris writes:

(I)t is taboo for a scientist to think such things, much less say them public.

I have good news for you, Sam: nobody thinks of you as a scientist.

Everyone thinks of you as a writer. I know you do neuroscience, which is ostensibly my field, but I don’t know what kind of research you do. I had to look, and I had to look pretty hard. You have a grand total of two peer-reviewed publications containing original data listed on your website (here’s one, and here’s the other). Sorry, but your list indicates that even you don’t think of yourself as a practicing scientist.

On to his points, and why I see them as trivial.

First, Harris attacks ethical relativism, and makes a big deal of his proposition that there are definite answers to moral questions. I have never met a philosopher or ethicist that seriously proposes or defends any form of ethical relativism. Harris claims to have met them, and I am sure that they exist. But the point is, this is not contentious or particularly insightful on Harris’s part.

Second, Harris says that point of ethics is to promote human flourishing. This sounds one heck of a lot like utilitarianism. Utilitarianism is a well-described and argued moral theory. Again, nothing controversial or new.

Third, I don’t see how Harris thinks science can answer moral questions, in this sense. Practicing scientists are always harping on about how science is a process. But Harris is, as far as I can see, mum on what processes we could use to answer moral questions.

Should we do double blind, ramdomized control experiments? Do we demand one group take a particular course of action, demand the other group not take this action, and measure them again at some point to see which group has undergone more flourishing? Because that’s empiricism, and that’s the way we do science. Maybe this is a good way to go (though I have doubts). But Harris doesn’t say.

If you want to say “science can do this,” you have to outline a research program. Harris doesn’t.

30 March 2010

Tuesday Crustie: Scrawny

An arrow crab, Stenorhynchus seticornis. One of the most uneven ratios of exoskeleton to everything else you’re likely to find in the crustacean world.

Photo by baltus15 on Flickr. Used under a Creative Commons license.

29 March 2010

Is Texas’s textbook buying power all that and a bag of chips?

The Texas Tribune reports that the much ballyhooed Texan influence on K-12 textbooks may be exaggerated.

(S)ince the mid-1990s and the rise of the state curriculum standards and testing movement, publishers have increasingly been forced to customize their books for different states, as well as for larger school districts in the roughly 30 states without statewide adoptions. Simultaneously, advances in publishing and printing technologies allow far more customization at lower cost, much like large newspapers that issue several geographically customized editions every day.

What’s more, rapidly shifting politics and the digital revolution in instructional materials promises to dilute the power of state school boards even further — both here in Texas and nationally.

On this point, a blog in Newsweek reaches a somewhat similar conclusion, and concludes with this cynical observation:

Besides, it's not like high-schoolers pay any attention to their textbooks anyway.

Open Lab 2010 ready for your choices

The Open Lab 2010 submission form is now live! Get cracking, people, you’ve already had almost a third of the year go by! There should be a couple of hundred prospective posts up there now!

Hat tip to Nerdy Christie and Greg Laden’s blog.

Desperado crickets

ResearchBlogging.orgIn Texas field crickets (Gryllus texensis), males come in two types: a flying long-winged form, and a non-flying short-winged form. These crickets’ forms are correlated with their interests in reproduction: short-wingers court females much more than fliers do. In this new paper, Guerra and Pollack predict the different interest of males in reproduction would be reflected in their willingness, and ability, to fight with other males.

Doesn’t that sound like a simple thing to test? You might think all you gotta get some crickets, put them together, watch them fight, and you’re ready to write up the paper! Not so fast, speedy. Watch the factors pile up, and you’ll get a sense of how performing a behavioural test of even a simple hypothesis can be trickier than you think.

Unfortunately, what appears to be a simple test is complicated by the flying males losing their ability to fly. So instead of a simple face-off between the mobile “colonists” and the flightless “desperados,” you have a more complex set of nine match-ups: each morph against the other two, and a control set of fights against the same morph.

There’s also the chance that the act of flight itself would affect the males’ aggression, because that had been shown to influence courtship.

To make things even more complicated, tn most studies of animal aggression, the number one factor in determining who wins and loses is not morph, but size. So the authors also have to track body size and account for it.

Ooooh, and hormones affect aggression, so testes size better be a variable to consider, too.

The results are tricky to summarize, since not only are there a lot of different match-ups, but fights are measured in different ways: Who starts the fight? Who wins the fight? How intense was the fight?

The trends, however, were that the short-winged males tended to be the most aggressive ones in terms of the initiation of aggression and the level of aggression, as predicted.

As to the question they might ask in the movies, “Are you going to bet on the man with the big muscles or the man with the big cajones?” I’m not sure about men, but in crickets, it was the case that both mattered. Indeed, those factors mattered more than the type of wings and flight capability the animals had.

Flying changed aggression levels of the long-winged males, but, surprisingly, not the probability of winning. This paper suggests that fighting can affect mating success, although there are no direct tests in this paper. There’s still a lot to work out in this system, not least of which is how all these variations are going to result in greater or lesser reproductive success. Is this a stable system? Or ar their conditions under which the colonists might out compete the desperadoes, and vice versa?


Guerra, P., & Pollack, G. (2010). Colonists and desperadoes: different fighting strategies in wing-dimorphic male Texas field crickets Animal Behaviour DOI: 10.1016/j.anbehav.2010.02.002

26 March 2010

No hurry

Because some days, you’re just all blogged out.

25 March 2010

Publishers and citation managers

I use a citation manager. Currently, it’s EndNote X3. I ♥ EndNote, and have told more than one person it was one of the best purchases I’ve ever made as a career scientist. And nobody paid me to say that, incidentally. (Other reference managers are available. Please sing their praises, but don’t be disappointed if I don’t convert.)

But I’ve noticed something weird. Most journals have a “download to citation manager” or “export citation” option for their articles, and most will specifically give you the option of downloading to EndNote.

Almost none of them gets the friggin’ digital object identifier (DOI) right.

I love DOIs. I love the idea of each scientific article having a uniform and permanent ID number, so that I don't have to constantly update my links or go trolling through Google Scholar when publishers rearrange their websites.

ScienceDirect journals put the doi in the “Type of article” field instead of EndNote’s “DOI” field. And they put, “doi: DOI:” before the actual DOI number.

Nature Publishing Group journals put the DOI under "Type of article", and put the link to supplemental information in EndNote’s DOI field .

Wiley Interscience journals stick the DOI under the “legal note” field.

What about that bastion of new ways of publishing and article level metrics including citation downloads, the Public Library of Science? PLoS journals don’t export a DOI into any field in EndNote, making me have to go cut and paste from the webpage.

Highwire Press seems to be the only one who gets it right. So there – it is possible!

Next time: And what about those keywords...?

24 March 2010

Research with undergrads

Last week, I was at an undergrad research meeting in Washington, D.C. On the whole, the trip was not highly useful, but I did get a lovely view from my balcony:

It was depressing to hear multiple people say that a lot of undergrad research mentors don’t benefit from working with undergraduates. They see it as a duty that they do somewhat reluctantly. Sort of like cleaning the toilets after a party. The mentors don’t even work directly with the students in some cases, leaving it to grad students and post-docs. I wonder how many students apply to a program and think they’re going to work with a faculty member, only to discover you’re going to get very little face time with the “listed” mentor.

Interestingly, most of the grants go to research intensive universities. A discussion about publishing with undergraduates, though, indicated that the ones at the mainly undergraduate institutions might have better success in publishing papers.

There was no discussion about long term career prospects; i.e., whether all these undergraduate researchers are going to be able to have career prospects at the end of this. To some degree, some people addressed this by asking, “If a student goes on to become a science teacher, is that as much a success as a student who goes into a Ph.D. Program?”

While at the meeting, someone asked if there was any drug violence around the region. I said I wasn’t aware of any, but little did I know that waiting on my iPod was a story from The Current about violence in Reynosa, which is right across the border from us.

I did have some time after the meeting to walk around the mall. I stuck to the outside exhibits rather than going into the Smithsonian museums, several of which had long lines and wanted me to check my bag. I did see the signs for a new hall on human origins in the Natural History Museum (right). As I was walking past, I saw one man point at the banners and say to his friend, “That’s where they try to tell you we came from monkeys,” and laugh. (More commentary on the exhibit by Jerry Coyne.)

Going through security was much less annoying than I expected. I got some useful data mining done on the flight between Memphis and McAllen, so I’m glad I brought my netbook after all.

Unfortunately, I seem to have walked past someone who had a virus either in DC or in an airport. I’ve been feeling a little woozy since getting back.

23 March 2010

Tuesday Crustie: Racing stripes

Not identified on the webpage, but based on some similar looking pictures, I think it’s Lysmata amboinensis. Lovely whatever its species!

Photo by David Panevin from Flickr, used under a Creative Commons license.

Research Blogging winners...

Research Blogging Awards 2010...are listed here. Congrats to Scicurious at Neurotopia blog for kicking my butt in the best neuroscience blog category!

22 March 2010

Beware, predator, I have ink!

ResearchBlogging.orgIf you were a predator trying to design the perfect food source, you’d probably want something that was slow moving, reasonably large, and had no annoying hard bits that you couldn’t really eat. In other words, it would probably looks something like an opisthobranch mollusk. Opisthobranch are also known as sea slugs or sea hares, and at first glance, they look like snack packs for predators.

Of course, opisthobranchs don’t take this lightly. Rather than physical defenses, they put up chemical ones. Besides any chemicals that they keep inside, many sea hares release chemicals, too. Sea hares have two chemicals they will squirt out in the presence of a predator: ink and opaline.

To test for how these two different chemicals affect predators, Nunsbaum and Derby looked at the inking behaviour of the California sea hare (Aplysia californica – a species well-known to neurobiologists for the many studies on memory that have been conducted on it; pictured above). They used blueheaded wrasse (Thalassoma bifasciatum; pictured right) as a predator.

The sea hare is a Pacific species (hence the species name “californica,” as in California) and the wrasse is an Atlantic species, so the authors obviously can’t mimic ecological interactions with 100% realism. The choice of species is almost certainly one of convenience, but you might expect that these chemicals and such are general enough that the exact species wouldn’t matter. That said, it does open up some possibilities to check whether there might be “arms races” where species in the same region have different inks or behavioural responses to animals they live with versus animals they don't.

To test the effect of the ink or opaline alone, without the actual sea hare in the tank to possibly confound things, Nunsbaum and Derby made “shrimp cubes” as a food item for the fish. They released them simultaneously with ink between the food and the fish. Ink made the fish less likely to get the food, but opaline didn’t, indicating that the ink is acting as a deterrent, partly visual.

Previous work had suggested that ink / opaline was a distraction to a predator, which would mistake it for food. They found that fish wouldn't eat alginate cubes, cubes with ink, cubes with opaline, but would eat pellets that had the amino acid components contained within ink and opaline.

What about when the ink and opaline are presented with actual food? Put any ink in it, and the fish wouldn’t eat it. Literally none. Zero. Put opaline alone in it, and the fish will eat it. All of them. 100%. This experiment (plotted right) is significant by IOT*. The more complex stats just seem like going through the motions...

When ink was around, fish took longer to get to food; this got shorter if the nose was blocked. This indicates that ink has some sort of olfactory blocking in addition to being a visual distraction.

Opaline appears to have no effect on fish at all. Curious. But this paper doesn’t speculate on what its job might be. A likely story is that opaline is a deterrent to non-fish predators, but the sea hares either can’t or don’t distinguish between predators bothering them enough to cause ink and opaline release.

* IOT = inter-ocular test. It’s something so obvious, it hits you right between the eyes.


Nusnbaum, M., & Derby, C. (2010). Ink secretion protects sea hares by acting on the olfactory and nonolfactory chemical senses of a predatory fish Animal Behaviour DOI: 10.1016/j.anbehav.2010.01.022

Wrasse picture by algaedoc on Flickr. Slug picture by user wanderinggnome on Flickr. Both are used under a Creative Commons license.

18 March 2010

Are big brains better for long trips?

ResearchBlogging.orgFor many birds, migration is a major component of life. You'd expect think that migration would have a whole cascade of effects on those birds, including the nervous system. But which way?

On the one hand, migration might be correlated with large brains to handle the the complex navigation tasks. On the other hand, migration might be correlated with small brains that are energetically efficient.

Sol and colleagues compared over six hundred species of birds (measuring over 4,000 skulls). Species ranged from non-migratory, to some members of a population where migratory, to some that were extensively migratory. They found, as had previous authors, that migratory birds tended to have smaller brains than non-migratory birds. Unsurprisingly, there is a substantial amount of variation from species to species. For instance, corvids (e.g., crows and allies) don't show this effect.

But what these authors are really trying to figure out is not the correlation, but the direction of causation. Do lineages become migratory because their small brains allow it, or does migration cause brains to become smaller, as neurons as jettisoned over evolutionary time for efficiency?

And here, there's a lot of math. It's not easy going for someone who doesn't do these kinds of models routinely, and I don't. Sol and colleagues argue that the models they tested indicate that migration causes brain size to reduce, rather than the other way around. Again, however, a good chunk of variation appears to be due to factors that were not included in the model. They also suggest that some brain areas may be more subject to selection pressures, and it's more complex than just the overall brain size alone.

When people think about the evolution of brains, the most common thing that leaps to mind is brains getting larger. Maybe that's just because that's such a major aspect of human evolution. This work is a nice example of selection pressure working to reduce brain size.


Sol, D., Garcia, N., Iwaniuk, A., Davis, K., Meade, A., Boyle, W., & Székely, T. (2010). Evolutionary Divergence in Brain Size between Migratory and Resident Birds PLoS ONE, 5 (3) DOI: 10.1371/journal.pone.0009617

Picture from user philip.bitnar on Flickr. Used under a Creative Commons license.

17 March 2010

The scientific-industrial complex

At the [citation needed] blog, Tal Yarkoni wrote about a recent fMRI paper (mphasis added):

I really do think that the prevalence of long author lists in a discipline are an important sign of a discipline’s maturity, and that the fact that you can get several dozen contributors to a single paper means you’re seeing a level of collaboration across different labs that previously didn’t exist.

I’m increasingly understanding how mom and pop shops felt about Wal-Mart, and how local booksellers felt about Barnes & Noble.

“I’m going to get crushed.”

This has been on my mind for almost five years now, if not longer: the effect of automation and increasing efficiency in data collection. Indeed, this has been going on for a while in biology. For instance, the amount of attention paid to model organism is an early indicator of this, even when there were many labs working independently.

But the argument above is that ever increasing numbers of authors on scientific papers is good, and as far as I can see, the reasoning is that economies of scale start to kick in. The result? I expect that you will increasingly see the same kind of positive feedback loop that you see in business. Small, independent businesses mostly lose to large corporations.

Of course, it’s long been the case that certain labs and universities outcompete all others in the question for federal funding. But I supposed that when a lot of labs had personnel numbering in the single digits, it seemed like a more even match in resources. And somehow, I never thought of the emergence of huge, multi-author papers as a sign of “maturity” of a research field.

As more and more papers have 50 authors or more, will researchers with small labs that don’t generate terabytes of data will have to sell their land to the cattle barons (so to speak)? Close up shop and join the factory (to use another metaphor)?

I’m terribly worried that the kind of biology I love, like neuroethology, is irrelevant. (I’m not so worried about myself, since I’ve known my place in the research world for a good long while.)

And, on another note, the increasing prevalence of papers with 50 or more authors really points to the need for reform of authorial credit.

Related posts

Science is a doozy
Long live the scientific method

16 March 2010

Tuesday Crustie: Glam

She’s arguably the hottest star in the music world right now, thanks to her amazing dance beats and wilder than life stage persona, and now, Lady Gaga brings crustaceans to the limelight...

Much cooler than the last crustacean-inspired headwear.

Spotted at The Daily Mail.

15 March 2010

Why science loses in the short term (but usually wins in the long term)

Over the last few months, there has been much weeping and wailing and gnashing of teeth about strategy and tactics over how to communicate with non-scientists, and how to regain public trust over issues like climate change. A good example of this was a recent email exchange between Matt Nisbet and Randy Olson.


When scientists... take action by responding with tit-for-tat attacks on climate skeptics, it... feeds a downward spiral of “war” and conflict rhetoric that appears as just more ideological rancor to the wider public.


There comes a point where the public DOES want to see the science community stand up for themselves.

People arguing that scientists are losing to denialists in areas like climate science because they have taken a poor approach to communication are perhaps mischaracterizing the problem. The problem of what approach scientists use to communicate with non-scientists is a real problem, but it is minuscule in these cases.

Scientists have to, you know, do science in addition to communication with non-scientists. Denialists, as far as I can tell, can devote 100% of their time to communication.

If scientists want to win, we need to find a way to support a dedicated crew of people whose job is to do nothing else but do public relations. Why don’t national academies and organizations for the advancement of science have full-time, professional communicators?

The only organization that I can think of that is even close to the sort of “think tank” person who seems to be so routinely called for media interviews is the National Center for Science Education. They do a heroic job, but there’s only sixteen people listed on staff, including some whose job is in no way related to science.

Allocation of resources is a major problem, and time is a 100% non-renewable resource. People who can devote time to that will, in the short term, win.

The good news may be that because scientists are responsible for generating new knowledge, that can help in the long term. Ultimately, denialists cannot create anything new.

Image from here.

Comments for first half of March 2010

Canadian Girl Postdoc has a great post about how power relationships filter into conversations in the academic blogosphere.

Miriam at Deep Sea News talks about how fact-based science communication is failing. Facts are good; a plan is better.

FlowingData shows the “How genetics works” picture, which should be called, “How genetics was thought to work in the eighteenth century or so.”

Biochem Bell asks if a bird in the hand is worth two in the bush. Or something. Doctor Becca then takes this and runs with it some more. (Actually, they’re both concerned with high prestige journals.)

David Crotty at The Scholarly Kitchen examines a wonky paper on science blogging, and asks, “If you knew people read your blog, would you blog differently?” (I’m paraphrasing there...)

Jeff Jarvis at BuzzMachine asks, “In the Google age, what is the point of teaching memorization?” An excellent question, and one I also struggle with.

Sheril Kirshenbaum asks at The Intersection what readers want to know about energy. I’m perpetually confused by nuclear power generation and whether it’s worth it or not.

Armin Schneider, in a book review in PLoS Biology, says neuroscientists must not be interested in the history of their field, because the aren’t a lot of people in the history poster sessions. He neglects to mention that the history posters are displayed all week long, while regular posters are only up for four hours. Visits to the history posters are going to be more spread out.

Nancy Duarte wanted feedback on the cover for her next book. It’ll be called Resonate, and I guarantee you I’ll be buying it whichever cover ends up on it.

13 March 2010

I’ve been trying to stay out of this

Yes, it’s about the Texas State Board of Education and the Texas K-12 education standards. Again. I’ve tried to limit my comments to stuff related to science, particularly biology, because that’s what I feel competent to make comments about.

As a faculty member at a university that has about 85% Hispanic students, however, I feel obligated to highlight this bit from a New York Times article yesterday. It concerns the ongoing review of the state’s social studies standards.

Efforts by Hispanic board members to include more Latino figures as role models for the state’s large Hispanic population were consistently defeated, prompting one member, Mary Helen Berlanga, to storm out of a meeting late Thursday night, saying, “They can just pretend this is a white America and Hispanics don’t exist.”

Ms. Berlanga is the representative for the area that includes my institution, by the way.

There’s much more of interest in the Times piece.

12 March 2010

Lab equipment love #3

Last equipment post for a while, but by no means least. Finally, something a little bit more high tech than forceps and a microscope.

A 60 cycle noise eliminator, the HumBug.

To understand how marvelous this little box is, I have to explain a little about electrophysiology.

Everything you’re using to read this blog post runs off a powerline. So do lights and other electrical appliances. Those electric powerlines generate noise, or a “hum,” that cycles 60 times a second in North American, and 50 times a second in Australia and, I think, the U.K. This “60 cycle” is picked up by recording electrodes, like those used to record neural activity.

Since biologists are interested in the biology and not power mains, the 60 cycle just gets in the way of seeing the actual biological signal. So eletrophysiologists have to spend huge amounts of time trying to eliminate that 60 cycle noise by grounding, using Faraday cages, tinfoil, alligator clamps, and offerings to minor deities.

Worse, it’s incredibly unpredictable. A set-up that is perfect one day may have horrible 60 cycle the next day.

Thus, anything that helps combat 60 cycle is a beautiful thing. And that is what this clever little device does. I had no idea it existed until I went to the annual Neuroscience meeting the year I was hired, and discovering it alone made the trip worthwhile.

11 March 2010

One degree of separation between fellow nerds

I had never met Carin Bondar until I followed her on Twitter. Only after that did I learn that we have several colleagues in common, so there is absolutely no “old boy’s club” networking behind her decision to put me in Nerd Corner this week.

Nerd Corner? It’s like a regular corner, only, you know, nerdier.

Actually, Carin thought I might be interesting enough to interview. I sure fooled her.

Carin has a great website, with lots of other interviews, career resources, and more. Tell her Zen sent ya!

P.S. – She’s not related to Canadian astronaut Roberta Bondar.

Lab equipment love #2

Continuing this week with some of my favourite things in the lab... Like my first selection, this is something that is basic but absolutely fundamental.

A good stereo dissecting microscope, with a mount for a camera.

Edward Tufte often argues that much of science is the story of increasing resolving power. The classic example was the telescope, which was celebrated in the last year’s 400th anniversary celebration of Galileo using the device for such great effect. Microscopes came slightly later, but also revolutionized thinking about the world.

When I bought this microscope, I bought a camera lucida for drawing pictures, something I’d use through much of doctoral and post-doctoral work. A good drawing could provide more information more efficiently than using 35 mm film then. I have rarely used it, since digital photography had made it faster and more efficient to take a lot of photographs and work with those.

10 March 2010

Tenure is not a job for life, continued

Last month, I complained about the common misconception that tenure was “a job for life.” Florida State University has just provided an example of why it’s a misconception. Twenty-five examples, in fact.

My sympathy to those losing their positions. The prospect of losing a job is always terrifying.

Texas textbooks tapering influence?

In the blogging I’ve been doing on the Texas K-12 science standards, one point that get repeatedly emphasized is that Texas influences textbooks outside the state, for many reasons.

That influence is declining, and may be ending, according to the Austin American-Statesman. Kate Alexander reports on how several factors have combined to weaken the likelihood that textbook publishers will be as attentive to Texas standards as in the past.

First, it’s the economy, stupid (emphasis added).

Bob Cassel... said publishers have tailored textbooks to Texas in the past because the state has been an enormous customer with a reliable source of textbook funding from the $22 billion Permanent School Fund.

Last year, no money was available from the school fund for textbooks because of significant investment losses, and legislators relied on federal stimulus money to pay for the books.

Second, people are waking up to limitations of print books (emphasis added).

Our entire purchasing philosophy right now is based on one thing, and that is the lifetime of a textbook binding,” Hochberg said.

That approach does not lend itself to providing students with the most up-to-date material, particularly in dynamic fields such as science and social studies, Hochberg said.

For example, elementary science books in Texas still say there are nine planets in the solar system even though Pluto lost full planet status in 2006.

Rattling neuroethology’s windows

ResearchBlogging.orgAs I’ve written recently, I don’t feel all that at home and comfortable in the field of neuroscience. I feel much more at home in the discipline of neuroethology, which investigates the neural bases of naturally occurring animal behaviour. It is populated by people who still appreciate diversity.

Having said that neuroethology is my intellectual home, I would like to rattle the windows in my own house a bit.

Neuroethology has a bunch of great people working on cool stories. And yet it is not a vibrant or growing discipline right now. This is partly due to neuroscience losing touch with comparative biology as it emerges as its own discipline. But I think it’s deeper than that. The field seems without direction.

Neuroethology’s sister discipline, animal behaviour, provides an interesting case study of how to galvanize a field. In the early 1980s, animal behaviour was hopping. Just a few years before that, E.O. Wilson’s Sociobiologyand Richard Dawkin’s The Selfish Gene had brought to many people’s attention a whole series of ideas that had been gestating in theoretical biology, or were just starting to emerge in the scientific literature. That had thrown up a whole series of hypotheses and ideas about altruism, fitness, optimal strategies, and kin selection that needed testing.

Wilson, Dawkins, and many more challenged the field. And researchers stepped up.

If that wasn’t enough, DNA technology arrived. For the first time, people really started to be able to pinpoint paternity, which was key to underlying explanations of so much of why animals did what they did. A technological revolution is always helpful in getting interest and excitement going.

The discipline of neuroethology needs a challenge. It needs some choice problems for its practitioners to grapple. Something that someone working with hawkmoths or archerfish can contribute to.

I don’t pretend to know what that problem might be. Just to get conversations going, here are a couple of examples.

How do animals analyze complex and biologically relevant signals? Animal behaviour is filled with examples of evidence that animals are attending to, and making decisions, based on quite complex sensory signals. Many experiments show that animals pay attention to symmetry, for instance. Others show individual recognition.

How do small circuits evolve? Neuroethologists have this catalog of fantastic case studies: bat echolocation, fish escape, songbird learning. But in keeping with the model organism tradition, people have tended to milk those case studies. Why not put our knowledge of those neural circuits to use, and use them to work on brain evolution in a more detailed way than more typical size size comparisons? (I freely admit to a bias here, which is obvious since I discussed this a bit in my last review article.)

I don’t know if those questions will galvanize my colleagues. I mean, Ted Bullock set questions similar to those out as “pregnant agendas” a decade ago, and I’m no Ted Bullock. But I’ll be listening closely if I manage to get to the next international congress to see if there’s anything that might galvanize them.


Bullock, T. (1999). Neuroethology has pregnant agendas Journal of Comparative Physiology A: Sensory, Neural, and Behavioral Physiology, 185 (4), 291-295 DOI: 10.1007/s003590050389

Image from here.

09 March 2010

Tuesday Crustie: Attack!

I haven't been so looking forward to a movie since Mega Shark vs. Giant Octopus.

Hat tip to Arthropoda.

A neuron for free will

ResearchBlogging.orgThe question for neuroscience is how nervous systems generate behaviour and cognition. In general, we think there’s a hierachical command scheme, as the quick and dirty sketch below shows.

It’s been hard to move from general principles and “black boxes” to real neurons. A good chunk of effort in neuroethology has gone into understanding the sensory capabilities of different animals, and cracking how pattern generators could generate the detailed plan for movements, especially rhythmic behaviours. Research on command neurons, though, has focused on neurons that generate simple behaviours that are strongly stimulus driven, like escape responses. But many behaviours are far more... subtle. Behaviour is often spontaneous, and no clear stimulus is visible to an external observer.

Ideally, to understand the linkages I showed above, you’d want to record from all those different layers simultaneously: you’d want to know what the neurons are doing while you are simultaneously recording behaviour. Command neurons are involved tend to be located deep in the animal, so it is hard to locate and record from them in a way where there is enough animal left to behave. Jim Larimer and colleagues published a series of nice articles back in the 1970s showing that such neurons existed in crayfish, and reliably stimulated certain behaviours, like walking (Bowerman and Larimer 1974a, b).

Invertebrate locomotion has been very influential in influencing our understanding of motor control. During grad school, I was heavily reading papers on crustacean walking. That line of research seems to have slowed a bit since then, but this paper by Kagaya and Takahata is an amazing update to the field. I am, quite frankly, in awe of its technical prowess.

Procambarus clarkiiKagaya and Takahata must have spent a very long time troubleshooting these experiments. Using Louisiana red swamp crayfish, they were able to record from neurons heading from the brain to the thorax (where the legs are attached and controlled) and stimulate them, record key leg muscles involved in walking, and record the final behaviour, the trajectory and speed of the crayfish walking.

The authors recorded from several kinds of neurons running from the brain toward the thorax that had interesting influences on walking. Perhaps the most interesting were the ones that started firing before any behaviour started, which they called the “readiness discharge.” They were also able to stimulate these neurons electrically, and show reasonably well that their stimulation would initiate walking.

Intuitively, you might expect that you would only need one neuron to initiate a particular behaviour, and it wouldn’t matter all that much whether the source feeding into that initiation was external or internal. But that's the fascinating thing is that the “readiness discharge” neurons were not active when crayfish were “encouraged” to walk by touching them; reflexive walking was correlated with other neurons descending from the brain.

The “readiness discharge” neurons seemed to be involved only in spontaneous walking, and not reflexive walking. And isn’t spontaneous behaviour the usual place where “free will” gets invoked to explain what happens in complex animals?

They also found a variety of other interesting neurons. They found neurons that seemed to stop walking. They found neurons that appeared to be involved in maintaining walking, including some neurons that would fire only when walking in a particular direction.

At this point, all we know about these cells is the firing patterns of their action potentials. And it’s very difficult to know how many neurons might be missed, or if perhaps these neurons are overcategorized. We don’t know anything about their anatomy in the brain or in the rest of the nervous system, how they might be modulated, or anything. But now that we know they’re there... maybe people will start to figure out some ways to track these down.

This is the kind of paper that you don’t see enough of: classic, hard-core neuroethology. But it’s tough going to read it. Having detailed physiological recordings at multiple levels means that the experiments defy easy summary. Consequently, this paper may be like jazz music: there may be more people who admire the technical virtuosity than there are people who “get it.”


Bowerman RF, Larimer JL. 1974b. Command fibres in the circumoesophageal connectives of crayfish II. Phasic fibres. The Journal of Experimental Biology 60:119-134. http://jeb.biologists.org/cgi/content/abstract/60/1/119

Kagaya K, Takahata M. 2010. Readiness discharge for spontaneous initiation of walking in crayfish Journal of Neuroscience 30(4): 1348-1362. DOI: 10.1523/jneurosci.4885-09.2010

Kagaya, K., & Takahata, M. (2010). Readiness Discharge for Spontaneous Initiation of Walking in Crayfish Journal of Neuroscience, 30 (4), 1348-1362 DOI: 10.1523/JNEUROSCI.4885-09.2010

[Crossposted at Marmorkrebs.]

08 March 2010

Lab equipment love #1

drdrA at Blue Lab Coats started a series on her favourite lab equipment. This seemed to me to be a spiffing idea. Even if I cannot bring myself to describe my lab equipment as “hot.”

Here is one of my favourite pieces of lab equipment: a simple, elegant, Swiss made precision instrument.

Dumont Number 5 forceps.

I’ve come to appreciate the pleasure of working with a new set of good, sharp forceps. It’s amazing what you can manipulate with them. Don Abbott was reported in the book Observing Marine Invertebrates as often saying something to the effect of, “There is no substitute for good forceps. None.” And he was right.

Forceps come in a lot of different materials. Most are steel. Titanium is good for people working with salt water or saline, because titanium is more rust resistant, but titanium is soft. I’ve found strength of the tips to be the most important factor for me, so am now usually using forceps made of an alloy called Dumostar.

Unfortunately, the pleasure of working with sharp new forceps is balanced out by the agony of trying to keep them sharp. It seems that no matter what you do, or what they’re made of, how carefully you try to handle them, those fine tips always end up getting bent somehow. Particularly because I work with crustaceans, I always have to be handling exoskeleton, which are prone to bend the tips of forceps because it’s hard.

And dropping them gives you that same visceral reaction as locking your keys in the car: You realize it the exact instant the forceps / car door has left your hand.

07 March 2010

Only a matter of time before this showed up

Your results:
You are Jean-Luc Picard
Jean-Luc Picard
James T. Kirk (Captain)
Will Riker
Geordi LaForge
An Expendable Character (Redshirt)
Deanna Troi
Mr. Sulu
Leonard McCoy (Bones)
Beverly Crusher
Mr. Scott
A lover of Shakespeare and other
fine literature. You have a decisive mind
and a firm hand in dealing with others.

Click here to take the "Which Star Trek character are you?" quiz...

05 March 2010

At last, microgrants

“Sit by the river long enough, and you will see the bodies of your enemies float by.”

I’m invoking this vengeful proverb about the virtues of patience because, two and a half years ago, I wrote:

(M)icro-loans have been so successful at creating wealth that some of the first to use this strategy were recognized with a Nobel Peace price in 2006.

Where are the equivalent micro-grants?

Finally, someone is making that a reality, and that someone is BenchFly.com. They have a program called “Search for Research.” And good on Sigma-Aldrich for supporting this initiative.

I hope this it will get people thinking seriously about new ways to grease the wheels of research.

04 March 2010

Like a fly in amber...


...Your copy of The Open Laboratory 2009 arrives perfectly preserved!

(Yes, I’m blogging about getting the book before actually breaking the seal and cracking open the book. ‘Cause I’m just that geeky.)

Can jellyfish see colour?

ResearchBlogging.org“Jellyfish? See colours? That’s crazy talk! They’d need eyes to do that! They don’t even have brains, do they?”

Some jellyfish do have eyes to go along with their well-developed central nervous system. These are box jellies, which are generally better known because some of their number contains rather deadly toxins. If that wasn’t scary enough, they have eyes. In fact, they have lots of eyes.

Rhophalia are sensory structures that you can see as black dots about two thirds of the way down the bell (pictured right). Close up, they look like part of an old-school movie monster (pictured below). Each rhophalium has six, count ‘em, six, eyes. Four of the eyes are quite simple, but two have lens eyes, just like vertebrates and cephalopods. These eyes are fairly crummy by human standards – they’re blurry and probably pretty low resolution – but they do the job well enough.

To see colour, you need to tell different wavelengths of light apart, and to do that, you need at least two different visual pigments. (Humans have three.) O’Connor and colleagues went looking for different visual pigments in Chiropsella bronzie (pictured above right). This involves firing light of all different colours at the eye, and looking to see how much is absorbed at each wavelength. They found only one absorbance peak – i.e., lights of one particular wavelength alone were being absorbed.

They also tried using labels for visual pigments taken from zebrafish. Zebrafish have at least six different visual pigments, and these molecules are often very similar across species. Again, only one of the five different immunolabels that they tried reacted with the cells in the largest lower camera eye.

All of which indicates that these animals are only seeing black and white – at least through their largest eye. I suppose it’s possible that they might have different pigments in different eyes, but if they don’t have multiple pigments in their largest eye, it seems unlikely they’d have them in their smaller eyes.

A side finding was that the jellyfish visual pigments “bleach,” meaning some chemical bonds are broken in the molecules. Most invertebrate visual pigments do not do this, but vertebrate pigments do. Thus, it’s another way that jellyfish eyes are resemble vertebrate eyes (camera eyes with bleaching pigments) more than most other invertebrate eyes (compound eyes with non-bleaching pigments).

A previous study had suggested that a box jellyfish might see colour, but that was a different species (Carybdea marsupialis). Maybe there’s some real diversity in the visual abilities of these different jellies, and some can see colour. But it seems that C. bronzie lives in a world of gray.


O'Connor, M., Garm, A., Marshall, J., Hart, N., Ekstrom, P., Skogh, C., & Nilsson, D. (2010). Visual pigment in the lens eyes of the box jellyfish Chiropsella bronzie Proceedings of the Royal Society B: Biological Sciences DOI: 10.1098/rspb.2009.2248

Rhophalia picture from here.

03 March 2010

Thank you for your service, Don McLeroy

Several sites today are reporting that Don McLeroy (pictured right) appears to have been defeated by Thomas Ratliff (left) in the primary for the Texas State Board of Education (SBoE). I have blogged extensively about how the SBoE have made a series of questionable decisions about K-12 science standards (at best), and how McLeroy has frequently misrepresented science in general and evolutionary biology in particular.

How much does this change the composition of the SBoE, which has had a strong religious right, conservative block of represenatives just a hair’s breadth from a majority (7 out of 15 members)? While McLeroy is out, George Clayton in in. Clayton has been quoted thus:

Clayton said evolution is and should remain in science classrooms, but he thinks the alternative theories supported by the religious right – intelligent design and creationism – can “find a real nice home” in humanities, philosophy or world history classes.

“It’s seems to me you can’t be taught the one [evolution] without the other [creationism],” Clayton said. “It’s an impossibility to talk about evolution without mentioning creationism.”

Right. Of course. You can't have physics without metaphysics. Can't teach marine biology without mentioning mermaids.

Honestly? I don’t think Clayton is being completely out in left field on that. These are important philosophical issues, and they have played a role in the biology historically. Darwin was highly influenced by Paley, and many eighteenth and nineteenth century geologists sought to support Noah’s flood scientifically. That they failed does not mean those efforts should never be talked about. The problem is putting them into their context: they are failed hypotheses that do not play a role in contemporary science.

The title of this post, by the way, is not intended as sarcasm. Needless to say, I disagree with a large amount of Mr. McLeroy’s actions and goals, but I do admire that he was willing to serve in public office. That is not an easy thing.

Pedestrian ponders parking prices

Because I walk to work 99% of the time, I normally have never had cause to pay attention to the cost of parking. So I was puzzled to learn that faculty parking permits cost ~33% more for Fall semester than the equally long Spring semester. Weirder, Summer session I costs more than 100% than the equally long Summer session II.

This makes zero sense to me. A popular theory was that this was because enrollment is higher in Fall then Spring, and Summer I than Summer II. But these are faculty parking rates, not student rates, and faculty don’t park in the same places as students. Even then, there aren’t one third more students in one semester than the other.

One of the things I think  we have to thank the Quakers for is the idea that things have a price. And that the price of an object doesn’t fluctuate depending on your haggling skills or how well off you are. It shouldn’t fluctuate in this way, either.

02 March 2010

So that’s where she’s been!

Following yesterday’s post about neuroscience leaving me, I find an interview with someone I recognize. Andrea Novicki who was once a fellow invertebrate neuroethologist. I first met Andrea at Western Nerve Net meetings, before that series vanished beneath the waves, and at a few conferences after that.

Then, she went sailing. (Meanwhile, I went through tenure.)

A post that shows how many twists and turns a career can take.

Tuesday Crustie: Boxed in

Calappa flammea, also known as a box crab or shame-faced crab.

Not sure what it has to be ashamed of – it has lovely colours!

From here.

Carnivals for March 2010

The Circus of the Spineless #48 is up at Matthew Sarver’s blog.

The Carnival of Evolution #21 is up at Mauka to Makai.

Bonus! Not exactly a carnival, but the final list of selections for the Young Australian Skeptics Blog Anthology has been announced.

The difference between experts and scientists

An expert compiles existing knowledge. A scientist generates new knowledge.

Comment made in response to Simon Bostock’s question on Twitter yesterday.

01 March 2010

Science is neither left-wing nor right-wing

On the eve of tomorrow’s primaries for the Texas State Board of Education, Mr. Don McLeroy yet again provides a choice quotation in an Associated Press wire story (emphasis added):

“There is nothing conservative about what we did in English. Nothing conservative about what we did in science,” McLeroy said of the board’s record. “It just shows how left things get with the uncritical examination of evolution.”

McLeroy’s tying of science and politics is disingenuous and dangerous. The data don’t vary with political beliefs. Science is about reality, not left or right wing politics.

Science is among the most conservative disciplines practiced by human beings. It demands scholarship and credit of past achievements. It realizes the tenuous nature of new discoveries, and tries over and over again to maintain practices and processes that have yielded real progress.

I guess McLeroy is right: what they did to science standards was not conservative. Everyone, please meet Mr. Don McLeory – radical liberal.

Such complete confidence combined with real misunderstanding I’ve come to expect from Mr. McLeory. I didn’t expect his opponent, Tom Ratliff, to say this:

Ratliff, his opponent, said he concedes that McLeroy never tried foisting his creationism beliefs into textbooks(.)

Seriously? Did he follow the same science standards adoption process that I did? I know Mr. Ratliff is in the same political party as McLeroy, but still, he’s glossing over McLeroy’s involvement way too much.

Curse you, Yopak!

D’oooooh... that Kara Yopak. Her paper got ahead of mine again... After a long time in the top three, my review paper has finally slipped down to #4.

One thing that drives me a bit batty about this list, though, is that half of the top 10 list is prefaces and notes rather than the actual articles that people should be reading the journal for.

Texas State Board of Education primaries tomorrow

I’m grateful to Michael Alvard for pointing out that:

  • Texas primary elections for the State Board of Education are tomorrow, 2 March 2010.
  • You do not have to be a registered member of a political party to vote.

The Texas State Board of Education wields a disproportionate amount of power to influence the teaching of kids in the United States. This vote matters.

Vote as you will, but please vote.

When is neuroscience not neuroscience? When it’s neurobiology

It was a great pleasure that I found out that this blog had been shortlisted for the “Best Neuroscience Blog” category of the ResearchBlogging.org awards.

I am soooo going to lose.

But I’m good with that. First, I’ve read some several of the other blogs, and already know they’re great. Second, this blog exists, much like I do, on a teetering precipice between disciplines. Neuro stuff is just one third (at best) of what this blog is about, scientifically.

And “neuroscience” is, increasingly, not a comfortable fit with me. I’ve thought more than a little about whether I am a neuroscientist, and more and more, I reckon the answer is, “No.”

Neuroscience has become a distinct discipline of science in the last couple of decades. It has ties to biology, psychology, medicine, computation, and more. But it isn’t a subdiscipline of biology any more, in the way that entomology or microbiology or mycology still is.

The enterprise of neuroscience as a mature independent discipline is to understand, as neuroscientists put it, “the” brain. The use of the definite article here is deliberate, because it’s that phrase is often used, and the implication is clear: the only kind of brain that really matters is the human brain. Sure, you can study other kinds of organisms, but they are little more than carnival sideshow unless there’s some sort of hint that what’s learned there will inform our understanding of human brains.

It’s gotten harder for people studying other kinds of animals to hold their own. In the 1970s and 1980s, I think there was more interest in studying non-humans, because you could more easily record neural activity. In the 1990s, fMRI hit the scene and the presence of its high resolution brain scans have been growing by leaps and bounds ever since. I think that’s directly cut into interest in non-human neuroscience at almost every level.

The emphasis on model organisms has also seemed to become stronger, probably brought about by the power of genetic analysis. Animals with sequenced genomes got attention. The genome club is getting bigger, but it’s still a small group.

Consequently, neuroscience (which should be the broad discipline) is in some ways narrower in scope than neurobiology. Neurobiology tends to pitch a bigger tent, species wise.

It may be too strong to say, “I didn’t leave neuroscience; neuroscience left me.” But I don’t see a way for neurobiology to make its way back to the mainline of the field of neuroscience, leaving me and my colleagues working increasingly distant from it.

Comments for second half of February 2010

Building Blogs of Science brings to light a nice paper on hearing that I missed. This is a sweet angle on some stuff I routinely talk about in my neuro classes.

Blue Lab Coats writes about that perennial favourite of NeuroDojo, the Texas State Board of Education and the Board’s upcoming elections.

Dr. Becca asks about whether short-term lectureships are worth it. They beat the dole, as the British might say.